Detection of iron-depositing Pedomicrobium species in native biofilms from the Odertal National Park by a new, specific FISH probe.

PubMed

Braun, Burga; Richert, Inga; Szewzyk, Ulrich

2009-10-01

Iron-depositing bacteria play an important role in technical water systems (water wells, distribution systems) due to their intense deposition of iron oxides and resulting clogging effects. Pedomicrobium is known as iron- and manganese-oxidizing and accumulating bacterium. The ability to detect and quantify members of this species in biofilm communities is therefore desirable. In this study the fluorescence in situ hybridization (FISH) method was used to detect Pedomicrobium in iron and manganese incrusted biofilms. Based on comparative sequence analysis, we designed and evaluated a specific oligonucleotide probe (Pedo 1250) complementary to the hypervariable region 8 of the 16S rRNA gene for Pedomicrobium. Probe specificities were tested against 3 different strains of Pedomicrobium and Sphingobium yanoikuyae as non-target organism. Using optimized conditions the probe hybridized with all tested strains of Pedomicrobium with an efficiency of 80%. The non-target organism showed no hybridization signals. The new FISH probe was applied successfully for the in situ detection of Pedomicrobium in different native, iron-depositing biofilms. The hybridization results of native bioflims using probe Pedo_1250 agreed with the results of the morphological structure of Pedomicrobium bioflims based on scanning electron microscopy.

Detection of aneurysmal subarachnoid hemorrhage 3 months after initial bleeding: evaluation of T2* and FLAIR MR sequences at 3 T in comparison with initial non-enhanced CT as a gold standard.

PubMed

Mulé, Sébastien; Soize, Sébastien; Benaissa, Azzedine; Portefaix, Christophe; Pierot, Laurent

2016-08-01

To investigate the ability of T2* and fluid-attenuated inversion recovery (FLAIR) MR sequences to detect hemosiderin deposition 3 months after aneurysmal subarachnoid hemorrhage (SAH) in comparison with early non-enhanced CT (NECT) as a gold standard. From September 2008 through May 2013, patients with aneurysmal SAH were included if a NECT less than 24 h after the onset of symptoms showed a SAH, and MRI, including T2* and FLAIR sequences, was performed 3 months later. All aneurysms were treated endovascularly. NECT and MR sequences were blindly analyzed for the presence of SAH (NECT) or hemosiderin deposition (MRI). When positive, details of the spatial distribution of SAH or hemosiderin deposits were noted. Sensitivities were calculated for each patient. Sensitivities, specificities, and positive predictive values (PPVs) were calculated for each location. Forty-nine patients (mean age 52.9 years) were included. Bleeding-related patterns were identified in 43 patients (87.8%) on T2* and 10 patients (20.4%) on FLAIR. T2* was highly predictive of the location of the initial hemorrhage, especially in the Sylvian cisterns (PPVs 95% and 100%) and the anterior interhemispheric fissure (PPV 90%). The T2* sequence can detect and localize a previous SAH a few months after aneurysmal bleeding. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Microfacies and depositional environments of the Late Ordovician Lianglitage Formation at the Tazhong Uplift in the Tarim Basin of Northwest China

NASA Astrophysics Data System (ADS)

Gao, Da; Lin, Changsong; Yang, Haijun; Zuo, Fanfan; Cai, Zhenzhong; Zhang, Lijuan; Liu, Jingyan; Li, Hong

2014-04-01

The Late Ordovician Lianglitage Formation comprises 13 microfacies (Mf1-Mf13) that were deposited on a carbonate platform at the Tazhong Uplift of the Tarim Basin in Northwest China. Each type of microfacies indicates a specific depositional environment with a certain level of wave energy. Four primary groups of microfacies associations (MA1-MA4) were determined. These associations represent different depositional facies, including reef-shoal facies in the platform margin (MA1), carbonate sand shoal facies (MA2) and oncoid shoal (MA3) on open platforms, and lagoon and tidal flat facies (MA4) in the platform interior. Each microfacies association was generated in a fourth-order sedimentary sequence developing within third-order sequences (SQ1, SQ2, and SQ3, from bottom to top), showing a shallowing-upward trend. High-frequency sequences and facies correlation between wells suggests that the reef-shoal facies more successively developed in the southeastern part of the platform margin, and high-energy microfacies were more strictly confined by the top boundary of fourth-order sequences in the northwestern part of the platform. The highstand systems tract (HST) of the SQ2 is characterized by reef-shoals that developed along the platform margin and tidal flats and lagoons that developed in the platform interior, while the SQ3 is characterized by the oncoid shoal facies that generally developed on the uplift due to a regionally extensive transgression that occurred during the latter part of the Late Ordovician. The results of this study can be used for investigating the development and distribution of potential reservoirs; the reservoirs in southeastern part of the platform margin may be of premium quality because the high-energy microfacies were best preserved there.

Facies analysis and sequence stratigraphic framework of upper Campanian strata (Neslen and Mount Garfield formations, Bluecastle Tongue of the Castlegate sandstone, and Mancos shale), Eastern Book cliffs, Colorado and Utah

USGS Publications Warehouse

Kirschbaum, Mark A.; Hettinger, Robert D.

2004-01-01

Facies and sequence-stratigraphic analysis identifies six high-resolution sequences within upper Campanian strata across about 120 miles of the Book Cliffs in western Colorado and eastern Utah. The six sequences are named after prominent sandstone units and include, in ascending order, upper Sego sequence, Neslen sequence, Corcoran sequence, Buck Canyon/lower Cozzette sequence, upper Cozzette sequence, and Cozzette/Rollins sequence. A seventh sequence, the Bluecastle sequence, is present in the extreme western part of the study area. Facies analysis documents deepening- and shallowing- upward successions, parasequence stacking patterns, downlap in subsurface cross sections, facies dislocations, basinward shifts in facies, and truncation of strata.All six sequences display major incision into shoreface deposits of the Sego Sandstone and sandstones of the Corcoran and Cozzette Members of the Mount Garfield Formation. The incised surfaces represent sequence-boundary unconformities that allowed bypass of sediment to lowstand shorelines that are either attached to the older highstand shorelines or are detached from the older highstand shorelines and located southeast of the main study area. The sequence boundary unconformities represent valley incisions that were cut during successive lowstands of relative sea level. The overlying valley-fill deposits generally consist of tidally influenced strata deposited during an overall base level rise. Transgressive surfaces can be traced or projected over, or locally into, estuarine deposits above and landward of their associated shoreface deposits. Maximum flooding surfaces can be traced or projected landward from offshore strata into, or above, coastal-plain deposits. With the exception of the Cozzette/Rollins sequence, the majority of coal-bearing coastal-plain strata was deposited before maximum flooding and is therefore within the transgressive systems tracts. Maximum flooding was followed by strong progradation of parasequences and low preservation potential of coastal-plain strata within the highstand systems tract. The large incised valleys, lack of transgressive retrogradational parasequences, strong progradational nature of highstand parasequences, and low preservation of coastal-plain strata in the highstand systems tracts argue for relatively low accommodation space during deposition of the Sego, Corcoran, and Cozzette sequences. The Buck Canyon/Cozzette and Cozzette/Rollins sequences contrast with other sequences in that the preservation of retrogradational parasequences and the development of large estuaries coincident with maximum flooding indicate a relative increase in accommodation space during deposition of these strata. Following maximum flooding, the Buck Canyon/Cozzette sequence follows the pattern of the other sequences, but the Cozzette/Rollins sequence exhibits a contrasting offlapping pattern with development of offshore clinoforms that downlap and eventually parallel its maximum flooding surface. This highstand systems tract preserves a thick coal-bearing section where the Rollins Sandstone Member of the Mount Garfield Formation parasequences prograde out of the study area, stepping up as much as 800 ft stratigraphically over a distance of about 90 miles. This progradational stacking pattern indicates a higher accommodation space and increased sedimentation rate compared to the previous sequences.

Tidal-bundle sequences in the Jordan Sandstone (Upper Cambrian), southeastern Minnesota, U.S.A.: Evidence for tides along inboard shorelines of the Sauk Epicontinental Sea

USGS Publications Warehouse

Tape, C.H.; Cowan, Clinton A.; Runkel, Anthony C.

2003-01-01

This study documents for the first time tidal bundling in a lower Paleozoic sheet sandstone from the cratonic interior of North America, providing insights into the hydrodynamics of ancient epicontinental seas. The Jordan Sandstone (Upper Cambrian) in the Upper Mississippi Valley contains large-scale planar tabular cross-sets with tidal-bundle sequences, which were analyzed in detail at an exceptional exposure. Tidal-bundle sequences (neap-spring-neap cycles) were delineated by foreset thickening-thinning patterns and composite shale drapes, the latter of which represent accumulations of mud during the neap tides of neap-spring-neap tidal cycles. Fourier analysis of the bundle thickness data from the 26 measurable bundle sequences revealed cycles ranging from 15 to 34 bundles per sequence, which suggests a semidiurnal or mixed tidal system along this part of the Late Cambrian shoreline. We extend the tidal interpretation to widespread occurrences of the same facies in outcrops of lesser quality, where the facies is recognizable but too few bundles are exposed for tidal cycles to be measured. By doing so, this study shows that tidally generated deposits have a significant geographic and temporal extent in Upper Cambrian strata of central mid-continent North America. The deposition and preservation of tidal facies was related to the intermittent development of shoreline embayments during transgressions. The tidally dominated deposits filled ravined topographies that were repeatedly developed on the updip parts of the shoreface. Resulting coastal geomorphologies, accompanied perhaps by larger-scale changes in basinal conditions and/or configuration, led to changes in depositional conditions from wave-dominated to tide-dominated. Outcrops of the Jordan Sandstone tidal facies in the Upper Mississippi Valley represent the farthest inboard recorded transmission of ocean-generated tides in the Laurentian epicontinental seas, demonstrating that tidal currents were significant agents in the transport of sand along the far cratonic interior shorelines of Cambrian North America. The results of this study improve the facies-level understanding of the genesis of sheet sandstones. Furthermore, tidalites documented here occur in a specific position within a sequence stratigraphic architecture for the Jordan Sandstone. This provides a framework to compare these ancient deposits and processes to younger (e.g., Carboniferous) epicontinental systems where stratal and sediment dynamics are better documented. ?? 2003, SEPM (Society for Sedimentary Geology).

Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)

PubMed Central

Ye, Manhong; Zhou, Bin; Wei, Shanshan; Ding, MengMeng; Lu, Xinghui; Shi, Xuehao; Ding, Jiatong; Yang, Shengmei; Wei, Wanhong

2016-01-01

Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs. PMID:27175015

Sequence stratigraphy of the Raha Formation, Bakr Oil Field, Gulf of Suez, Egypt: Insights from electrical well log and palynological data

NASA Astrophysics Data System (ADS)

Mansour, Ahmed; Mohamed, Omar; Tahoun, Sameh S.; Elewa, Ashraf M. T.

2018-03-01

The current paper provides a high resolution sequence stratigraphic study of the Raha Formation from the productive Bakr Oil Field, central Gulf of Suez, Egypt. Sixty cutting rock samples spanning the Cenomanian from three wells (Bakr-114, B-115 and B-109) in the Bakr Basin, were palynologically investigated. The documented palynomorphs assemblage of either terrestrially-derived sporomorphs or marine inhabited dinocysts, allowed two palynological zones as well as their encompassing depositional palaeoenvironment to be recognized. These zones are Afropollis jardinus-Crybelosporites pannuceus Assemblage Zone (early-middle Cenomanian) and Classopollis brasiliensis-Tricolpites sagax Assemblage Zone (late Cenomanian). Detailed analysis of the particulate organic matter compositions suggested that the depositional palaeoenvironment of the Raha Formation was fluctuating between supratidal and distal-inner neritic conditions, due to successive oscillations of the Neo-Tethyan Ocean during the Cenomanian. The pronounced peaks of particulate organic matter versus gamma ray are markedly used in delineating the depositional sequences of the Raha Formation and their bounding surfaces. The Raha Formation probably corresponds to a second-order depositional sequence, which can be further subdivided into eight third-order depositional sequences, of which six are complete and two are incomplete ones. These depositional sequences are significantly synchronized based on a simple 2-D correlation model between the three wells. According to the hierarchical duration system, the Cenomanian herein was approximately attributed to 6 Myr, each of which has lower order depositional sequences that took approximately 0.9 Myr. Based on the sequence stratigraphic approach together with palynofacies analysis and gamma ray data, a condensed section was defined in the B-115.

The Automated Array Assembly Task of the Low-cost Silicon Solar Array Project, Phase 2

NASA Technical Reports Server (NTRS)

Coleman, M. G.; Grenon, L.; Pastirik, E. M.; Pryor, R. A.; Sparks, T. G.

1978-01-01

An advanced process sequence for manufacturing high efficiency solar cells and modules in a cost-effective manner is discussed. Emphasis is on process simplicity and minimizing consumed materials. The process sequence incorporates texture etching, plasma processes for damage removal and patterning, ion implantation, low pressure silicon nitride deposition, and plated metal. A reliable module design is presented. Specific process step developments are given. A detailed cost analysis was performed to indicate future areas of fruitful cost reduction effort. Recommendations for advanced investigations are included.

Facies architecture and high resolution sequence stratigraphy of an aeolian, fluvial and shallow marine system in the Pennsylvanian Piauí Formation, Parnaíba Basin, Brazil

NASA Astrophysics Data System (ADS)

Vieira, Lucas Valadares; Scherer, Claiton Marlon dos Santos

2017-07-01

The Pennsylvanian Piauí Formation records the deposition of aeolian, fluvial and shallow marine systems accumulated in the cratonic sag Parnaíba basin. Characterization of the facies associations and sequence stratigraphic framework was done by detailed description and logging of outcrops. Six facies associations were recognized: aeolian dunes and interdunes, aeolian sandsheets, fluvial channels, tidally-influenced fluvial channels, shoreface and shoreface-shelf transition. Through correlation of stratigraphic surfaces, the facies associations were organized in system tracts, which formed eight high frequency depositional sequences, bounded by subaerial unconformities. These sequences are composed of a lowstand system tract (LST), that is aeolian-dominated or fluvial-dominated, a transgressive system tract (TST) that is formed by tidally-influenced fluvial channels and/or shoreface and shoreface-shelf transition deposits with retrogradational stacking, and a highstand system tract (HST), which is formed by shoreface-shelf transition and shoreface deposits with progradational stacking. Two low frequency cycles were determined by observing the stacking of the high frequency cycles. The Lower Sequence is characterized by aeolian deposits of the LST and an aggradational base followed by a progressive transgression, defining a general TST. The Upper Sequence is characterized by fluvial deposits and interfluve pedogenesis concurring with the aeolian deposits of the LST and records a subtle regression followed by transgression. The main control on sedimentation in the Piauí Formation was glacioeustasy, which was responsible for the changes in relative sea level. Even though, climate changes were associated with glacioeustatic phases and influenced the aeolian and fluvial deposition.

Stratigraphy of the Grande Savane Ignimbrite Sequence, Dominica, Lesser Antilles

NASA Astrophysics Data System (ADS)

Schneider, S.; Smith, A. L.; Deuerling, K.; Killingsworth, N.; Daly, G.

2007-12-01

The island of Dominica, located in the central part of the Lesser Antilles island arc has eight potentially active volcanoes. One of these, Morne Diablotins, is a composite stratovolcano with several superimposed stratigraphic sequences ranging in age from Pliocene (4-2 Ma) to "Younger" Pleistocene (<1.8 Ma). The most recent major eruptive activity from this volcano was a series of Plinian eruptions that produced ignimbrites that gave dates of >22,000 and >40,000 years B.P. The ignimbrite sequences form four flow fans that reached both the east and west coasts of the island. One of these flow fans, the Grande Savane, on the west coast of the island, also extends off-shore for a distance of at least 14 km as a distinctive submarine fan. Stratigraphical studies of the on- shore deposits that make up this fan indicate an older sequence of block and ash flow deposits, within which occurs a distinctive vulcanian fall deposit. These are overlain, with no evidence of an intervening paleosol, by a sequence of ignimbrites containing welded horizons (ranging in thickness from around 4 m to 16m). The lack of fall deposits beneath the ignimbrites suggest they may have been formed by instantaneous continuous collapse of the eruption column. This whole succession is overlain by a series of planar and dune bedded pumiceous surge deposits with interbedded pumiceous lapilli fall and ash fall deposits, that extend laterally outside of the main area of ignimbrite deposition. Beds within this upper sequence often contain accretionary lapilli and gas cavities suggesting magma-water interaction. The youngest deposits from Morne Diablotins appear to be valley- fill deposits of both ignimbrite and block and ash flow. A comparison of the of the Grande Savane pyroclastic sequence with the Pointe Ronde (west coast) and Londonderry (east coast) pyroclastic flow fans will provide information on the eruptive history of this major Plinian episode.

Relationships between palaeogeography and opal occurrence in Australia: A data-mining approach

NASA Astrophysics Data System (ADS)

Landgrebe, T. C. W.; Merdith, A.; Dutkiewicz, A.; Müller, R. D.

2013-07-01

Age-coded multi-layered geological datasets are becoming increasingly prevalent with the surge in open-access geodata, yet there are few methodologies for extracting geological information and knowledge from these data. We present a novel methodology, based on the open-source GPlates software in which age-coded digital palaeogeographic maps are used to “data-mine” spatio-temporal patterns related to the occurrence of Australian opal. Our aim is to test the concept that only a particular sequence of depositional/erosional environments may lead to conditions suitable for the formation of gem quality sedimentary opal. Time-varying geographic environment properties are extracted from a digital palaeogeographic dataset of the eastern Australian Great Artesian Basin (GAB) at 1036 opal localities. We obtain a total of 52 independent ordinal sequences sampling 19 time slices from the Early Cretaceous to the present-day. We find that 95% of the known opal deposits are tied to only 27 sequences all comprising fluvial and shallow marine depositional sequences followed by a prolonged phase of erosion. We then map the total area of the GAB that matches these 27 opal-specific sequences, resulting in an opal-prospective region of only about 10% of the total area of the basin. The key patterns underlying this association involve only a small number of key environmental transitions. We demonstrate that these key associations are generally absent at arbitrary locations in the basin. This new methodology allows for the simplification of a complex time-varying geological dataset into a single map view, enabling straightforward application for opal exploration and for future co-assessment with other datasets/geological criteria. This approach may help unravel the poorly understood opal formation process using an empirical spatio-temporal data-mining methodology and readily available datasets to aid hypothesis testing.

Integrated sequence stratigraphy of the postimpact sediments from the Eyreville core holes, Chesapeake Bay impact structure inner basin

USGS Publications Warehouse

Browning, J.V.; Miller, K.G.; McLaughlin, P.P.; Edwards, L.E.; Kulpecz, A.A.; Powars, D.S.; Wade, B.S.; Feigenson, M.D.; Wright, J.D.

2009-01-01

The Eyreville core holes provide the first continuously cored record of postimpact sequences from within the deepest part of the central Chesapeake Bay impact crater. We analyzed the upper Eocene to Pliocene postimpact sediments from the Eyreville A and C core holes for lithology (semiquantitative measurements of grain size and composition), sequence stratigraphy, and chronostratigraphy. Age is based primarily on Sr isotope stratigraphy supplemented by biostratigraphy (dinocysts, nannofossils, and planktonic foraminifers); age resolution is approximately ??0.5 Ma for early Miocene sequences and approximately ??1.0 Ma for younger and older sequences. Eocene-lower Miocene sequences are subtle, upper middle to lower upper Miocene sequences are more clearly distinguished, and upper Miocene- Pliocene sequences display a distinct facies pattern within sequences. We recognize two upper Eocene, two Oligocene, nine Miocene, three Pliocene, and one Pleistocene sequence and correlate them with those in New Jersey and Delaware. The upper Eocene through Pleistocene strata at Eyreville record changes from: (1) rapidly deposited, extremely fi ne-grained Eocene strata that probably represent two sequences deposited in a deep (>200 m) basin; to (2) highly dissected Oligocene (two very thin sequences) to lower Miocene (three thin sequences) with a long hiatus; to (3) a thick, rapidly deposited (43-73 m/Ma), very fi ne-grained, biosiliceous middle Miocene (16.5-14 Ma) section divided into three sequences (V5-V3) deposited in middle neritic paleoenvironments; to (4) a 4.5-Ma-long hiatus (12.8-8.3 Ma); to (5) sandy, shelly upper Miocene to Pliocene strata (8.3-2.0 Ma) divided into six sequences deposited in shelf and shoreface environments; and, last, to (6) a sandy middle Pleistocene paralic sequence (~400 ka). The Eyreville cores thus record the fi lling of a deep impact-generated basin where the timing of sequence boundaries is heavily infl uenced by eustasy. ?? 2009 The Geological Society of America.

A novel monoclonal Perkinsus chesapeaki in vitro isolate from an Australian cockle, Anadara trapezia.

PubMed

Reece, Kimberly S; Scott, Gail P; Dang, Cécile; Dungan, Christopher F

2017-09-01

A monoclonal Perkinsus chesapeaki isolate was established from 1 of 10 infected Australian Anadara trapezia cockles. Morphological features were similar to those of described P. chesapeaki isolates, and also included a unique vermiform schizont cell-type. Perkinsus olseni-specific PCR primers amplified DNAs from all 10 cockles. Perkinsus chesapeaki-specific primers also amplified DNAs from 4/10 cockles, including DNA from the isolate source cockle. Three different sets of DNA sequences from the monoclonal isolate grouped with the homologous, previously deposited, P. chesapeaki sequences in phylogenetic analyses. In situ hybridization assays detected both P. chesapeaki and P. olseni cells in histological sections from the source cockle for monoclonal isolate ATCC PRA-425. Copyright © 2017 Elsevier Inc. All rights reserved.

Sulfate-reducing bacteria inhabiting natural corrosion deposits from marine steel structures.

PubMed

Païssé, Sandrine; Ghiglione, Jean-François; Marty, Florence; Abbas, Ben; Gueuné, Hervé; Amaya, José Maria Sanchez; Muyzer, Gerard; Quillet, Laurent

2013-08-01

In the present study, investigations were conducted on natural corrosion deposits to better understand the role of sulfate-reducing bacteria (SRB) in the accelerated corrosion process of carbon steel sheet piles in port environments. We describe the abundance and diversity of total and metabolically active SRB within five natural corrosion deposits located within tidal or low water zone and showing either normal or accelerated corrosion. By using molecular techniques, such as quantitative real-time polymerase chain reaction, denaturing gel gradient electrophoresis, and sequence cloning based on 16S rRNA, dsrB genes, and their transcripts, we demonstrated a clear distinction between SRB population structure inhabiting normal or accelerated low-water corrosion deposits. Although SRB were present in both normal and accelerated low-water corrosion deposits, they dominated and were exclusively active in the inner and intermediate layers of accelerated corrosion deposits. We also highlighted that some of these SRB populations are specific to the accelerated low-water corrosion deposit environment in which they probably play a dominant role in the sulfured corrosion product enrichment.

Sedimentology of the fluvial and fluvio-marine facies of the Bahariya Formation (Early Cenomanian), Bahariya Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Khalifa, M. A.; Catuneanu, O.

2008-05-01

The Lower Cenomanian Bahariya Formation in the Bahariya Oasis, Western Desert, Egypt, was deposited under two coeval environmental conditions. A fully fluvial system occurs in the southern portion of the Bahariya Oasis, including depositional products of meandering and braided streams, and a coeval fluvio-marine setting is dominant to the north. These deposits are organized into four unconformity-bounded depositional sequences, whose architecture is shaped by a complex system of incised valleys. The fluvial portion of the lower two depositional sequences is dominated by low-energy, meandering systems with a tabular geometry, dominated by overbank facies. The fluvial deposits of the upper two sequences represent the product of sedimentation within braided streams, and consist mainly of amalgamated channel-fills. The braided fluvial systems form the fill of incised valleys whose orientation follows a southeast-northwest trending direction, and which truncate the underlying sequences. Four sedimentary facies have been identified within the braided-channel systems, namely thin-laminated sandstones (Sh), cross-bedded sandstones (Sp, St), massive ferruginous sandstones (Sm) and variegated mudstones (Fm). The exposed off-channel overbank facies of the meandering systems include floodplain (Fm) and crevasse splay (Sl) facies. The fluvio-marine depositional systems consist of interbedded floodplain, coastal and shallow-marine deposits. The floodplain facies include fine-grained sandstones (Sf), laminated siltstones (Stf) and mudstones (Mf) that show fining-upward cycles. The coastal to shallow-marine facies consist primarily of mudstones (Mc) and glauconitic sandstones (Gc) organized vertically in coarsening-upward prograding cyclothems topped by thin crusts of ferricrete (Fc). The four depositional sequences are present across the Bahariya Oasis, albeit with varying degrees of preservation related to post-depositional erosion associated with the formation of sequence boundaries. These unconformities may be overlain by braided-stream channel sandstones at the base of incised valleys, or marked by ferricrete paleosols (lithofacies Fc) in the interfluve areas.

Stratigraphy and conodont biostratigraphy of the uppermost Carboniferous and Lower Permian from the North American Midcontinent

USGS Publications Warehouse

Boardman, Darwin R.; Wardlaw, Bruce R.; Nestell, Merlynd K.

2009-01-01

Part A The uppermost Wabaunsee, Admire, Council Grove, and lower Chase Groups of Kansas, Oklahoma, and Nebraska are placed into three third-order depositional sequences: a Gzhelian late-highstand sequence set, a Council Grove transgressive and highstand sequence set, and a Chase transgressive sequence set. Sequences are defined by bounding maximum-exposure surfaces and are placed within the zone of exposure surfaces (typically, stacked paleosols). Conodonts are abundant in open-marine deposits and most marine units have a differing and characteristic faunal make-up. Eleven species are described as new: Streptognathodus binodosus, S. denticulatus, S. elongianus, S. florensis, S. lineatus, S. nevaensis, S. postconstrictus, S. postelongatus, S. robustus, S. translinearis, and S. trimilus. Part B Maximum-marine flooding levels and marine-condensed sections from uppermost Carboniferous and Lower Permian fourth-order (0.1-1 m.y.) depositional sequences of the North American midcontinent reveal a rich stratigraphic succession of species of Streptognathodus and Sweetognathus conodonts that permits high-precision correlation of the Carboniferous-Permian boundary as well as the Asselian-Sakmarian and Sakmarian-Artinskian boundaries. Eleven new species of Streptognathodus are described: Streptognathodus binodosus, S. denticulatus, S. elongianus, S. florensis, S. lineatus, S. nevaensis, S. postconstrictus, S. postelongatus, S. robustus, S. translinearis, and S. trimilus. Seventeen species are redescribed and clarified and include Streptognathodus alius, S. barskovi, S. bellus, S. brownvillensis, S. conjunctus, S. constrictus, S. elongatus, S. farmeri, S. flexuosus, S. fuchengensis, S. fusus, S. invaginatus, S. isolatus, S. longissimus, S. minacutus, S. nodulinearis, and S. wabaunsensis. The correlated level of the Carboniferous-Permian boundary is recognized in the lower part of the Red Eagle Depositional Sequence based on the introduction of Streptognathodus isolatus Chernykh, Ritter, and Wardlaw; Streptognathodus minacutus Barskov and Reimers; Streptognathodus invaginatus Reshetkova and Chernykh; Streptognathodus fuchengensis Zhao; and Streptognathodus nodulinearis Reshetkova and Chernykh. The correlated Carboniferous-Permian boundary occurs in the depositional sequence that represents the maximum-marine highstand of the Council Grove Composite Third Order Sequence. This level represents a significant marine-flooding event that should be correlatable in numerous shelfal sections throughout the world. Although the Asselian-Sakmarian boundary has not been rigorously defined, Sweetognathus merrilli has been informally utilized as a Sakmarian indicator. Due to the ecologically controlled distribution of species of Sweetognathus, we prefer to use a species of Streptognathodus as a defining species. We propose that Streptognathodus barskovi (Kozur) Reshetkova be considered as a potentially defining or ancillary defining species for the Sakmarian Stage. In the North American midcontinent, Streptognathodus barskovi appears in the same depositional sequence with Sweetognathus merrilli in the Eiss (Lower Bader) Depositional Sequence. Historically, Sweetognathus whitei has been used to mark the Sakmarian-Artinskian boundary. In our succession Sweetognathus whitei and Streptognathodus florensis appear in the basal part of the Barneston Depositional Sequence. We suggest that Streptognathodus florensis be further investigated as a possible defining or ancillary defining taxon for the base of the Artinskian Stage. This depositional sequence also forms the maximum-marine highstand of the Chase Third-Order Composite Depositional Sequence suggesting that this level is a significant marine-flooding event that should be widely traceable in numerous shelfal sections.

Sedimentological indicators of paleoenvironments and siliciclastic stratigraphic sequences in some Miocene deposits of the Calvert Cliffs, southern Maryland

USGS Publications Warehouse

Shideler, G.L.

1994-01-01

Middle Miocene siliciclastic deposits comprising the Calvert Cliffs section at the Baltimore Gas and Electric Company's (BG&E) nuclear power plant site in southern Maryland were analyzed in terms of lithostratigraphy, sedimentary structures, and granulometric parameters, to interprete paleo-environments within a sequence-stratigraphic framework. In terms of sequence-stratigraphic models, the BG&E section can be interpreted as consisting of two genetic stratigraphic sequences (Galloway model), namely, a shelf sequence and an overlying deltaic sequence. Using the Exxon model, the section consists of two third-order (1-5 m.y. duration) depositional sequences. The stratigraphic sequences of the BG&E section reflect both relatively short-term eustatic transgressive events, as well as a long-term regressive trend with associated local deltation and coastal progradation. The regression probably signified a regional basinward shift of depocenters within the Salisbury embayment during Miocene time. -from Author

Quaternary geology and sapphire deposits from the BO PHLOI gem field, Kanchanaburi Province, Western Thailand

NASA Astrophysics Data System (ADS)

Choowong, Montri

2002-01-01

One of the most famous blue sapphire deposits in Thailand and SE Asia is from the Bo Phloi District, Kanchanaburi Province, Western Thailand. This paper presents the results of our gemstone investigation as well as establishing the Bo Phloi depositional sequence as one of the Quaternary Type Sections in the region. Relationships among the sedimentology, depositional sequences and geomorphology were investigated in order to understand the gemstone depositional features. Sedimentary structures and textures of the sequences show that the deposition of gemstones is related genetically to fluvial processes. Gemstones are recognized in floodplain and low terrace deposits where gemstone paystreaks concentrate mostly inside layers of gravel beds and foreset-bedded gravels lithofacies. C-14 dating of wood and peat within gemstone-bearing layers indicated that the deposit formed during the middle to late Pleistocene. The gemstone-bearing gravel bed defines a north-south trend along the incised palaeo-channel of an ancient braided river system in the middle part of the basin.

Collaborative development for setup, execution, sharing and analytics of complex NMR experiments.

PubMed

Irvine, Alistair G; Slynko, Vadim; Nikolaev, Yaroslav; Senthamarai, Russell R P; Pervushin, Konstantin

2014-02-01

Factory settings of NMR pulse sequences are rarely ideal for every scenario in which they are utilised. The optimisation of NMR experiments has for many years been performed locally, with implementations often specific to an individual spectrometer. Furthermore, these optimised experiments are normally retained solely for the use of an individual laboratory, spectrometer or even single user. Here we introduce a web-based service that provides a database for the deposition, annotation and optimisation of NMR experiments. The application uses a Wiki environment to enable the collaborative development of pulse sequences. It also provides a flexible mechanism to automatically generate NMR experiments from deposited sequences. Multidimensional NMR experiments of proteins and other macromolecules consume significant resources, in terms of both spectrometer time and effort required to analyse the results. Systematic analysis of simulated experiments can enable optimal allocation of NMR resources for structural analysis of proteins. Our web-based application (http://nmrplus.org) provides all the necessary information, includes the auxiliaries (waveforms, decoupling sequences etc.), for analysis of experiments by accurate numerical simulation of multidimensional NMR experiments. The online database of the NMR experiments, together with a systematic evaluation of their sensitivity, provides a framework for selection of the most efficient pulse sequences. The development of such a framework provides a basis for the collaborative optimisation of pulse sequences by the NMR community, with the benefits of this collective effort being available to the whole community. Copyright © 2013 Elsevier Inc. All rights reserved.

Sequence and facies architecture of the upper Blackhawk Formation and the Lower Castlegate Sandstone (Upper Cretaceous), Book Cliffs, Utah, USA

NASA Astrophysics Data System (ADS)

Yoshida, S.

2000-11-01

High-frequency stratigraphic sequences that comprise the Desert Member of the Blackhawk Formation, the Lower Castlegate Sandstone, and the Buck Tongue in the Green River area of Utah display changes in sequence architecture from marine deposits to marginal marine deposits to an entirely nonmarine section. Facies and sequence architecture differ above and below the regionally extensive Castlegate sequence boundary, which separates two low-frequency (106-year cyclicity) sequences. Below this surface, high-frequency sequences are identified and interpreted as comprising the highstand systems tract of the low-frequency Blackhawk sequence. Each high-frequency sequence has a local incised valley system on top of the wave-dominated delta, and coastal plain to shallow marine deposits are preserved. Above the Castlegate sequence boundary, in contrast, a regionally extensive sheet sandstone of fluvial to estuarine origin with laterally continuous internal erosional surfaces occurs. These deposits above the Castlegate sequence boundary are interpreted as the late lowstand to early transgressive systems tracts of the low-frequency Castlegate sequence. The base-level changes that generated both the low- and high-frequency sequences are attributed to crustal response to fluctuations in compressive intraplate stress on two different time scales. The low-frequency stratigraphic sequences are attributed to changes in the long-term regional subsidence rate and regional tilting of foreland basin fill. High-frequency sequences probably reflect the response of anisotropic basement to tectonism. Sequence architecture changes rapidly across the faulted margin of the underlying Paleozoic Paradox Basin. The high-frequency sequences are deeply eroded and stack above the Paradox Basin, but display less relief and become conformable updip. These features indicate that the area above the Paradox Basin was more prone to vertical structural movements during formation of the Blackhawk-Lower Castlegate succession.

Sequence stratigraphy and reservoir architecture of the J18/20 and J15 sequences in PM-9, Malay Basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahman, R.A.; Said, Md.J.; Bedingfield, J.R.

1994-07-01

The group J stratigraphic interval is lower Miocene (18.5-21 Ma) in age and was deposited during the early sag phase of the Malay Basin structural development. Reduction in depositional relief and first evidence of widespread marine influence characterize the transition into this interval. Twelve group J sequences have been identified. Reservoirs consist of progradational to aggradational tidally-dominated paralic to shallow marine sands deposited in the lowstand systems tract. Transgressive and highstand deposits are dominantly offshore shales. In PM-9, the original lift-related depocenters, coupled with changes in relative sea level, have strongly influenced group J unit thickness and the distribution ofmore » reservoir and seal facies. Two important reservoir intervals in PM-9 are the J18/20 and J15 sands. The reservoirs in these intervals are contained within the lowstand systems tracts of fourth-order sequences. These fourth-order sequences stack to form sequence sets in response to a third-order change in relative sea level. The sequences of the J18/20 interval stack to form part of a lowstand sequence set, whereas the J15 interval forms part of the transgressive sequence set. Reservoir facies range from tidal bars and subtidal shoals in the J18/20 interval to lower shoreface sands in the J15. Reservoir quality and continuity in group J reservoirs are dependent on depositional facies. An understanding of the controls on the distribution of facies types is crucial to the success of the current phase of field development and exploration programs in PM-9.« less

Late Pleistocene sediments and fossils near the mouth of Mad River, Humboldt County, California: Facies analysis, sequence development, and possible age correlation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, E.W.

Study of late Pleistocene-age sediments near the mouth of the Mad River revealed a sequence of nearshore marine and shallow bay deposits. This sequence, bounded by unconformities, is informally named the Mouth of Mad unit. The Mouth of mad unit can be divided into four distinct depositional facies at the study site. The lowest facies are the Nearshore Sand and Estuarine Mud, which lie unconformably on a paleosol. The sand facies grades upward into a high-energy, interbedded Nearshore Sand and Gravel facies containing storm and rip-channel deposits. Above the sand and gravel is a Strand-Plain Sand facies. This sand ismore » overlain by a laterally variable sequence of shell-rich Bay facies. The bay deposits can be further divided into five subfacies: (1) a Bioturbated Sand; (2) a Lower Tidal Flat Mud; (3) a Mixed Sand and Mud; (4) an oyster-rich Bay Mud; and (5) an Upper Tidal Flat Mud. The bay sequence is overlain unconformably by younger late Pleistocene-age marine terrace deposits. The depositional environments represented by these facies progress from a shoreline estuary to nearshore deposits, above storm wave base, and slowly back to shoreline and finally shallow bay conditions. The Mouth of Mad unit represents a transgressive-regressive sequence, involving the development of a protective spit. The uppermost mud within the Mouth of Mad unit has been dated, using thermoluminescence age estimation, at 176 [+-] 33 ka, placing it in the late Pleistocene. The Mouth of Mad unit appears to be younger than the fossiliferous deposits at Elk Head, Crannell Junction, Trinidad Head, Moonstone Beach, and the Falor Formation near Maple Creek, and possibly time equivalent with gravel deposits exposed at the western end of School Road in McKinleyville.« less

Three-dimensional T1rho-weighted MRI at 1.5 Tesla.

PubMed

Borthakur, Arijitt; Wheaton, Andrew; Charagundla, Sridhar R; Shapiro, Erik M; Regatte, Ravinder R; Akella, Sarma V S; Kneeland, J Bruce; Reddy, Ravinder

2003-06-01

To design and implement a magnetic resonance imaging (MRI) pulse sequence capable of performing three-dimensional T(1rho)-weighted MRI on a 1.5-T clinical scanner, and determine the optimal sequence parameters, both theoretically and experimentally, so that the energy deposition by the radiofrequency pulses in the sequence, measured as the specific absorption rate (SAR), does not exceed safety guidelines for imaging human subjects. A three-pulse cluster was pre-encoded to a three-dimensional gradient-echo imaging sequence to create a three-dimensional, T(1rho)-weighted MRI pulse sequence. Imaging experiments were performed on a GE clinical scanner with a custom-built knee-coil. We validated the performance of this sequence by imaging articular cartilage of a bovine patella and comparing T(1rho) values measured by this sequence to those obtained with a previously tested two-dimensional imaging sequence. Using a previously developed model for SAR calculation, the imaging parameters were adjusted such that the energy deposition by the radiofrequency pulses in the sequence did not exceed safety guidelines for imaging human subjects. The actual temperature increase due to the sequence was measured in a phantom by a MRI-based temperature mapping technique. Following these experiments, the performance of this sequence was demonstrated in vivo by obtaining T(1rho)-weighted images of the knee joint of a healthy individual. Calculated T(1rho) of articular cartilage in the specimen was similar for both and three-dimensional and two-dimensional methods (84 +/- 2 msec and 80 +/- 3 msec, respectively). The temperature increase in the phantom resulting from the sequence was 0.015 degrees C, which is well below the established safety guidelines. Images of the human knee joint in vivo demonstrate a clear delineation of cartilage from surrounding tissues. We developed and implemented a three-dimensional T(1rho)-weighted pulse sequence on a 1.5-T clinical scanner. Copyright 2003 Wiley-Liss, Inc.

Remote Stratigraphic Analysis: Combined TM and AIS Results in the Wind River/bighorn Basin Area, Wyoming

NASA Technical Reports Server (NTRS)

Lang, H. R.; Paylor, E. D.; Adams, S.

1985-01-01

An in-progress study demonstrates the utility of airborne imaging spectrometer (AIS) data for unraveling the stratigraphic evolution of a North American, western interior foreland basin. AIS data are used to determine the stratigraphic distribution of mineralogical facies that are diagnostic of specific depositional environments. After wavelength and amplitude calibration using natural ground targets with known spectral characteristics, AIS data identify calcite, dolomite, gypsum and montmorillonite-bearing strata in the Permian-Cretaceous sequence. Combined AIS and TM results illustrate the feasibility of spectral stratigraphy, remote analysis of stratigraphic sequences.

The problems and promise of DNA barcodes for species diagnosis of primate biomaterials

PubMed Central

Lorenz, Joseph G; Jackson, Whitney E; Beck, Jeanne C; Hanner, Robert

2005-01-01

The Integrated Primate Biomaterials and Information Resource (www.IPBIR.org) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome c oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics. PMID:16214744

MR Fingerprinting Using The Quick Echo Splitting NMR Imaging Technique

PubMed Central

Jiang, Yun; Ma, Dan; Jerecic, Renate; Duerk, Jeffrey; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A.

2016-01-01

Purpose The purpose of the study is to develop a quantitative method for the relaxation properties with a reduced radio frequency (RF) power deposition by combining Magnetic Resonance Fingerprinting (MRF) technique with Quick Echo Splitting NMR Imaging Technique (QUEST). Methods A QUEST-based MRF sequence was implemented to acquire high order echoes by increasing the gaps between RF pulses. Bloch simulations were used to calculate a dictionary containing the range of physically plausible signal evolutions using a range of T1 and T2 values based on the pulse sequence. MRF-QUEST was evaluated by comparing to the results of spin-echo methods. The SAR of QUEST-MRF was compared to the clinically available methods. Results MRF-QUEST quantifies the relaxation properties with good accuracy at the estimated head Specific Absorption Rate (SAR) of 0.03 W/kg. T1 and T2 values estimated by MRF-QUEST are in good agreement with the traditional methods. Conclusion The combination of the MRF and the QUEST provides an accurate quantification of T1 and T2 simultaneously with reduced RF power deposition. The resulting lower SAR may provide a new acquisition strategy for MRF when RF energy deposition is problematic. PMID:26924639

The terminal Permian in European Russia: Vyaznikovian Horizon, Nedubrovo Member, and Permian-Triassic boundary

NASA Astrophysics Data System (ADS)

Lozovsky, V. R.; Balabanov, Yu. P.; Karasev, E. V.; Novikov, I. V.; Ponomarenko, A. G.; Yaroshenko, O. P.

2016-07-01

The comprehensive analysis of the data obtained on terrestrial vertebrata, ostracods, entomologic fauna, megaflora, and microflora in deposits of the Vyaznikovian Horizon and Nedubrovo Member, as well as the paleomagnetic data measured in enclosing rocks, confirms heterogeneity of these deposits. Accordingly, it is necessary to distinguish these two stratons in the terminal Permian of the East European Platform. The combined sequence of Triassic-Permian boundary deposits in the Moscow Syneclise, which is considered to be the most complete sequence in the East European Platform, is as follows (from bottom upward): Vyatkian deposits; Vyaznikovian Horizon, including Sokovka and Zhukovo members; Nedubrovo Member (Upper Permian); Astashikha and Ryabi members of the Vokhmian Horizon (Lower Triassic). None of the sequences of Permian-Triassic boundary deposits known in the area of study characterizes this sequence in full volume. In the north, the Triassic deposits are underlain by the Nedubrovo Member; in the south (the Klyazma River basin), the sections are underlain by the Vyaznikovian Horizon. The Permian-Triassic boundary adopted in the General Stratigraphic Scale of Russia for continental deposits of the East European platform (the lower boundary of the Astashikha Member) is more ancient than the one adopted in the International Stratigraphic Chart. The same geological situation is observed in the German Basin and other localities where Triassic continental deposits are developed. The ways of solving this problem are discussed in this article.

Sedimentology and hydrodynamic implications of a coarse-grained hurricane sequence in a carbonate reef setting

USGS Publications Warehouse

Spiske, M.; Jaffe, B.E.

2009-01-01

Storms and associated surges are major coast-shaping processes. Nevertheless, no typical sequences for storm surge deposits in different coastal settings have been established. This study interprets a coarse-grained hurricane ridge deposit on the island of Bonaire, Netherlands Antilles. The sequence was deposited during Hurricane Lenny in November 1999. Insight is gained into the hydrodynamics of surge flow by interpreting textural trends, particle imbrication, and deposit geometry. Vertical textural variations, caused by time-dependent hydrodynamic changes, were used to subdivide the deposit into depositional units that correspond to different stages of the surge, such as setup, peak, and return flow. Particle size and imbrication trends and geometry of the units reflect landward bed-load transport of components during the setup, a nondirectional flow with sediment falling out of suspension during the peak, and a seaward bedload transport during the return flow. Formation of a ridge during setup affected the texture of the return flow unit. Changing angles of imbrication reflect alternating flow velocities during each phase. Normal grading during setup and inverse grading during return flow are caused by decelerating and accelerating flow, respectively. Hence, the interpreted deposit seems to represent the first described complete hurricane surge sequence from a carbonate environment. ?? 2009 Geological Society of America.

Geochemical imprint of depositional conditions on organic matter in laminated-Bioturbated interbeds from fine-grained marine sequences

USGS Publications Warehouse

Pratt, L.M.; Claypool, G.E.; King, J.D.

1986-01-01

Laminated organic-rich shales are interbedded at a scale of centimeters to a few meters with bioturbated organic-poor mudstones or limestones in some fine-grained marine sequences. We have analyzed the organic matter in pairs of laminated/bioturbated interbeds from Cretaceous and Devonian rocks deposited in epicontinental and oceanic settings for the purpose of studying the influence of depositional and early diagenetic environment on the organic geochemical properties of marine shales. Results of these analyses indicate that for rocks that are still in a diagenetic stage of thermal alteration, the relative abundance of biomarker compounds and specific biomarker indices can be useful indicators of depositional and early diagenetic conditions. Pristane/phytane ratios are generally highest for laminated rocks from epicontinental basins and appear to reflect the input of isoprenoid precursors more than oxygenated versus anoxic depositional conditions. The thermally immature laminated rocks are characterized by relatively high contents of 17??(H), 21??(H)-hopanes, hopenes, sterenes and diasterenes, and by strong predominance of the 22R over 22S homohopane isomers. Thermally immature bioturbated samples are characterized by absence of the ??,??-hopanes, by low contents of both saturated and unsaturated polycyclic hydrocarbons, and by slight or no predominance of the 22R over 22S homohopane isomers. There are less obvious compositional differences between the saturated hydrocarbons in the laminated and bioturbated units from the thermally mature sequences. For both the thermally mature and immature laminated samples, the degree of isomerization at the 22C position for hopanes and at the 20C position for steranes is generally consistent with the degree of thermal maturity interpreted from other properties of the organic matter. The bioturbated samples, however, exhibit inconsistent and anomalously high degrees of isomerization for the homohopanes, resulting either from reworking and oxidation of the primary organic matter or from the presence of older recycled organic matter. ?? 1986.

High-sensitive electrochemical detection of point mutation based on polymerization-induced enzymatic amplification.

PubMed

Feng, Kejun; Zhao, Jingjin; Wu, Zai-Sheng; Jiang, Jianhui; Shen, Guoli; Yu, Ruqin

2011-03-15

Here a highly sensitive electrochemical method is described for the detection of point mutation in DNA. Polymerization extension reaction is applied to specifically initiate enzymatic electrochemical amplification to improve the sensitivity and enhance the performance of point mutation detection. In this work, 5'-thiolated DNA probe sequences complementary to the wild target DNA are assembled on the gold electrode. In the presence of wild target DNA, the probe is extended by DNA polymerase over the free segment of target as the template. After washing with NaOH solution, the target DNA is removed while the elongated probe sequence remains on the sensing surface. Via hybridizing to the designed biotin-labeled detection probe, the extended sequence is capable of capturing detection probe. After introducing streptavidin-conjugated alkaline phosphatase (SA-ALP), the specific binding between streptavidin and biotin mediates a catalytic reaction of ascorbic acid 2-phosphate (AA-P) substrate to produce a reducing agent ascorbic acid (AA). Then the silver ions in solution are reduced by AA, leading to the deposition of silver metal onto the electrode surface. The amount of deposited silver which is determined by the amount of wild target can be quantified by the linear sweep voltammetry (LSV). The present approach proved to be capable of detecting the wild target DNA down to a detection limit of 1.0×10(-14) M in a wide target concentration range and identifying -28 site (A to G) of the β-thalassemia gene, demonstrating that this scheme offers a highly sensitive and specific approach for point mutation detection. Copyright © 2010 Elsevier B.V. All rights reserved.

Gallium plasmonic nanoparticles for label-free DNA and single nucleotide polymorphism sensing

NASA Astrophysics Data System (ADS)

Marín, Antonio García; García-Mendiola, Tania; Bernabeu, Cristina Navio; Hernández, María Jesús; Piqueras, Juan; Pau, Jose Luis; Pariente, Félix; Lorenzo, Encarnación

2016-05-01

A label-free DNA and single nucleotide polymorphism (SNP) sensing method is described. It is based on the use of the pseudodielectric function of gallium plasmonic nanoparticles (GaNPs) deposited on Si (100) substrates under reversal of the polarization handedness condition. Under this condition, the pseudodielectric function is extremely sensitive to changes in the surrounding medium of the nanoparticle surface providing an excellent sensing platform competitive to conventional surface plasmon resonance. DNA sensing has been carried out by immobilizing a thiolated capture probe sequence from Helicobacter pylori onto GaNP/Si substrates; complementary target sequences of Helicobacter pylori can be quantified over the range of 10 pM to 3.0 nM with a detection limit of 6.0 pM and a linear correlation coefficient of R2 = 0.990. The selectivity of the device allows the detection of a single nucleotide polymorphism (SNP) in a specific sequence of Helicobacter pylori, without the need for a hybridization suppressor in solution such as formamide. Furthermore, it also allows the detection of this sequence in the presence of other pathogens, such as Escherichia coli in the sample. The broad applicability of the system was demonstrated by the detection of a specific gene mutation directly associated with cystic fibrosis in large genomic DNA isolated from blood cells.A label-free DNA and single nucleotide polymorphism (SNP) sensing method is described. It is based on the use of the pseudodielectric function of gallium plasmonic nanoparticles (GaNPs) deposited on Si (100) substrates under reversal of the polarization handedness condition. Under this condition, the pseudodielectric function is extremely sensitive to changes in the surrounding medium of the nanoparticle surface providing an excellent sensing platform competitive to conventional surface plasmon resonance. DNA sensing has been carried out by immobilizing a thiolated capture probe sequence from Helicobacter pylori onto GaNP/Si substrates; complementary target sequences of Helicobacter pylori can be quantified over the range of 10 pM to 3.0 nM with a detection limit of 6.0 pM and a linear correlation coefficient of R2 = 0.990. The selectivity of the device allows the detection of a single nucleotide polymorphism (SNP) in a specific sequence of Helicobacter pylori, without the need for a hybridization suppressor in solution such as formamide. Furthermore, it also allows the detection of this sequence in the presence of other pathogens, such as Escherichia coli in the sample. The broad applicability of the system was demonstrated by the detection of a specific gene mutation directly associated with cystic fibrosis in large genomic DNA isolated from blood cells. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00926c

Sedimentary evolution of the Pliocene and Pleistocene Ebro margin, northeastern Spain

USGS Publications Warehouse

Alonso, B.; Field, M.E.; Gardner, J.V.; Maldonado, A.

1990-01-01

The Pliocene and Pleistocene deposits of the Spanish Ebro margin overlie a regional unconformity and contain a major disconformity. These unconformities, named Reflector M and Reflector G, mark the bases of two seismic sequences. Except for close to the upper boundary where a few small channel deposits are recognized, the lower sequence lacks channels. The upper sequence contains nine channel-levee complexes as well as base-of-slope aprons that represent the proximal part of the Valencia turbidite system. Diverse geometries and variations in seismic units distinguish shelf, slope, base-of-slope and basin-floor facies. Four events characterize the late Miocene to Pleistocene evolution of the Ebro margin: (a) formation of a paleodrainage system and an extensive erosion-to-depositional surface during the latest Miocene (Messinian), (b) deposition of hemipelagic units during the early Pliocene, (c) development of canyons during the late Pliocene to early Pleistocene, and (d) deposition of slope wedges, channel-levee complexes, and base-of-slope aprons alternating with hemipelagic deposition during the Pleistocene. Sea-level fluctuations influenced the evolution of the sedimentary sequences of the Ebro margin, but the major control was the sediment supply from the Ebro River. ?? 1990.

Stratigraphy and sedimentology of the K/T boundary deposit in Haiti

NASA Technical Reports Server (NTRS)

Carey, S.; Sigurdsson, H.; Dhondt, S.; Espindola, J. M.

1993-01-01

The K/T boundary sequence is exposed in uplifted carbonate sediments of the southwest peninsula of Haiti. It is found at 15 localities within the Beloc formation, a sequence of limestone and marls interpreted as a monoclinal nappe structure thrust to the north. This tectonic deformation has affected the K/T boundary deposit to varying degrees. In some cases the less competent K/T deposit has acted as a slip plane leading to extensive shearing of the boundary layer, as well as duplication of the section. The presence of glassy tektites, shocked quartz, and an Ir anomaly directly link the deposit to a bolide impact. Stratigraphic and sedimentological features of the tripartite sequence indicate that it was formed by deposition from ballistic fallout of coarse tektites, emplacement of particle gravity flows and fine grained fallout of widely dispersed impact ejecta.

Integrated biostratigraphic and sequence stratigraphic framework for Upper Cretaceous strata of the eastern Gulf Coastal Plain, USA

USGS Publications Warehouse

Mancini, E.A.; Puckett, T.M.; Tew, B.H.

1996-01-01

Upper Cretaceous (Santonian-Maastrichtian stages) strata of the eastern US Gulf Coastal Plain represent a relatively complete section of marine to nonmarine mixed siliciclastic and carbonate sediments. This section includes three depositional sequences which display characteristic systems tracts and distinct physical defining surfaces. The marine lithofacies are rich in calcareous nannoplankton and planktonic foraminifera which can be used for biostratigraphic zonation. Integration of this zonation with the lithostratigraphy and sequence stratigraphy of these strata results in a framework that can be used for local and regional intrabasin correlation and potentially for global interbasin correlation. Only the synchronous maximum flooding surfaces of these depositional sequences, however, have chronostratigraphic significance. The sequence boundaries and initial flooding surfaces are diachronous, and their use for correlation can produce conflicting results. The availability of high resolution biostratigraphy is critical for global correlation of depositional sequences. ?? 1996 Academic Press Limited.

Leg 67: the Deep Sea Drilling Project Mid-America Trench transect off Guatemala.

USGS Publications Warehouse

von Huene, Roland E.

1980-01-01

Drilling on the Cocos plate recovered a basal chalk sequence deposited during early and mid-Miocene time, a short interval of abyssal red clay, and an upper sequence of late Miocene and younger sediment deposited within an area influenced by a terrigenous source. In the trench, a mud and sand fill less than 400,000 yr old overlies the oceanic sequence. The entire section shows no evidence of compressive deformation. In contrast, the section cored on the trench's landward slope 3 km from the trench axis is affected by tectonism. The section contains a Cretaceous to Pliocene claystone sequence capped by Pliocene to Quaternary hemipelagic slope deposits.- from Authors

Actinobacterial diversity across a marine transgression in the deep subsurface off Shimokita Peninsula, Japan

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Bailey, J. V.

2013-12-01

Sediment horizons represent a significant - but not permanent - barrier to microbial transport. Cells commonly attach to mineral surfaces in unconsolidated sediments. However, by taxis, growth, or passive migration under advecting fluids, some portion of the microbial community may transgress sedimentary boundaries. Few studies have attempted to constrain such transport of community signatures in the marine subsurface and its potential impact on biogeography. Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula recovered sediments over a greater than 1km interval representing a gradual decrease of terrestrial influence, from tidal to continental shelf depositional settings. This sequence represents a key opportunity to link subsurface microbial communities to lithological variability and investigate the permanence of community signatures characteristic of distinct depositional regimes. The phylogenetic connectivity between marine and terrestrially-influenced deposits may demonstrate to what degree sediments offer a substantial barrier to cell transport in the subsurface. Previous work has demonstrated that the Actinobacterial phylum is broadly distributed in marine sediments (Maldonado et al., 2005), present and active in the deep subsurface (Orsi et al., 2013), and that marine and terrestrial lineages may potentially be distinguished by 16S rRNA gene sequencing (e.g. Prieto-Davó et al., 2013). We report on Actinobacteria-specific 16S rRNA gene diversity recovered between 1370 and 2642 mbsf with high-throughput sequencing using the Illumina MiSeq platform, as well as selective assembly and analysis of environmental clone libraries.

Sequence stratigraphy of the Kingak Shale (Jurassic-Lower Cretaceous), National Petroleum Reserve in Alaska

USGS Publications Warehouse

Houseknecht, D.W.; Bird, K.J.

2004-01-01

Beaufortian strata (Jurassic-Lower Cretaceous) in the National Petroleum Reserve in Alaska (NPRA) are a focus of exploration since the 1994 discovery of the nearby Alpine oil field (>400 MMBO). These strata include the Kingak Shale, a succession of depositional sequences influenced by rift opening of the Arctic Ocean Basin. Interpretation of sequence stratigraphy and depositional facies from a regional two-dimensional seismic grid and well data allows the definition of four sequence sets that each displays unique stratal geometries and thickness trends across NPRA. A Lower to Middle Jurassic sequence set includes numerous transgressive-regressive sequences that collectively built a clastic shelf in north-central NPRA. Along the south-facing, lobate shelf margin, condensed shales in transgressive systems tracts downlap and coalesce into a basinal condensed section that is likely an important hydrocarbon source rock. An Oxfordian-Kimmeridgian sequence set, deposited during pulses of uplift on the Barrow arch, includes multiple transgressive-regressive sequences that locally contain well-winnowed, shoreface sandstones at the base of transgressive systems tracts. These shoreface sandstones and overlying shales, deposited during maximum flooding, form stratigraphic traps that are the main objective of exploration in the Alpine play in NPRA. A Valanginian sequence set includes at least two transgressive-regressive sequences that display relatively distal characteristics, suggesting high relative sea level. An important exception is the presence of a basal transgressive systems tract that locally contains shoreface sandstones of reservoir quality. A Hauterivian sequence set includes two transgressive-regressive sequences that constitute a shelf-margin wedge developed as the result of tectonic uplift along the Barrow arch during rift opening of the Arctic Ocean Basin. This sequence set displays stratal geometries suggesting incision and synsedimentary collapse of the shelf margin. ?? 2004. The American Association of Petroleum Geologists. All rights reserved.

Seismic sequence stratigraphy of Miocene deposits related to eustatic, tectonic and climatic events, Cap Bon Peninsula, northeastern Tunisia

NASA Astrophysics Data System (ADS)

Gharsalli, Ramzi; Zouaghi, Taher; Soussi, Mohamed; Chebbi, Riadh; Khomsi, Sami; Bédir, Mourad

2013-09-01

The Cap Bon Peninsula, belonging to northeastern Tunisia, is located in the Maghrebian Alpine foreland and in the North of the Pelagian block. By its paleoposition, during the Cenozoic, in the edge of the southern Tethyan margin, this peninsula constitutes a geological entity that fossilized the eustatic, tectonic and climatic interactions. Surface and subsurface study carried out in the Cap Bon onshore area and surrounding offshore of Hammamet interests the Miocene deposits from the Langhian-to-Messinian interval time. Related to the basin and the platform positions, sequence and seismic stratigraphy studies have been conducted to identify seven third-order seismic sequences in subsurface (SM1-SM7), six depositional sequences on the Zinnia-1 petroleum well (SDM1-SDM6), and five depositional sequences on the El Oudiane section of the Jebel Abderrahmane (SDM1-SDM5). Each sequence shows a succession of high-frequency systems tract and parasequences. These sequences are separated by remarkable sequence boundaries and maximum flooding surfaces (SB and MFS) that have been correlated to the eustatic cycles and supercycles of the Global Sea Level Chart of Haq et al. (1987). The sequences have been also correlated with Sequence Chronostratigraphic Chart of Hardenbol et al. (1998), related to European basins, allows us to arise some major differences in number and in size. The major discontinuities, which limit the sequences resulted from the interplay between tectonic and climatic phenomena. It thus appears very judicious to bring back these chronological surfaces to eustatic and/or local tectonic activity and global eustatic and climatic controls.

Seismic stratigraphy, tectonics and depositional history in the Halk el Menzel region, NE Tunisia

NASA Astrophysics Data System (ADS)

Sebei, Kawthar; Inoubli, Mohamed Hédi; Boussiga, Haïfa; Tlig, Said; Alouani, Rabah; Boujamaoui, Mustapha

2007-01-01

In the Halk el Menzel area, the proximal- to pelagic platform transition and related tectonic events during the Upper Cretaceous-Lower Miocene have not been taken into adequate consideration. The integrated interpretation of outcrop and subsurface data help define a seismic stratigraphic model and clarify the geodynamic evolution of the Halk el Menzel block. The sedimentary column comprises marls and limestones of the Campanian to Upper Eocene, overlain by Oligocene to Lower Miocene aged siliciclastics and carbonates. Well to well correlations show sedimentary sequences vary considerably in lithofacies and thicknesses over short distances with remarkable gaps. The comparison of sedimentary sequences cut by borehole and seismic stratigraphic modelling as well help define ten third order depositional sequences (S1-S10). Sequences S1 through S6 (Campanian-Paleocene) are mainly characterized by oblique to sigmoid configurations with prograding sedimentary structures, whereas, sequences S7-S10 (Ypresian to Middle Miocene) are organized in shallow water deposits with marked clinoform ramp geometry. Sedimentary discontinuities developed at sequence boundaries are thought to indicate widespread fall in relative sea level. Angular unconformities record a transpressive tectonic regime that operated from the Campanian to Upper Eocene. The geometry of sequences with reduced thicknesses, differential dipping of internal seismic reflections and associated normal faulting located westerly in the area, draw attention to a depositional sedimentary system developed on a gentle slope evolving from a tectonically driven steepening towards the Northwest. The seismic profiles help delimit normal faulting control environments of deposition. In contrast, reef build-ups in the Eastern parts occupy paleohighs NE-SW in strike with bordering Upper Maastrichtian-Ypresian seismic facies onlapping Upper Cretaceous counterparts. During the Middle-Upper Eocene, transpressive stress caused reactivation of faults from normal to reverse play. This has culminated in propagation folds located to the west; whereas, the eastern part of the block has suffered progressive subsidence. Transgressive carbonate depositional sequences have predominated during the Middle Miocene and have sealed pre-existing tectonic structures.

DNA Barcoding Identifies Illegal Parrot Trade.

PubMed

Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

2015-01-01

Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Structural evolution and petroleum productivity of the Baltic basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulmishek, G.F.

The Baltic basin is an oval depression located in the western part of the Russian craton; it occupies the eastern Baltic Sea and adjacent onshore areas. The basin contains more than 5,000 m of sedimentary rocks ranging from latest Proterozoic to Tertiary in age. These rocks consist of four tectonostratigraphic sequences deposited during major tectonic episodes of basin evolution. Principal unconformities separate the sequences. The basin is underlain by a rift probably filled with Upper Proterozoic rocks. Vendian and Lower Cambrian rocks (Baikalian sequence) form two northeast-trending depressions. The principal stage of the basin development was during deposition of amore » thick Middle Cambrian-Lower Devonian (Caledonian) sequence. This stage was terminated by the most intense deformations in the basin history. The Middle Devonian-Carboniferous (Hercynian) and Permian-Tertiary (Kimmerian-Alpine) tectonic and depositional cycles only slightly modified the basin geometry and left intact the main structural framework of underlying rocks. The petroleum productivity of the basin is related to the Caledonian tectonostratigraphic sequence that contains both source rocks and reservoirs. However, maturation of source rocks, migration of oil, and formation of fields took place mostly during deposition of the Hercynian sequence.« less

Direct deposition of silver nanoplates on quartz surface by sequence pre-treatment hydroxylation and silanisation.

PubMed

Abu Bakar, Norhayati; Mat Salleh, Muhamad; Ali Umar, Akrajas; Shapter, Joseph George

2017-01-01

Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface. •Sequence hydroxylation and silanisation pre-treatment assists the deposition of the nanoplate on the surface.•Various immersion times of the quartz surface into the colloidal nanoplates determined size distributions and density surface of the nanoplates on the surface.

Paleo­geographic implications of molluscan assemblages in the Upper Cretaceous (Campanian) Pigeon Point Formation, California

USGS Publications Warehouse

Elder, William P.; Saul, LouElla

1993-01-01

The Pigeon Point Formation crops out along the San Mateo County coastline in a northern and southern sequence of folded and faulted strata. Correlation of the two sequences remains somewhat equivocal, although on the basis of biostratigraphy and a reversed magnetic interval both appear to have been deposited during the early to middle Campanian. Sedimentary structures suggest that the northern sequence was deposited by turbidity currents in a continental rise setting, whereas the southern sequence primarily reflects deposition in shelf and slope environments . Right-lateral offset on the San Andreas and subsidiary faults to the east of the Pigeon Point Formation can account for 100's of km of northward transport since its deposition. However, Champion and others (1984) suggested 2500 km of northward transport from a tropical setting of about 21°N. Molluscan assemblages in the formation argue strongly for a less tropical site of deposition. Relative abundances of warm and temperate taxa and the presence or absence of key species are similar to those of the Santa Ana Mountains Cretaceous section, and are indicative of a war

Transgressive systems tract development and incised-valley fills within a quaternary estuary-shelf system: Virginia inner shelf, USA

USGS Publications Warehouse

Foyle, A.M.; Oertel, G.F.

1997-01-01

High-frequency Quaternary glacioeustasy resulted in the incision of six moderate- to high-relief fluvial erosion surfaces beneath the Virginia inner shelf and coastal zone along the updip edges of the Atlantic continental margin. Fluvial valleys up to 5 km wide, with up to 37 m of relief and thalweg depths of up to 72 m below modern mean sea level, cut through underlying Pleistocene and Mio-Pliocene strata in response to drops in baselevel on the order of 100 m. Fluvially incised valleys were significantly modified during subsequent marine transgressions as fluvial drainage basins evolved into estuarine embayments (ancestral generations of the Chesapeake Bay). Complex incised-valley fill successions are bounded by, or contain, up to four stacked erosional surfaces (basal fluvial erosion surface, bay ravinement, tidal ravinement, and ebb-flood channel-base diastem) in vertical succession. These surfaces, combined with the transgressive oceanic ravinement that generally caps incised-valley fills, control the lateral and vertical development of intervening seismic facies (depositional systems). Transgressive stratigraphy characterizes the Quaternary section beneath the Virginia inner shelf where six depositional sequences (Sequences I-VI) are identified. Depositional sequences consist primarily of estuarine depositional systems (subjacent to the transgressive oceanic ravinement) and shoreface-shelf depositional systems; highstand systems tract coastal systems are thinly developed. The Quaternary section can be broadly subdivided into two parts. The upper part contains sequences consisting predominantly of inner shelf facies, whereas sequences in the lower part of the section consist predominantly of estuarine facies. Three styles of sequence preservation are identified. Style 1, represented by Sequences VI and V, is characterized by large estuarine systems (ancestral generations of the Chesapeake Bay) that are up to 40 m thick, have hemicylindrical wedge geometries, and occur within large, coast-oblique trending depressions (paleo-estuaries). Style 1 is dominated by fluvial through estuary-mouth depositional systems (Seismic Facies 1-4). Style 2 sequence preservation, represented by Sequences III and II, is dominantly an inner shelf and shoreface succession with a seaward-thickening tabular wedge geometry that does not exceed 15 m in thickness. These shoreface and inner shelf depositional systems of the upper transgressive systems tract (Seismic Facies 9) and highstand systems tract (Seismic Facies 7 and 11) are not associated with paleo-estuaries. Style 3 sequence preservation is represented by Sequence 1, the Holocene Sequence. It consists of lower transgressive systems tract fluvial-estuarine, lagoonal, and tidal-inlet fill deposits (Seismic Facies 1-6, and 8) overlain by upper transgressive systems tract shelf and shoreface sands (Seismic Facies 9). Style 3 has a crenulated wedge geometry, and is thickest beneath and seaward of the modern Chesapeake Bay mouth. It thins northward and landward onto Late Pleistocene interfluvial highs on the basinward side of the southern Delmarva Peninsula.

Cleavage of rRNA ensures translational cessation in sperm at fertilization

PubMed Central

Johnson, G.D.; Sendler, E.; Lalancette, C.; Hauser, R.; Diamond, M.P.; Krawetz, S.A.

2011-01-01

Intact ribosomal RNAs (rRNAs) comprise the majority of somatic transcripts, yet appear conspicuously absent in spermatozoa, perhaps reflecting cytoplasmic expulsion during spermatogenesis. To discern their fate, total RNA retained in mature spermatozoa from three fertile donors was characterized by Next Generation Sequencing. In all samples, >75% of total sequence reads aligned to rRNAs. The distribution of reads along the length of these transcripts exhibited a high degree of non-uniformity that was reiterated between donors. The coverage of sequencing reads was inversely correlated with guanine-cytosine (GC)-richness such that sequences greater than ∼70% GC were virtually absent in all sperm RNA samples. To confirm the loss of sequence, the relative abundance of specific regions of the 28S transcripts in sperm was established by 7-Deaza-2′-deoxy-guanosine-5′-triphosphate RT–PCR. The inability to amplify specific regions of the 28S sequence from sperm despite the abundant representation of this transcript in the sequencing libraries demonstrates that approximately three-quarters of RNA retained in the mature male gamete are products of rRNA fragmentation. Hence, cleavage (not expulsion of the RNA component of the translational machinery) is responsible for preventing spurious translation following spermiogenesis. These results highlight the potential importance of those transcripts, including many mRNAs, which evade fragmentation and remain intact when sperm are delivered at fertilization. Sequencing data are deposited in GEO as: GSE29160. PMID:21831882

High resolution luminescence chronology for Xiashu Loess deposits of Southeastern China

NASA Astrophysics Data System (ADS)

Yi, Shuangwen; Li, Xusheng; Han, Zhiyong; Lu, Huayu; Liu, Jinfeng; Wu, Jiang

2018-04-01

Loess deposits in Xiashu are representative of such deposits in Southeastern China that are mainly distributed in the middle and lower reaches of the Yangtze River valley. These loess-paleosol sequences provide a key archive of past climate change in humid, subtropical regions. However, the ages of the sequences are not well constrained. In this study, the standard quartz single-aliquot regenerative (SAR) dose optically stimulated luminescence (OSL) and K-feldspar post-infrared infrared stimulated luminescence (post-IR IRSL; pIRIR290) methods are used to date two loess sequences in Nanjing region. Our results show that quartz SAR OSL and K-feldspar pIRIR290 ages are more or less indistinguishable from one another up to ∼50 ka. Beyond this age, the K-feldspar pIRIR ages increased systematically with deposition depth, agreeing well with the expected ages as far as ∼200 ka. On the basis of a fully independently-dated timescale, we are therefore able to propose, for the first time, a new age model for the Xiashu Loess deposits accumulated since the penultimate interglacial period. Using our newly obtained luminescence dating ages, we observe a marked difference between the loess accumulation rates in the two sequences, potentially forced by regional depositional processes and loess preservation.

Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands.

PubMed

Magnusson, Karin; Simon, Rozalyn; Sjölander, Daniel; Sigurdson, Christina J; Hammarström, Per; Nilsson, K Peter R

2014-01-01

The disease-associated prion protein (PrP) forms aggregates which vary in structural conformation yet share an identical primary sequence. These variations in PrP conformation are believed to manifest in prion strains exhibiting distinctly different periods of disease incubation as well as regionally specific aggregate deposition within the brain. The anionic luminescent conjugated polythiophene (LCP), polythiophene acetic acid (PTAA) has previously been used to distinguish PrP deposits associated with distinct mouse adapted strains via distinct fluorescence emission profiles from the dye. Here, we employed PTAA and 3 structurally related chemically defined luminescent conjugated oligothiophenes (LCOs) to stain brain tissue sections from mice inoculated with 2 distinct prion strains. Our results showed that in addition to emission spectra, excitation, and fluorescence lifetime imaging microscopy (FLIM) can fruitfully be assessed for optical distinction of PrP deposits associated with distinct prion strains. Our findings support the theory that alterations in LCP/LCO fluorescence are due to distinct conformational restriction of the thiophene backbone upon interaction with PrP aggregates associated with distinct prion strains. We foresee that LCP and LCO staining in combination with multimodal fluorescence microscopy might aid in detecting structural differences among discrete protein aggregates and in linking protein conformational features with disease phenotypes for a variety of neurodegenerative proteinopathies.

Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands

PubMed Central

Magnusson, Karin; Simon, Rozalyn; Sjölander, Daniel; Sigurdson, Christina J; Hammarström, Per; Nilsson, K Peter R

2014-01-01

The disease-associated prion protein (PrP) forms aggregates which vary in structural conformation yet share an identical primary sequence. These variations in PrP conformation are believed to manifest in prion strains exhibiting distinctly different periods of disease incubation as well as regionally specific aggregate deposition within the brain. The anionic luminescent conjugated polythiophene (LCP), polythiophene acetic acid (PTAA) has previously been used to distinguish PrP deposits associated with distinct mouse adapted strains via distinct fluorescence emission profiles from the dye. Here, we employed PTAA and 3 structurally related chemically defined luminescent conjugated oligothiophenes (LCOs) to stain brain tissue sections from mice inoculated with 2 distinct prion strains. Our results showed that in addition to emission spectra, excitation, and fluorescence lifetime imaging microscopy (FLIM) can fruitfully be assessed for optical distinction of PrP deposits associated with distinct prion strains. Our findings support the theory that alterations in LCP/LCO fluorescence are due to distinct conformational restriction of the thiophene backbone upon interaction with PrP aggregates associated with distinct prion strains. We foresee that LCP and LCO staining in combination with multimodal fluorescence microscopy might aid in detecting structural differences among discrete protein aggregates and in linking protein conformational features with disease phenotypes for a variety of neurodegenerative proteinopathies. PMID:25495506

A buried marine depositional sequence (Presumpscot FM. ) N. of the marine limit, Waterboro, Maine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morency, R.E.

Subsurface investigations conducted in Waterboro, ME (York Co.) in connection with studies of two hazardous waste sites and a municipal water supply exploration project, have demonstrated that a laterally extensive sequence of marine deposits underlies surficial sediments mapped as non-esker ice contact glacio-fluvial deposits. The marine deposits consist of a fining-downwards sequence of grey, micaceous sands (fine to medium, grading down to a silty-fine sand), which grade downward into a thick ([plus minus] 30 feet) grey silt/clay unit, which itself shows a fining-downward trend. The stratigraphy is likely correlative to the Presumpscot Formation, as described by Bloom (1963). The bottommore » of the regressive marine sequence is marked at several locations by a thin layer of sand-sized biotite mica. Lodgement till was encountered only at scattered localities (in boreholes) at each site. The bedrock surface is of considerable relief, with changes of 200--300 feet over short distances detected. The sequence appears to be the record of a rapidly transgressing sea which inundated a valley where outwash had been deposited by meltwater ahead of retreating ice. As the sea retreated, up to 70 feet of sediment was deposited in a continuous, coarsening-upwards sequence. Subsequent to the marine regression, the sediments were reworked in a subaerial (braided stream) environment. The Surficial Geologic Map of Maine shows that the inland limit of late-glacial marine submergence is located approximately 8 miles southwest of Waterboro, in Alfred, Maine. The marine limit in Alfred takes the form of a NNE trending, blunt-ended embayment. The results of this study suggest that the marine embayment once extended northward from Alfred, and is now a buried feature, possibly representing a preglacial valley, which hosted an estuary in late Wisconsonian time.« less

Sequence stratigraphic principles applied to the Miocene Hawthorn Group, west-central Florida

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norton, V.L.; Randazzo, A.F.

1993-03-01

Sequence boundaries for the Miocene Hawthorn Group in the ROMP 20 drill core from Osprey, Sarasota County, FL were generally delineated by lithologic variations recognized from core slabs, thin section analysis, and geophysical logs. At least six depositional sequences representing third order sea level fluctuations were identified. Depositional environments were determined on the basis of the characteristic lithologic constituents including rip-up clasts, pellets, fossils, laminations, burrow, degree of induration, and grain sorting. The sequence boundaries appear to have formed when the rate of the eustatic fall exceeded basin subsidence rates producing a relative sea level fall at a depositional shorelinemore » break. As a result of the basinward facies shift associated with this sequence type, peritidal facies may directly overlie deeper water facies. Subaerial exposure and erosion can be expected. The sequence of facies representing progressively deeper water depositional environments, followed by a progressive shallowing, were present between bounding surfaces. Among the six sequences recognized, four were clearly delineated as representative of regression, subaerial exposure, and subsequent transgression. Two sequences were less clearly defined and probably represent transitional facies which had exposure surfaces developed. Comparison of the petrologically established sequence stratigraphy with published sea level curves resulted in a strong correlation between the number of sequences recognized and the number of coastal on-lap/off-lap cycles depicted for the early to middle Miocene. This correlation suggests that petrologic examination of core slabs, with supplemental thin section data, can provide useful information regarding the recognition of stratigraphic sequences and relative sea level fluctuations, particularly, in situations where seismic data may not be available.« less

Austrian phase on the northern African margin inferred from sequence stratigraphy and sedimentary records in southern Tunisia (Chotts and Djeffara areas)

NASA Astrophysics Data System (ADS)

Lazzez, Marzouk; Zouaghi, Taher; Ben Youssef, Mohamed

2008-08-01

A multidisciplinary study concerning Aptian and Albian deposits is reported from petroleum wells and the exposed section. The biostratigraphic and sedimentological analysis defined four sedimentary units. Well-logging signals' analysis allows us to refine the record resolution on Aptian series and reveals, in the Djeffara field, a transgressive system tract (TST) and a highstand system tract (HST). Exceptionally, the first sequence (S1) in the Mareth 1 well and the fifth sequence in the two wells Mareth 1 and Gourine 1 reveal the lower-stand system tract (LST). The unconformities characterized by the absence of Upper Aptian (Clansayesian) and Lower to Middle Albian deposits signed by a significant gamma-ray reduction. The Middle and Upper Albian is represented by only one deposit sequence (S6) in Mareth 1. Towards the south, in the Gourine well, two deposit sequences were identified (S6 and S7); to specify the Aptian and Albian evolution of the deposit sequences, a tentative correlation has been established between the Chotts and Djeffara areas. This correlation allows us to characterize the sedimentary unconformities related to the tectonics and eustatic events. The Chotts and the Djeffara deposition areas were developed, characterized by an irregular subsidence and separated by the Tebaga Medenine high area. The Aptian-Albian subsidence platform of southern Tunisia may be considered as a block diagram of environmental deposit with regressive and transgressive trends, showing the impact of tectonic deformations on the palaeogeographic evolution of southeastern Tunisia during the Austrian phase. This study also must be replaced within regional structural patterns that may explain both the sequential and sedimentological evolution of the area. Deformations regionally identified are integrated in the more general context of both Tethyan and Atlantic areas related to the drift of the African platform.

MR fingerprinting using the quick echo splitting NMR imaging technique.

PubMed

Jiang, Yun; Ma, Dan; Jerecic, Renate; Duerk, Jeffrey; Seiberlich, Nicole; Gulani, Vikas; Griswold, Mark A

2017-03-01

The purpose of the study is to develop a quantitative method for the relaxation properties with a reduced radio frequency (RF) power deposition by combining magnetic resonance fingerprinting (MRF) technique with quick echo splitting NMR imaging technique (QUEST). A QUEST-based MRF sequence was implemented to acquire high-order echoes by increasing the gaps between RF pulses. Bloch simulations were used to calculate a dictionary containing the range of physically plausible signal evolutions using a range of T 1 and T 2 values based on the pulse sequence. MRF-QUEST was evaluated by comparing to the results of spin-echo methods. The specific absorption rate (SAR) of MRF-QUEST was compared with the clinically available methods. MRF-QUEST quantifies the relaxation properties with good accuracy at the estimated head SAR of 0.03 W/kg. T 1 and T 2 values estimated by MRF-QUEST are in good agreement with the traditional methods. The combination of the MRF and the QUEST provides an accurate quantification of T 1 and T 2 simultaneously with reduced RF power deposition. The resulting lower SAR may provide a new acquisition strategy for MRF when RF energy deposition is problematic. Magn Reson Med 77:979-988, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Depositional History and Sequence Stratigraphy of the Middle Ordovician Yeongheung Formation (Yeongweol Group), Taebaeksan Basin, mid-east Korea

NASA Astrophysics Data System (ADS)

Kwon, Yoo Jin; Kwon, Yi Kyun

2017-04-01

The Middle Ordovician Yeongheung Formation consists of numerous meter-scale, shallowing-upward cycles which were deposited on a shallow-marine carbonate platform. Many diagnostic sedimentary textures and structures such as supratidal laminite, tepee structure, and solution-collapsed breccia are observed, which enable to infer the dry climate and high salinity conditions during deposition of the formation. In order to understand its depositional history, this study focuses on vertical and spatial stacking patterns of the second- to third-order sequences through the detailed outcrop description and geologic mapping. A total 19 lithofacies have been recognized, which can be grouped into 5 facies associations (FAs): FA1 (Supratidal flat), FA2 (Supratidal or dolomitization of peritidal facies), FA3 (Intertidal flat), FA4 (Shallow subtidal to peritidal platform), FA5 (Shallow subtidal shoal). Global mega-sequence boundary (Sauk-Tippecanoe) occurs in solution-collapsed breccia zone in the lower part of the formation. Correlation of the shallowing-upward cycle stacking pattern across the study area defines 6 transgressive-regressive depositional sequences. Each depositional sequences comprises a package of vertical and spatial staking of shallow subtidal cycles in the lower part and peritidal cycles in the upper part of the formation. According to sequence stratigraphic interpretation, the reconstructed relative sea-level curve of the Yeongweol platform is very similar to that of the Taebaek platform. Based on the absence of siliciclastic sequence such as the Jigunsan Formation and the lithologic & stratigraphic differences, however, the Yeongweol and Taebaek groups might not belong to a single depositional system within the North China platform. The Yeongweol Group can be divided by the four subunits into their unique lithologic successions and geographic distributions. The Eastern subunit of the Yeongweol Group is composed dominantly of carbonate rocks with a high composition ratio of siliciclastic materials dominated facies in the upper part of the Yeongheung Formation. The Middle1 subunit is pervasively recognized by subaerial exposures facies (carbonate breccia, paleosol), whereas the Middle2 subunit is similar to the Middle1 subunit except for the absence of subaerial exposure features. The Western subunit lost some of its primary sedimentary structure and texture in comparison to other subunits, because of the active recrystallization, metamorphism, structural deformation and carbonate diagenesis. This study reveals depositional history and refines sequence stratigraphy of the Yeongheung Formation, promoting understanding of the basin evolution of the Yeongweol Group.

Depositional sequence stratigraphy and architecture of the cretaceous ferron sandstone: Implications for coal and coalbed methane resources - A field excursion

USGS Publications Warehouse

Garrison, J.R.; Van Den, Bergh; Barker, C.E.; Tabet, D.E.

1997-01-01

This Field Excursion will visit outcrops of the fluvial-deltaic Upper Cretaceous (Turonian) Ferron Sandstone Member of the Mancos Shale, known as the Last Chance delta or Upper Ferron Sandstone. This field guide and the field stops will outline the architecture and depositional sequence stratigraphy of the Upper Ferron Sandstone clastic wedge and explore the stratigraphic positions and compositions of major coal zones. The implications of the architecture and stratigraphy of the Ferron fluvial-deltaic complex for coal and coalbed methane resources will be discussed. Early works suggested that the southwesterly derived deltaic deposits of the the upper Ferron Sandstone clastic wedge were a Type-2 third-order depositional sequence, informally called the Ferron Sequence. These works suggested that the Ferron Sequence is separated by a type-2 sequence boundary from the underlying 3rd-order Hyatti Sequence, which has its sediment source from the northwest. Within the 3rd-order depositional sequence, the deltaic events of the Ferron clastic wedge, recognized as parasequence sets, appear to be stacked into progradational, aggradational, and retrogradational patterns reflecting a generally decreasing sediment supply during an overall slow sea-level rise. The architecture of both near-marine facies and non-marine fluvial facies exhibit well defined trends in response to this decrease in available sediment. Recent studies have concluded that, unless coincident with a depositional sequence boundary, regionally extensive coal zones occur at the tops of the parasequence sets within the Ferron clastic wedge. These coal zones consist of coal seams and their laterally equivalent fissile carbonaceous shales, mudstones, and siltstones, paleosols, and flood plain mudstones. Although the compositions of coal zones vary along depositional dip, the presence of these laterally extensive stratigraphic horizons, above parasequence sets, provides a means of correlating and defining the tops of depositional parasequence sets in both near-marine and non-marine parts of fluvial-deltaic depositional sequences. Ongoing field studies, based on this concept of coal zone stratigraphy, and detailed stratigraphic mapping, have documented the existence of at least 12 parasequence sets within the Last Chance delta clastic wedge. These parasequence sets appear to form four high frequency, 4th-order depositional sequences. The dramatic erosional unconformities, associated with these 4th-order sequence boundaries, indicate that there was up to 20-30 m of erosion, signifying locally substantial base-level drops. These base-level drops were accompanied by a basin ward shift in paleo-shorelines by as much as 5-7 km. These 4th-order Upper Ferron Sequences are superimposed on the 3rd-order sea-level rise event and the 3rd-order, sediment supply/accommodation space driven, stratigraphie architecture of the Upper Ferron Sandstone. The fluvial deltaic architecture shows little response to these 4th-order sea-level events. Coal zones generally thicken landward relative to the mean position of the landward pinch-out of the underlying parasequence set, but after some distance landward, they decrease in thickness. Coal zones also generally thin seaward relative to the mean position of the landward pinch-out of the underlying parasequence set. The coal is thickest in the region between this landward pinch-out and the position of maximum zone thickness. Data indicate that the proportion of coal in the coal zone decreases progressively landward from the landward pinch-out. The effects of differential compaction and differences in original pre-peat swamp topography have the effect of adding perturbations to the general trends. These coal zone systematics have major impact on approaches to exploration and production, and the resource accessment of both coal and coalbed methane.

A short review of paleoenvironments for Lower Beaufort (Upper Permian) Karoo sequences from southern to central Africa: A major Gondwana Lacustrine episode

NASA Astrophysics Data System (ADS)

Yemane, K.; Kelts, K.

This paper compares Karoo deposits within the Lower Beaufort (Late Permian) time interval from southern to central Africa. Facies aspects are summarized for selected sequences and depositional environments assessed in connection with the palaeogeography. The comparison shows that thickness of Lower Beaufort sequences varies greatly; sequences are over a kilometre thick at the southern tip, but decrease drastically to the north, northwest and northeast, and is commonly absent from the western part of the subcontinent. Depositional environments are continental except for small estuarine intervals from a sequence in Tanzania. The commonest lithologies comprise mudstones, siltstones, arkoses and carbonates. In spite of the dominance of fluvial facies, the records preserved by intervals of lacustrine sequences suggest that large lakes were major features of the palaeogeography, and that lacustrine environments may have been dominant deposition environments. The Lower Beaufort landscape is generally interpreted as an expansive cratonic lowland with meandering rivers and streams crossing vast floodplains, which were indented by concomitant shallow lakes of various sizes. The lakes from the Karoo tectono-sedimentary terrain were often ephemeral and closely linked with fluvial processes, but large, anoxic lakers are also documented. On the other hand, giant, freshwater lakes, covered large areas of the Zambezian tectono-sedimentary terrain and may have been locally connected. Evidence from abundant freshwater fossil assemblages, particularly from the Zambezian tectono-sedimentary terrain suggest that in spite of the generally semi-arid global climate of the Upper Permian, seasonal precipitation (monsoonal?) supplied enough moisture to sustain large perennial lakes. Because of the unique nature of the Permian cotinental configuration and palaeogeography, however, modern analogues of large systems are lacking. The general lithological and palaeontological correlability of Lower Beaufort sequences suggests a similar regional palaeoclimate, whereas the differences in distribution are taken to be a result of control of tectonic settings. From the widespread occurrences of lake deposits in the African subcontinent, over relatively long interval, we conclude that lake deposits provide more information for a better understanding of Karoo palaeogeography than previously thought, since such lacustrine sequences should hold sensitive, high resolution records for palaeoenvironmental interpretations.

Tectonostratigraphy and depositional history of the Neoproterozoic volcano-sedimentary sequences in Kid area, southeastern Sinai, Egypt: Implications for intra-arc to foreland basin in the northern Arabian-Nubian Shield

NASA Astrophysics Data System (ADS)

Khalaf, E. A.; Obeid, M. A.

2013-09-01

This paper presents a stratigraphic and sedimentary study of Neoproterozoic successions of the South Sinai, at the northernmost segment of the Arabian-Nubian Shield (ANS), including the Kid complex. This complex is composed predominantly of thick volcano-sedimentary successions representing different depositional and tectonic environments, followed by four deformational phases including folding and brittle faults (D1-D4). The whole Kid area is divisible from north to south into the lower, middle, and upper rock sequences. The higher metamorphic grade and extensive deformational styles of the lower sequence distinguishes them from the middle and upper sequences. Principal lithofacies in the lower sequence include thrust-imbricated tectonic slice of metasediments and metavolcanics, whereas the middle and upper sequences are made up of clastic sediments, intermediate-felsic lavas, volcaniclastics, and dike swarms. Two distinct Paleo- depositional environments are observed: deep-marine and alluvial fan regime. The former occurred mainly during the lower sequence, whereas the latter developed during the other two sequences. These alternations of depositional conditions in the volcano-sedimentary deposits suggest that the Kid area may have formed under a transitional climate regime fluctuating gradually from warm and dry to warm and humid conditions. Geochemical and petrographical data, in conjunction with field relationships, suggest that the investigated volcano-sedimentary rocks were built from detritus derived from a wide range of sources, ranging from Paleoproterozoic to Neoproterozoic continental crust. Deposition within the ancient Kid basin reflects a complete basin cycle from rifting and passive margin development, to intra-arc and foreland basin development and, finally, basin closure. The early phase of basin evolution is similar to various basins in the Taupo volcanics, whereas the later phases are similar to the Cordilleran-type foreland basin. The progressive change in lithofacies from marine intra-arc basin to continental molasses foreland basin and from compression to extension setting respectively, imply that the source area became peneplained, where the Kid basin became stabilized as sedimentation progressed following uplift. The scenario proposed of the study area supports the role of volcanic and tectonic events in architecting the facies and stratigraphic development.

Sedimentology and sequence stratigraphy of the Lower Jurassic Kayenta Formation, Colorado Plateau, United States

NASA Astrophysics Data System (ADS)

Sanabria, Diego Ignacio

2001-07-01

Detailed outcrop analysis of the Lower Jurassic Kayenta Formation provides the basis for the formulation of a new sequence stratigraphic model for arid to semi-arid continental deposits and the generation of a comprehensive set of sedimentologic criteria for the recognition of ephemeral stream deposits. Criteria for the recognition of ephemeral deposits in the ancient record were divided into three categories according to the scale of the feature being considered. The first category takes into account sedimentary structures commonly found in the record of ephemeral stream deposits including hyperconcentrated and debris flow deposits, planar parallel bedding, sigmoidal cross-bedding, hummocky cross-bedding, climbing ripple lamination, scour-and-fill structures, convolute bedding, overturned cross-bedding, ball-and-pillow structures, pocket structures, pillars, mud curls, flaser lamination, algal lamination, termite nests, and vertebrate tracks. The second category is concerned with the mesoscale facies architecture of ephemeral stream deposits and includes waning flow successions, bedform climb, downstream accretion, terminal wadi splays, and channel-fill successions indicating catastrophic flooding. At the large-scale facies architecture level, the third category, ephemeral stream deposits are commonly arranged in depositional units characterized by a downstream decrease in grain size and scale of sedimentary structures resulting from deposition in terminal fan systems. Outcrops of the Kayenta Formation and its transition to the Navajo Sandstone along the Vermilion and Echo Cliffs of Northern Arizona indicate that wet/dry climatic cyclicity exerted a major control on regional facies architecture. Two scales of wet/dry climatic cyclicity can be recognized in northern Arizona. Three sequence sets composed of rocks accumulated under predominantly dry or wet conditions are the expression of long-term climatic cyclicity. Short-term climatic cyclicity, on the other hand, is represented by high-frequency sequences composed of eolian or ephemeral fluvial deposits overlain by perennial fluvial sediments. Increased evapotranspiration rates, depressed water tables, and accumulation of eolian or ephemeral fluvial deposits characterize the dry portion of these cycles. The wet part of the cycles is marked by an increase in precipitation and the establishment of perennial fluvial systems and lacustrine basins. This depositional model constitutes a valuable tool for correlation of similar deposits in the subsurface.

Radiocarbon Dates from Volcanic Deposits of the Chaos Crags and Cinder Cone Eruptive Sequences and Other Deposits, Lassen Volcanic National Park and Vicinity, California

USGS Publications Warehouse

Clynne, Michael A.; Christiansen, Robert L.; Trimble, Deborah A.; McGeehin, John P.

2008-01-01

This contribution reports radiocarbon ages obtained from charcoal, wood and other samples collected between 1979 and 2001 in Lassen Volcanic National Park and vicinity and a few samples from other nearby localities. Most of the samples are from the Chaos Crags and Cinder Cone eruptive sequences. Brief summaries are given of the Chaos Crags and Cinder Cone eruptive sequences.

Recognition of the DNA sequence by an inorganic crystal surface

PubMed Central

Sampaolese, Beatrice; Bergia, Anna; Scipioni, Anita; Zuccheri, Giampaolo; Savino, Maria; Samorì, Bruno; De Santis, Pasquale

2002-01-01

The sequence-dependent curvature is generally recognized as an important and biologically relevant property of DNA because it is involved in the formation and stability of association complexes with proteins. When a DNA tract, intrinsically curved for the periodical recurrence on the same strand of A-tracts phased with the B-DNA periodicity, is deposited on a flat surface, it exposes to that surface either a T- or an A-rich face. The surface of a freshly cleaved mica crystal recognizes those two faces and preferentially interacts with the former one. Statistical analysis of scanning force microscopy (SFM) images provides evidence of this recognition between an inorganic crystal surface and nanoscale structures of double-stranded DNA. This finding could open the way toward the use of the sequence-dependent adhesion to specific crystal faces for nanotechnological purposes. PMID:12361979

Evolution of the arginase fold and functional diversity

PubMed Central

Dowling, Daniel P.; Costanzo, Luigi Di; Gennadios, Heather A.; Christianson, David W.

2009-01-01

The large number of protein structures deposited in the Protein Data Bank allows for the identification of novel structural superfamilies based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique α/β fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel 8 stranded β-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core α/β fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes. PMID:18360740

Coupling molecules and morphology to discover new clades of ciliates.

NASA Astrophysics Data System (ADS)

Grattepanche, J. D.; Maurer-Alcalá, X. X.; Tucker, S. J.; McManus, G. B.; Katz, L. A.

2016-02-01

In a previous study using high-throughput sequencing (Grattepanche et al submitted, oral presentation?), we observe the presence of two clades of spirotrich ciliates mainly present in marine deep-water along the New England coast. These clades, clusters X1 and X2, are characterized by several deletions in their SSU-rDNA and have been observed elsewhere as both identical and similar sequences have been deposited on GenBank from other environmental studies, but lack morphological description. In order to link molecules (SSU-rDNA sequence) to their morphology, we sample below the photic zone (between 60 to 400m of depth) in the New England coast (Northeast Atlantic) in a transect crossing the continental shelf. We designed an oligonucleotide probe specific for choreotrich and oligotrich ciliates and another specific to clusters X1 and X2 to describe these clades through a combination of Fluorescence In Situ Hybridization (FISH) and light microscopy. Our aim is to increase our knowledge on the morphology of these `unknown' clades of ciliates, which will allow for future ecological studies.

Characteristics, stratigraphic architecture, and time framework of multi-order mixed siliciclastic and carbonate depositional sequences, outcropping Cisco Group (Late Pennsylvanian and Early Permian), Eastern Shelf, north-central Texas, USA

NASA Astrophysics Data System (ADS)

Yang, Wan; Kominz, Michelle A.

2003-01-01

The Cisco Group on the Eastern Shelf of the Midland Basin is composed of fluvial, deltaic, shelf, shelf-margin, and slope-to-basin carbonate and siliciclastic rocks. Sedimentologic and stratigraphic analyses of 181 meter-to-decimeter-scale depositional sequences exposed in the up-dip shelf indicated that the siliciclastic and carbonate parasequences in the transgressive systems tracts (TST) are thin and upward deepening, whereas those in highstand systems tracts (HST) are thick and upward shallowing. The sequences can be subdivided into five types on the basis of principal lithofacies, and exhibit variable magnitude of facies shift corresponding to variable extents of marine transgression and regression on the shelf. The sequence stacking patterns and their regional persistence suggest a three-level sequence hierarchy controlled by eustasy, whereas local and regional changes in lithology, thickness, and sequence type, magnitude, and absence were controlled by interplay of eustasy, differential shelf subsidence, depositional topography, and pattern of siliciclastic supply. The outcropping Cisco Group is highly incomplete with an estimated 6-11% stratigraphic completeness. The average duration of deposition of the major (third-order) sequences is estimated as 67-102 ka on the up-dip shelf and increases down dip, while the average duration of the major sequence boundaries (SB) is estimated as 831-1066 ka and decreases down dip. The nondepositional and erosional hiatus on the up-dip shelf was represented by lowstand deltaic systems in the basin and slope.

Sequence stratigraphy of the Maastrichtian-Paleocene succession at the Dakhla Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Hewaidy, Abdel Galil A.; Farouk, Sherif; Bazeen, Youssef S.

2017-12-01

The Maastrichtian-Paleocene succession at the Dakhla Oasis is marked by the presence of a typical Nile Valley Facies represented by the Dakhla and Tarawan formations in Edmonstone and Qur El Malik sections in the central and western parts of the oasis, while a mixed Nile Valley and Garra Al-Arbain facies represented by Dakhla, Kurkur and Tarawan formations in Teneida section in the eastern part of the oasis adjacent to the Abu Tartur Plateau. These sections were examined for their foraminiferal contents, lithologic characters and stratigraphic boundaries. The distribution of foraminifera in the studied sections is variable and inconstant, as the planktonics are concentrated only at certain levels, which may be considered as a time intervals of transgression and maximum flooding surfaces. Eight planktonic biozones are distinguished in this work; of theses two are of Maastrichtain age and six are of Paleocene age. Eight 3rd order depositional sequences are recognized in the studied Maastrichtian-Paleocene succession based on the time stratigraphic boundaries released from the planktonic foraminifera and sea level changes which are released from the paleoecologic interpretations. The distinguished sequences are subdivided into their systems tracts based on the paleobathymetric interpretations of P/B% and benthic biofacies analysis. These sequences are bounded by eight sequence boundaries (SB A - SB H) represented by unconformity surfaces and depositional hiatuses. The correlation of the sequence boundaries of the established depositional sequences with the eustatic sea level curve, suggesting that these depositional sequences were resulted from the interplay of eustatic sea-level changes and local tectonic activities.

Sequence stratigraphic controls on reservoir characterization and architecture: case study of the Messinian Abu Madi incised-valley fill, Egypt

NASA Astrophysics Data System (ADS)

Abdel-Fattah, Mohamed I.; Slatt, Roger M.

2013-12-01

Understanding sequence stratigraphy architecture in the incised-valley is a crucial step to understanding the effect of relative sea level changes on reservoir characterization and architecture. This paper presents a sequence stratigraphic framework of the incised-valley strata within the late Messinian Abu Madi Formation based on seismic and borehole data. Analysis of sand-body distribution reveals that fluvial channel sandstones in the Abu Madi Formation in the Baltim Fields, offshore Nile Delta, Egypt, are not randomly distributed but are predictable in their spatial and stratigraphic position. Elucidation of the distribution of sandstones in the Abu Madi incised-valley fill within a sequence stratigraphic framework allows a better understanding of their characterization and architecture during burial. Strata of the Abu Madi Formation are interpreted to comprise two sequences, which are the most complex stratigraphically; their deposits comprise a complex incised valley fill. The lower sequence (SQ1) consists of a thick incised valley-fill of a Lowstand Systems Tract (LST1)) overlain by a Transgressive Systems Tract (TST1) and Highstand Systems Tract (HST1). The upper sequence (SQ2) contains channel-fill and is interpreted as a LST2 which has a thin sandstone channel deposits. Above this, channel-fill sandstone and related strata with tidal influence delineates the base of TST2, which is overlain by a HST2. Gas reservoirs of the Abu Madi Formation (present-day depth ˜3552 m), the Baltim Fields, Egypt, consist of fluvial lowstand systems tract (LST) sandstones deposited in an incised valley. LST sandstones have a wide range of porosity (15 to 28%) and permeability (1 to 5080mD), which reflect both depositional facies and diagenetic controls. This work demonstrates the value of constraining and evaluating the impact of sequence stratigraphic distribution on reservoir characterization and architecture in incised-valley deposits, and thus has an important impact on reservoir quality evolution in hydrocarbon exploration in such settings.

Chemical Vapor Deposition Of Silicon Carbide

NASA Technical Reports Server (NTRS)

Powell, J. Anthony; Larkin, David J.; Matus, Lawrence G.; Petit, Jeremy B.

1993-01-01

Large single-crystal SiC boules from which wafers of large area cut now being produced commerically. Availability of wafers opens door for development of SiC semiconductor devices. Recently developed chemical vapor deposition (CVD) process produces thin single-crystal SiC films on SiC wafers. Essential step in sequence of steps used to fabricate semiconductor devices. Further development required for specific devices. Some potential high-temperature applications include sensors and control electronics for advanced turbine engines and automobile engines, power electronics for electromechanical actuators for advanced aircraft and for space power systems, and equipment used in drilling of deep wells. High-frequency applications include communication systems, high-speed computers, and microwave power transistors. High-radiation applications include sensors and controls for nuclear reactors.

A middle Pleistocene through middle Miocene moraine sequence in the central Transantarctic Mountains, Antarctica

NASA Astrophysics Data System (ADS)

Balter, A.; Bromley, G. R.; Balco, G.; Thomas, H.; Jackson, M. S.

2017-12-01

Ice-free areas at high elevation in the central Transantarctic Mountains preserve extensive moraine sequences and drift deposits that comprise a geologic record of former East Antarctic Ice Sheet thickness and extent. We are applying cosmogenic-nuclide exposure dating to determine the ages of these moraine sequences at Roberts Massif and Otway Massif, at the heads of the Shackleton and Beardmore Glaciers, respectively. Moraines at these sites are for the most part openwork boulder belts characteristic of deposition by cold-based ice, which is consistent with present climate and glaciological conditions. To develop our chronology, we collected samples from 30 distinct ice-marginal landforms and have so far measured >100 3He, 10Be, and 21Ne exposure ages. Apparent exposure ages range from 1-14 Ma, which shows that these landforms record glacial events between the middle Pleistocene and middle Miocene. These data show that the thickness of the East Antarctic Ice Sheet in this region was similar to or thicker than present for long periods between the middle Miocene and today. The time range represented by these moraine sequences indicates that they may also provide direct geologic evidence for East Antarctic Ice Sheet behavior during past periods of warmer-than-present climate, specifically the Miocene and Pliocene. As the East Antarctic Ice Sheet is the largest ice sheet on earth, understanding its sensitivity to warm-climate conditions is critical for projections of ice sheet behavior and sea-level rise in future warm climates.

Seismic sequence stratigraphy and platform to basin reservoir structuring of Lower Cretaceous deposits in the Sidi Aïch-Majoura region (Central Tunisia)

NASA Astrophysics Data System (ADS)

Azaïez, Hajer; Bédir, Mourad; Tanfous, Dorra; Soussi, Mohamed

2007-05-01

In central Tunisia, Lower Cretaceous deposits represent carbonate and sandstone reservoir series that correspond to proven oil fields. The main problems for hydrocarbon exploration of these levels are their basin tectonic configuration and their sequence distribution in addition to the source rock availability. The Central Atlas of Tunisia is characterized by deep seated faults directed northeast-southwest, northwest-southeast and north-south. These faults limit inherited tectonic blocks and show intruded Triassic salt domes. Lower Cretaceous series outcropping in the region along the anticline flanks present platform deposits. The seismic interpretation has followed the Exxon methodologies in the 26th A.A.P.G. Memoir. The defined Lower Cretaceous seismic units were calibrated with petroleum well data and tied to stratigraphic sequences established by outcrop studies. This allows the subsurface identification of subsiding zones and thus sequence deposit distribution. Seismic mapping of these units boundary shows a structuring from a platform to basin blocks zones and helps to understand the hydrocarbon reservoir systems-tract and horizon distribution around these domains.

The Array Automated Assembly Task for the Low Cost Solar Array Project, Phase 2

NASA Technical Reports Server (NTRS)

Campbell, R. B. (Editor); Farukhi, S. (Editor)

1978-01-01

During the program a process sequence was proposed and tested for the fabrication of dendritic welb silicon into solar modules. This sequence was analyzed as to yield and cost and these data suggest that the price goals of 1986 are attainable. Specifically, it was shown that a low cost POCL3 is a suitable replacement for the semiconductor grade, and that a suitable CVD oxide can be deposited from a silane/air mixture using a Silox reactor. A dip coating method was developed for depositing an antireflection coating from a metalorganic precursor. Application of photoresist to define contact grids was made cost effective through use of a dip coating technique. Electroplating of both Ag and Cu was shown feasible and cost effective for producing the conductive metal grids on the solar cells. Laser scribing was used to separate the cells from the dendrites without degradation. Ultrasonic welding methods were shown to be feasible for interconnecting the cells. A study of suitable low cost materials for encapsulation suggest that soda lime glass and phenolic filled board are preferred.

Recognition of maximum flooding events in mixed siliciclastic-carbonate systems: Key to global chronostratigraphic correlation

USGS Publications Warehouse

Mancini, E.A.; Tew, B.H.

1997-01-01

The maximum flooding event within a depositional sequence is an important datum for correlation because it represents a virtually synchronous horizon. This event is typically recognized by a distinctive physical surface and/or a significant change in microfossil assemblages (relative fossil abundance peaks) in siliciclastic deposits from shoreline to continental slope environments in a passive margin setting. Recognition of maximum flooding events in mixed siliciclastic-carbonate sediments is more complicated because the entire section usually represents deposition in continental shelf environments with varying rates of biologic and carbonate productivity versus siliciclastic influx. Hence, this event cannot be consistently identified simply by relative fossil abundance peaks. Factors such as siliciclastic input, carbonate productivity, sediment accumulation rates, and paleoenvironmental conditions dramatically affect the relative abundances of microfossils. Failure to recognize these complications can lead to a sequence stratigraphic interpretation that substantially overestimates the number of depositional sequences of 1 to 10 m.y. duration.

Oligocene lacustrine tuff facies, Abu Treifeya, Cairo-Suez Road, Egypt

NASA Astrophysics Data System (ADS)

Abdel-Motelib, Ali; Kabesh, Mona; El Manawi, Abdel Hamid; Said, Amir

2015-02-01

Field investigations in the Abu Treifeya area, Cairo-Suez District, revealed the presence of Oligocene lacustrine volcaniclastic deposits of lacustrine sequences associated with an Oligocene rift regime. The present study represents a new record of lacustrine zeolite deposits associated with saponite clay minerals contained within reworked clastic vitric tuffs. The different lithofacies associations of these clastic sequences are identified and described: volcaniclastic sedimentary facies represent episodic volcaniclastic reworking, redistribution and redeposition in a lacustrine environment and these deposits are subdivided into proximal and medial facies. Zeolite and smectite minerals are mainly found as authigenic crystals formed in vugs or crusts due to the reaction of volcanic glasses with saline-alkaline water or as alteration products of feldspars. The presence of abundant smectite (saponite) may be attributed to a warm climate, with alternating humid and dry conditions characterised by the existence of kaolinite. Reddish iron-rich paleosols record periods of non-deposition intercalated with the volcaniclastic tuff sequence.

Paleocene to Middle Miocene planktic foraminifera of the southwestern Salisbury Embayment, Virginia and Maryland: biostratigraphy, allostratigraphy, and sequence stratigraphy

USGS Publications Warehouse

Poag, C.W.; Commeau, J.A.

1995-01-01

The Paleocene to Middle Miocene sedimentary fill of the southwestern Salisbury Embayment contains a fragmental depositional record, interrupted by numerous local diastems and regional unconformities. Using planktic foraminiferal biostratigraphy, 15 unconformity-bounded depositional units have been identified, assigned to six formations and seven alloformations previously recognized in the embayment. The units correlate with second- and third-order sequences of the Exxon sequence stratigraphy model, and include transgressive and highstand systems tracts. Alloformation, formation, and sequence boundaries are marked by abrupt, scoured, burrowed, erosional surfaces, which display lag deposits, biostratigraphic gaps, and intense reworking of microfossils above and below the boundaries.Paleocene deposits represent the upper parts of upper Pleocene Biochronozones P4 and P5, and rest uncomformably  on Cretaceous sedimentary beds of various ages (Maastrichtian to Albian). Lower Eocene deposits represent parts of Biochronozones P6 and P9. Middle Eocene strata represent mainly parts of Biochronozones P11, P12, and P14. Upper Eocene sediments include parts of Biochronozones P15, P16, and P17. Oligocene deposits encompass parts of Biochronozones. N4b to N7 undifferentiated, P21a, and, perhaps, N4a. Lower Miocene deposits encompass parts of Biochronozones N4b to N7 undifferentiated. Middle Miocene strata represent mainly parts of Biochronorones N8, N9, and N10.Nine plates of scanning electron micrographs illustrate the principal planktic foraminifera used to establish the biostratigraphic framework. Two new informal formine of Praeterenuitella praegemma Li, 1987, are introduced.

Ramp Creek and Harrodsburg Limestones: A shoaling-upward sequence with storm-produced features in southern Indiana, U.S.A.. Carbonate petrology seminar, Indiana University

NASA Astrophysics Data System (ADS)

1987-05-01

Most previously described examples of storm-produced stratification have been reported from siliciclastic rocks. However, such features should also be common in carbonate rocks. The Mississippian (Valmeyeran) Ramp Creek and Harrodsburg Limestones, deposited on the east margin of the Illinois Basin on top of the Borden Delta, contain storm-produced features. The dolomitic, geode-bearing Ramp Creek Limestone contains muddying-upward sequences, commonly with scoured bases overlain by grainstones, packstones, wackestones, and burrowed mudstones. These sequences are similar to hummocky sequences formed by storm waves below fair-weather wave base. The middle portion of the section including the upper Ramp Creek and lower Harrodsburg Limestones contains dolomitized mud lenses of uncertain origin. They may have formed by the baffling effect of bryozoans and/or unpreserved algae. The Harrodsburg is gradational with the Ramp Creek and consists predominantly of grainstones and packstones deposited in shallower water. Low-angle cross-stratification and truncation surfaces suggest a foreshore depositional environment for the Harrodsburg. Neither formation contains any indication of supratidal deposition as has been previously suggested. Open marine conditions during deposition of both formations are indicated by the fauna which includes crinoids, bryozoans, brachiopods, corals, ostracods, echinoids, trilobites, molluscs, fish (sharks), and trace fossils.

The Miocene Sommières basin, SE France: Bioclastic carbonates in a tide-dominated depositional system

NASA Astrophysics Data System (ADS)

Reynaud, Jean-Yves; James, Noël P.

2012-12-01

The Miocene Sommières Basin in SE France is a semi-enclosed depression that was connected to the Mediterranean Sea by a flooded paleo-incised valley and then filled by a suite of sediments comprising carbonate grains coming from temperate factories that were largely deposited in tidal-dominated paleoenvironments. The strata are partitioned into two sequences that reflect repeated flooding of the incised valley system, one of several similar situations in this region of France. The carbonate grains are mostly bioclasts, namely from barnacles, bryozoans, coralline algae (encrusting, branching, and rhodoliths), echinoids, and benthic foraminifers (large and small) with ostracods, sponge spicules and planktic foraminifers prominent in muddy facies. Particles were produced by shallow water carbonate factories on hard substrates (valley walls in particular), associated with subaqueous dunes, and in deeper water basinal settings. Each depositional sequence is underlain by an eroded and bored hard surface that is progressively overlain by TST subaqueous tidal dunes or storm deposits that grade up, in one case, into HST marls (the HST of the upper sequence has been removed by erosion). The lower sequence is ebb tide dominated whereas the upper sequence is flood tide dominated. The succession is interpreted to represent a TST whose tidal currents were focused by the narrow valley and a HST that reflected flooding of the overbanks. This stratigraphic and depositional motif is comparable to that in other spatially separated Neogene paleovalleys that are filled with tide-dominated clastic carbonates in the region. Together with other recently documented similar systems, these limestones constitute an important new group of carbonate sand bodies in the carbonate depositional realm.

The relationship between shellbed type and sequence architecture: examples from Japan and New Zealand

NASA Astrophysics Data System (ADS)

Kondo, Yasuo; Abbott, Stephen T.; Kitamura, Akihisa; Kamp, Peter J. J.; Naish, Tim R.; Kamataki, Takanobu; Saul, Gordon S.

1998-12-01

Examples of lithology, fossil content and taphonomic features of shellbeds and intervening less fossiliferous intervals are presented from four Plio-Pleistocene successions (Shimosa Group, Boso Peninsula, Omma Formation, Hokuriku area, Japan, and Okehu, Kai-iwi, and Shakespeare groups in Wanganui, and the Rangitikei Group along the Rangitikei River in New Zealand). As for pre-Pliocene 3rd- and 4th-order depositional sequences, Plio-Pleistocene 5th- to 7th-order depositional sequences contain a variety of shellbeds which are often associated with surfaces or intervals that are characterized by sedimentary condensation, omission or erosion (e.g. sequence boundaries, ravinement surfaces, downlap surfaces and condensed sections). Stratigraphic patterns of shellbed type tend to be similar and repetitive within a basin and a locality. This demonstrates that a specific palaeogeography played an important role in determining the nature of shellbeds. For example, shellbeds formed in the context of toplap are common only in the Shimosa Group, which was deposited in a moderately sheltered sea, the palaeo-Tokyo Bay. Toplap shellbeds are rare in other sequences formed in more open conditions. Despite the variability resulting from such basin characteristics, common styles of shellbeds can be recognized that formed under conditions of marine onlap, backlap, downlap and toplap. Each type of shellbed has a characteristic fossil composition and taphonomy. Onlap and toplap shellbeds contain low-diversity macrobenthic associations including Glycymeris, Mercenaria, Paphies or other bivalves having robust shells, which are often abraded or fragmented. Backlap shellbeds, which are equivalent to the condensed section formed at the maximum transgression, are characterized by dominance of epifaunal macrobenthos such as bryozoa, brachiopoda, pectinid and ostreid bivalves, preserved in a slightly cemented, glauconitic muddy matrix. In contrast to fossils in such condensed sections, the shell density and species diversity of downlap shellbed associations are rather low, and in a few examples the macrobenthic association was buried rapidly in a lower unit of the highstand systems tract (HST) stratigraphically located above the condensed sections. Variations in the stratigraphic distribution of shellbed types are reflected in symmetrical and asymmetrical sequence architectures. Symmetrical sequences have roughly the same thickness of transgressive systems tracts (TST) and highstand systems tracts (HST), and have well segregated shellbeds that were formed during marine onlap and backlap. Asymmetrical cycles have very thin TSTs and much thicker HSTs, and are characterized by the amalgamation of condensed onlap and backlap shellbeds. Such contrasting cycle architectures are interpreted to reflect inner (symmetrical) and outer (asymmetrical) shelf palaeodepositional settings. The amalgamated onlap/backlap shellbeds appear to be common in Plio-Pleistocene sequences. Owing to the short duration of glacio-eustatic sea-level changes with dominant frequencies of 20,000, 40,000 or 100,000 years, shellbeds in the Plio-Pleistocene are relatively simple and thin compared to those formed in ordinary third-order depositional sequences. Infauna-dominated benthic associations are generally more common than in third-order cycles, and epifaunal associations facilitated by taphonomic feedback on sediment-starved shell-gravel substrates occur only in the condensed section corresponding to maximum transgression in most Plio-Pleistocene sequences.

Impact of beaver ponds on river discharge and sediment deposition along the Chevral River, Ardennes, Belgium

NASA Astrophysics Data System (ADS)

Nyssen, Jan; Frankl, Amaury; Pontzeele, Jolien; De Visscher, Maarten; Billi, Paolo

2013-04-01

With the recovery of the European beaver (Castor fiber) and their capacity to engineer fluvial landscapes, questions arise as to how they influence river discharge and sediment transport. The Chevral river (Ardennes, Belgium) contains two beaver dam sequences which appeared in 2004 and count now about 30 dams. Flow discharges and sediment fluxes were measured at the in- and outflow of each dam sequence. Volumes of sediment deposited behind the dams were measured. Between 2004 and 2011, peak flows were topped off, and the magnitude of extreme events decreased. 1710 m³ of sediment were deposited behind the beaver dams, with an average sediment thickness of 25 cm. The thickness of the sediment layer is related to the area of the beaver ponds. Along the stream, beaver pond sediment thickness displayed a sinusoidal deposition pattern, in which ponds with thick sediment layers were preceded by a series of ponds with thinner sediment layers. A downstream textural coarsening in the dam sequences was also observed, probably due to dam failures subsequent to surges. Differences in sediment flux between the in- and outflow at the beaver pond sequence were related to the river hydrograph, with deposition taking place during the rising limbs and slight erosion during the falling limbs. The seven-year-old sequences have filtered 190 tons of sediment out of the Chevral river, which is of the same order of magnitude as the 374 tons measured in pond deposits, with the difference between the values corresponding to beaver excavations (60 tons), inflow from small tributaries, and runoff from the valley flanks. Hydrogeomorphic effects of C. fiber and C. canadensis activity are similar in magnitude. The detailed analysis of changes to hydrology in beaver pond sequences confirms the potential of beavers to contribute to river and wetland restoration and catchment management.

Depletion of Unwanted Nucleic Acid Templates by Selective Cleavage: LNAzymes, Catalytically Active Oligonucleotides Containing Locked Nucleic Acids, Open a New Window for Detecting Rare Microbial Community Members

PubMed Central

Dolinšek, Jan; Dorninger, Christiane; Lagkouvardos, Ilias; Wagner, Michael

2013-01-01

Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer “Candidatus Nitrospira defluvii.” In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition. PMID:23263968

Carbonate sedimentation in an extensional active margin: Cretaceous history of the Haymana region, Pontides

NASA Astrophysics Data System (ADS)

Okay, Aral I.; Altiner, Demir

2016-10-01

The Haymana region in Central Anatolia is located in the southern part of the Pontides close to the İzmir-Ankara suture. During the Cretaceous, the region formed part of the south-facing active margin of the Eurasia. The area preserves a nearly complete record of the Cretaceous system. Shallow marine carbonates of earliest Cretaceous age are overlain by a 700-m-thick Cretaceous sequence, dominated by deep marine limestones. Three unconformity-bounded pelagic carbonate sequences of Berriasian, Albian-Cenomanian and Turonian-Santonian ages are recognized: Each depositional sequence is preceded by a period of tilting and submarine erosion during the Berriasian, early Albian and late Cenomanian, which corresponds to phases of local extension in the active continental margin. Carbonate breccias mark the base of the sequences and each carbonate sequence steps down on older units. The deep marine carbonate deposition ended in the late Santonian followed by tilting, erosion and folding during the Campanian. Deposition of thick siliciclastic turbidites started in the late Campanian and continued into the Tertiary. Unlike most forearc basins, the Haymana region was a site of deep marine carbonate deposition until the Campanian. This was because the Pontide arc was extensional and the volcanic detritus was trapped in the intra-arc basins and did not reach the forearc or the trench. The extensional nature of the arc is also shown by the opening of the Black Sea as a backarc basin in the Turonian-Santonian. The carbonate sedimentation in an active margin is characterized by synsedimentary vertical displacements, which results in submarine erosion, carbonate breccias and in the lateral discontinuity of the sequences, and differs from blanket like carbonate deposition in the passive margins.

STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

PubMed Central

Neshich, Goran; Togawa, Roberto C.; Mancini, Adauto L.; Kuser, Paula R.; Yamagishi, Michel E. B.; Pappas, Georgios; Torres, Wellington V.; Campos, Tharsis Fonseca e; Ferreira, Leonardo L.; Luna, Fabio M.; Oliveira, Adilton G.; Miura, Ronald T.; Inoue, Marcus K.; Horita, Luiz G.; de Souza, Dimas F.; Dominiquini, Fabiana; Álvaro, Alexandre; Lima, Cleber S.; Ogawa, Fabio O.; Gomes, Gabriel B.; Palandrani, Juliana F.; dos Santos, Gabriela F.; de Freitas, Esther M.; Mattiuz, Amanda R.; Costa, Ivan C.; de Almeida, Celso L.; Souza, Savio; Baudet, Christian; Higa, Roberto H.

2003-01-01

STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Cα–Cα and Cβ–Cβ distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)—amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS. PMID:12824333

Sequence stratigraphy of upper Paleogene to Neogene carbonates exposed from Guánica bay to Guayanilla, Southern Puerto Rico.

NASA Astrophysics Data System (ADS)

Flores Hots, V. E.; Santos, H.

2016-12-01

Detailed stratigraphic columns were measured and microfacies analysis was performed in southwestern Puerto Rico to conduct a sequence stratigraphic analysis of Paleogene to Neogene strata. Two of the best exposed outcrops include the Guánica Bay and outcrops along Highway PR-132 in Guayanilla. Three depositional sequences, separated by two major sequence boundaries were found. The lower sequence occurs within the Juana Díaz Formation and is an open shelf to reef facies indicative of a Transgressive System Tract (TST), that is overlain by a High Stand System Tract (HST) marked by reef progradation. The HST in both Guánica Bay and Guayanilla is characterized by coral-rhodolith cyclicity however sections in Guánica Bay show pervasive recrystallization due to diagenetic alteration as a result of a long periods of exposure. This first sequence is Oligocene in age. The middle sequence, exposed at the eastern section of the Guánica Bay is also part of the Juana Díaz Formation and includes a turbiditic Lowstand System Tract (LST) of slope-like deposits flow, a TST constituted by coral rubble and skeletal grainstones belonging to a shallow island slope environment; and a HST that consists of an island slope chalk facies intercalated with turbidite grainstones derived storm events at the Guayanilla location. During the deposition of the middle sequence the Guánica Bay west section was topographically higher and exposed. The upper depositional sequence is Miocene in age and is composed of a TST with the transgression starting distally in the Guánica area and transgressing northward toward the Guayanilla area. These was correlated using high resolution 87Sr/86Sr isotope concentrations of shallow marine mollusks Kuphus incrassatus in the Ponce Formation at the Guánica Bay and Guayanilla locations. Facies patterns like the ones in the studied outcrops of southwestern Puerto Rico provide an exemplary environmental model of variability of paleodepositional relief, tectonic setting, variability in depositional setting of reef Sediment acumulations, the influence of storm events and variability in rock porosity by diagenetic processes yielding valuable models that may apply to potential Oligocene - Miocene hydrocarbon reservoirs.

Stratigraphy, facies architecture, and palaeoenvironment of Neoproterozoic volcanics and volcaniclastic deposits in Fatira area, Central Eastern Desert, Egypt

NASA Astrophysics Data System (ADS)

Khalaf, Ezz El Din Abdel Hakim

Fatira area in the Central Eastern Desert, Egypt, is a composite terrane consisting of Neoproterozoic volcanics and sediments laid down in submarine to subaerial environment, intruded by voluminous old to young granitic rocks. The various lithofacies of the study area can be grouped in three distinct lithostratigraphic sequences, which are described here in stratigraphic order, from base to top as the Fatira El Beida, Fatira El Zarqa and Gabal Fatira sequences. Each depositional sequence, is intimately related to volcanic activity separated by time intervals of volcanic inactivity, such as marked hiatuses, reworked volcaniclasts, and or turbidite sedimentation. Four submarine facies groups have been recognized within the oldest, folded eruption sequence of Fatira El Beida. The southern part of the study area is occupied by sheet lava (SL), pillow lavas (PL), pillow breccias (PB), and overlying Bouma turbiditic volcaniclastites (VC). The four facies groups of Fatira El Beida sequence occur in a predictable upward-deepening succession, essentially from base to top, an SL-PL-PB-VC stacking pattern. The coeval tholeiitic mafic and felsic volcaniclastic rocks of this sequence indicate an extensional back-arc tectonic setting. The El Beida depositional sequence appears to fit a submarine-fan and slope-apron environment in an intra-arc site. The Fatira El Zarqa sequence involves a large volume of subaerial calc-alkaline intermediate to felsic volcanics and an unconformably overlying siliciclastic succession comprising clast-supported conglomerates (Gm), massive sandstone sheet floods (Sm) and mudstones (FI), together with a lateritic argillite paleosol (P) top formed in an alluvial-fan system. The youngest rock of Gabal Fatira sequence comprises anorogenic trachydacites and rhyolites with locally emergent domes associated with autobrecciation and sill-dyke rock swarms that could be interpreted as feeders and subvolcanic intrusions. Unconformity and lithofacies assemblages define seven events and three unconformity-bounded tectonic stages that record uplift-subsidence cycles in the study area. A proximal-distal relationship has been established within the depositional products, based on the relative dominance of erosional and depositional features.

Depositional model and seismic expression of turbidites in Campos basin, offshore Brazil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guardado, L.R.; Peres, W.E.; Souza Cruz, C.E.

1986-05-01

The Campos basin, located at the southeastern coast of Brazil, is one of the most prolific hydrocarbon areas along the Brazilian margin. The producing reservoirs range from the Neocomian to the early Miocene and were deposited in various environments. However, on deep-water submarine fans (turbidites), these reservoirs reach their maximum expression. The ratio between subsidence and sediment influx, associated to halokinesis, generated two major depositional styles for the sections before and after the early Oligocene, which affect the geometry of the turbidite bodies. Albian, Campanian, and Eocene turbidites occur mainly under the present continental shelf and are confined to thatmore » area. However, the Oligocene-Miocene turbidites occur mainly under the present slope. These younger turbidites were deposited as large submarine fans in broad subbasins as blankets, at the base of deep-water prograding sequences, and they have the potential for large hydrocarbon accumulations. These submarine fans are well defined on the seismic data, and specific processing improves the definition of anomalous amplitudes related to the presence of oil in the reservoirs.« less

The recent pumice eruptions of Mt. Pelée volcano, Martinique. Part I: Depositional sequences, description of pumiceous deposits

NASA Astrophysics Data System (ADS)

Traineau, Hervé; Westercamp, Denis; Bardintzeff, Jacques-Marie; Miskovsky, Jean-Claude

1989-08-01

Mount Pelée is one of the most active volcanoes of the Lesser Antilles arc, with more than twenty eruptions over the last 5000 years. Both nuée ardente-type eruptions, which are well known, and pumice eruptions, although little known, are very common in the stratigraphic record. The four younger pumice eruptions, P4 (2440 y.B.P.), P3 (2010 y.B.P.), P2 (1670 y.B.P.) and P1 (650 y.B.P.) can be used to reconstruct the eruption sequences. The various pumiceous deposits can be described as fine lithic ash layer, Plinian fall deposits, pumice and ash flow deposits with associated ash cloud fall deposits, and pumice surge deposits. Three kinds of depositional sequences have been defined. The distinctions between them are based on the occurrence of an initial Plinian phase and the generation of intraflow pyroclastic surges. The pumice eruptions of Mt. Pelée are small in intensity and magnitude, as expressed by the dispersal of their products and by the total mass of erupted material which is estimated to be less than 1 km 3 in each case. The pumice fall deposits have dispersal characteristics of small Plinian eruptions, close to the sub-Plinian type. Nevertheless, the probability of an occurrence of a new pumice eruption at Mt. Pelée is high, and the widespread distribution of pumice deposits around the volcano suggests that such an eruption is a major volcanic risk during the present stage of activity.

Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan

PubMed Central

Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi

2012-01-01

A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3. PMID:22815442

Complete genome sequence of Leptospirillum ferrooxidans strain C2-3, isolated from a fresh volcanic ash deposit on the island of Miyake, Japan.

PubMed

Fujimura, Reiko; Sato, Yoshinori; Nishizawa, Tomoyasu; Oshima, Kenshiro; Kim, Seok-Won; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

2012-08-01

A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans, known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3.

The age of the Keystone thrust: laser-fusion 40Ar/39Ar dating of foreland basin deposits, southern Spring Mountains, Nevada

USGS Publications Warehouse

Fleck, R.J.; Carr, M.D.

1990-01-01

Nonmarine sedimentary and volcaniclastic foreland-basin deposits in the Spring Mountains are cut by the Contact and Keystone thrusts. These synorogenic deposits, informally designated the Lavinia Wash sequence by Carr (1980), previously were assigned a Late Jurassic to Early Cretaceous(?) age. New 40Ar.39Ar laser-fusion and incremental-heating studies of a tuff bed in the Lavinia Wash sequence support a best estimate age of 99.0 ?? 0.4 Ma, indicating that the Lavinia Wash sequence is actually late Early Cretaceous in age and establishing a maximum age for final emplacement of the Contact and Keystone thrust plates consistent with the remainder of the Mesozoic foreland thrust belt. -from Authors

Depositional framework and sequence stratigraphic aspects of the Coniacian Santonian mixed siliciclastic/carbonate Matulla sediments in Nezzazat and Ekma blocks, Gulf of Suez, Egypt

NASA Astrophysics Data System (ADS)

El-Azabi, M. H.; El-Araby, A.

2007-04-01

Superb outcrops of mixed siliciclastic/carbonate rocks mark the Coniacian-Santonian Matulla Formation exposed in Nezzazat and Ekma blocks, west central Sinai. They are built up of various lithofacies that reflect minor fluctuations in relative sea-level from lower intertidal to slightly deep subtidal settings. Relying on the facies characteristics and stratal geometries, the siliciclastic rocks are divided into seven depositional facies, including beach foreshore laminated sands, upper shoreface cross-bedded sandstone, lower shoreface massive bioturbated and wave-rippled sandstones, shallow subtidal siltstone and deep subtidal shale/claystone. The carbonate rocks comprise lower intertidal lime-mudstone, floatstone and dolostone, shallow subtidal skeletal shoal of oyster rudstone/bioclastic grainstone, and shoal margin packstone. Oolitic grain-ironstone and ferribands are partially intervened the facies types. Deposition has taken place under varied conditions of restricted, partly open marine circulation, low to high wave energy and normal to raised salinity during alternating periods of abundant and ceased clastic supply. The facies types are arranged into asymmetric upward-shallowing cycles that record multiple small-scale transgressive-regressive events. Lime-mudstone and sandstone normally terminate the regressive events. Four sequence boundaries marking regional relative sea-level falls divide the Matulla Formation into three stratigraphic units. These boundaries are Turonian/Coniacian, intra-Coniacian, Coniacian/Santonian and Santonian/Campanian. They do not fit with those sequence boundaries proposed in Haq et al.'s global eustatic curves (1988) except for the sea-level fall associated with the intra-Coniacian boundary. Other sequence boundaries have resulted from regional tectonic impact of the Syrian Arc Fold System that has been initiated in north Egypt during the Latest Turonian-Coniacian. These boundaries enclose three well-defined 3rd order depositional sequences; their enclosing shallowing-upward cycles (i.e. parasequences) record the 4th order relative sea-level fluctuations. 34 and 20 parasequence sets, in the order of a few meters to tens of meters thick, mark the Matulla sequences in Nezzazat and Ekma blocks respectively. Each sequence shows an initial phase of rapid sea-level rise with retrogradational sets, followed by lowering sea-level and progradation/aggradation of the parasequence sets. The transgressive deposits display predominance of deep subtidal lagoonal facies, while highstand deposits show an increase in siliciclastic and carbonate facies with the progressive decrease of lagoonal facies. The sedimentary patterns and environments suggest that the regional, partly eustatic sea-level (i.e. intra-Coniacian) changes controlled the overall architecture of the sequence distribution, whereas changes in the clastic input controlled the variations in facies associations within each depositional sequence.

The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka.

PubMed

Behera, Pratiksha; Vaishampayan, Parag; Singh, Nitin K; Mishra, Samir R; Raina, Vishakha; Suar, Mrutyunjay; Pattnaik, Ajit K; Rastogi, Gurdeep

2016-09-01

Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka (P. karka), an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria that grows optimally at 37 °C, 7.0 pH, and 1% NaCl concentration. The draft genome sequence of strain MP23 contains 4,947,475 bp with an estimated G + C content of 49.9% and total 4392 protein coding genes. The genome sequence has provided information on putative genes that code for proteins involved in oxidative stress, uptake of nutrients, and nitrogen fixation that might offer niche specific ecological fitness and explain the invasive success of P. karka in Chilika Lagoon. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number LYRP00000000.

Sampling and evaluation of specific absorption rates during patient examinations performed on 1.5-Tesla MR systems.

PubMed

Brix, G; Reinl, M; Brinker, G

2001-07-01

It was the purpose of present study, to evaluate a large number of exposure-time courses measured during patient examinations in clinical routine in relation to the current IEC standard and the draft version of the revised standard and, moreover, to investigate whether there is a correlation between the subjective heat perception of the patients during the MR examination and the intensity of RF power deposition. To this end, radiofrequency exposure to 591 patients undergoing MR examinations performed on 1.5-Tesla MR systems was monitored in five clinics and evaluated in accordance with both IEC standards. For each of the 7902 sequences applied, whole body and partial body SARs were estimated on the basis of a simple patient model. Following the examinations, 149 patients were willing to provide information in a questionnaire regarding their body weight and their subjective heat perception during the examination. Although patient masses entered into the MR system were in some cases too high, reliable masses could be estimated by the SAR monitor. In relation to our data, the revision of the IEC standard results in a tightening of the restrictions, but still more than 96% of the examinations did not exceed the SAR limits recommended for the normal operating mode. For the exposure conditions examined, no statistically significant correlation was found between the subjective heat perception of the patients and the intensity of power deposition. Taking advantage of the possibility to compute running SAR averages, MR sequences can be employed in clinical practice for which SAR levels exceed the defined IEC limits, if the acquisition time is short in relation to the averaging period and energy deposition has been low previous to the applied high-power sequence.

Regional stratigraphy of the south polar layered deposits (Promethei Lingula, Mars): "Discontinuity-bounded" units in images and radargrams

NASA Astrophysics Data System (ADS)

Guallini, Luca; Rossi, Angelo Pio; Forget, François; Marinangeli, Lucia; Lauro, Sebastian Emanuel; Pettinelli, Elena; Seu, Roberto; Thomas, Nicolas

2018-07-01

The Mars South Polar Layered Deposits (SPLD) are the result of depositional and erosional events, which are marked by different stratigraphic sequences and erosional surfaces. To unambiguously define the stratigraphic units at regional scale, we mapped the SPLD on the basis of observed discontinuities (i.e., unconformities, correlative discontinuities and conformities), as commonly done in terrestrial modern stratigraphy. This methodology is defined as "Discontinuity-Bounded Units" or allostratigraphy, and is complemented by geomorphological mapping. Our study focuses on Promethei Lingula (PL) and uses both high-resolution images (CTX, HiRISE) and radargrams (SHARAD) to combine surface and sub-surface observations and obtain a 3D geological reconstruction of the SPLD. One regional discontinuity (named AUR1) was defined within the studied stratigraphic succession and is exposed in several non-contiguous outcrops around PL as well as observed at depth within the ice sheet. This is the primary contact between two major depositional sequences, showing a different texture at CTX resolution. The lower sequence is characterized mainly by a "ridge and trough" morphology (Ridge and Trough Sequence; RTS) and the upper sequence shows mainly by a "stair-stepped" morphology (Stair-Stepped Sequence; SSS). On the basis of the observations, we defined two regional "discontinuity-bounded" units in PL, respectively coinciding with RTS and SSS sequences. Our stratigraphic reconstruction provides new hints on the major scale events that shaped this region. Oscillations in Martian axial obliquity could have controlled local climate conditions in the past, affecting the PL geological record.

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

PubMed Central

Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A.; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M.; Kyrpides, Nikos C.

2012-01-01

The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11 472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond. PMID:22135293

Palynology and organic/isotope geochemistry of the Mae Moh Basin, Northern Thailand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minh, L.V.; Abrajano, T.; Burden, E.

The Mae Moh basin is one of several Tertiary intermontane basins in northern Thailand, whose evolution has been linked to the collision of the Indian plate with the Eurasian plate since the early Eocene. As in most of these basins, lacustrine/swamp sedimentation in the Mae Moh basin can be broadly divided into an Oligocene to Miocene synrift sequence and a Miocene to Quarternary postrift sequence. The dominance of swamp flora recognized from spore and pollen assemblages (e.g., Polypodiidites usmensis, Verrucatosporites, Cyrtostachys), as well as the abundance of macrophytes and woody debris, indicate overwhelming hot and humid swamp conditions, with lakemore » development restricted to relatively small areas. The distribution of alkanes and their compound-specific carbon isotope compositions are used to further show climatic variations affecting the lake/swamp ecology during the deposition of the synrift sequence.« less

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

PubMed

Liolios, Konstantinos; Chen, I-Min A; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M; Kyrpides, Nikos C

2010-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.

PubMed

Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos C

2012-01-01

The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11,472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond.

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

PubMed Central

Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M.; Kyrpides, Nikos C.

2010-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ PMID:19914934

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

PubMed Central

Li, Li; Brunk, Brian P.; Kissinger, Jessica C.; Pape, Deana; Tang, Keliang; Cole, Robert H.; Martin, John; Wylie, Todd; Dante, Mike; Fogarty, Steven J.; Howe, Daniel K.; Liberator, Paul; Diaz, Carmen; Anderson, Jennifer; White, Michael; Jerome, Maria E.; Johnson, Emily A.; Radke, Jay A.; Stoeckert, Christian J.; Waterston, Robert H.; Clifton, Sandra W.; Roos, David S.; Sibley, L. David

2003-01-01

Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%–20% represent putative homologs with a conservative cutoff of p < 10−9, thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets. [The sequence data from this study have been submitted to dbEST division of GenBank under accession nos.: Toxoplasma gondii: –, –, –, –, – , –, –, –, –. Plasmodium falciparum: –, –, –, –. Sarcocystis neurona: , , , , , , , , , , , , , –, –, –, –, –. Eimeria tenella: –, –, –, –, –, –, –, –, – , –, –, –, –, –, –, –, –, –, –, –. Neospora caninum: –, –, , – , –, –.] PMID:12618375

A palynostratigraphic approach to the SW Anatolian molasse basin: Kale-Tavas molasse and Denizli molasse

NASA Astrophysics Data System (ADS)

Akgün, Funda; Sözbilir, Hasan

The study, explains stratigraphy of the Oligo-Miocene molasse around the Denizli province (SW Anatolia), based on the palynology which is also supported by the detailed mapping and correlation of the measured sections from the coal-bearing sequences of the molasse deposits. For this purpose, two huge depressions named as the Kale-Tavas molasse and Denizli molasse basins were examined. The Kale-Tavas molasse deposits has a basal unconformity with the underlying pre-Oligocene basement and begins with the Chattian Karadere and Mortuma formations which are covered unconformably by the Aquitanian Yenidere formation. An angular unconformity between the Chattian and the Burdigalian is only observed in the middle part of the basin, around Kale. In the Tavas section, the Aquitanian and the Burdigalian are absent. The Denizli molasse is characterized by Chattian-Aquitanian sequence consisting of distinctive sedimentary facies, alluvial fan and deltaic-shallow marine deposits with carbonate patch reefs. Palynostratigraphic studies, which have given the Chattian age, have been carried out from the coal lenses of alluvial fan and delta plain deposits. In addition to the palynological determinations, coral and foraminiferal content of the carbonate patch reefs which rest conformably on the coal-bearing sequences have yielded the Chattian-Aquitanian age. Two different palynomorph associations have been determined from the molasse deposits. The first palynomorph association which is established in the samples from the Sağdere and Mortuma formations, corresponds to the Chattian age, whilst the second is of the Aquitanian age. The Late Oligocene-Early Miocene which is claimed as the time of N-S-extensional tectonics in western Turkey, is related to the depositional time of the molasse sequences in the study area. Thus, the molasse is older than the basal deposits of the Gediz and Büyük Menderes grabens.

Valley-fill sequences and onlap geometries, Lower Cretaceous Muddy Sandstone, Kitty Field, Powder River basin, Wyoming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, M.H.; Gustason, E.R.

1987-05-01

The Muddy Sandstone at Kitty field is a valley-fill sequence that records a late Albian sea level rise and accompanying transgression. The valley was cut during a preceding sea level lowstand. Stratal geometries and facies successions within the valley fill demonstrate the history of transgression was not gradual and progressive. Rather, the valley fill comprises a series of discrete, time-bounded, depositional units which onlap the erosional surface. Five time-bounded depositional units were defined by facies successions and were used to define onlap geometries. Facies successions within individual units record progressive shoaling. Capping each succession, there may be a planar disconformity,more » a thin bioturbated interval, or the deepest water facies of the next depositional event. Thus, the termination of each depositional event is marked by an episode of rapid deepening. At a single geographic location, stratal successions within older depositional units represent more landward facies than those within younger units. Therefore, the onlap geometry of the valley-fill sequence consists of a landward-stepping arrangement of depositional units. The primary reservoirs within the valley-fill sequence, at Kitty field, are laterally coalesced, channel-belt sandstones at the base and barrier island sandstones at the top. Reservoir sandstones of lesser quality occur within the intermediate estuarine facies. The stacking pattern, developed by onlap of the units, results in multiple pay zones within mid-valley reaches. The boundaries of each depositional unit define a high-resolution, chronostratigraphic correlation of valley-fill strata, a correlation corroborated by bentonites. This correlation method gives an accurate description of the internal geometry of valley-fill strata and, therefore, provides a basis for understanding the process of transgressive onlap.« less

Tectonics and metallogenesis of Proterozoic rocks of the Reading Prong

USGS Publications Warehouse

Gundersen, L.C.S.

2004-01-01

Detailed geologic mapping, petrography, and major and trace-element analyses of Proterozoic rocks from the Greenwood Lake Quadrangle, New York are compared with chemical analyses and stratigraphic information compiled for the entire Reading Prong. A persistent regional stratigraphy is evident in the mapped area whose geochemistry indicates protoliths consistent with a back-arc marginal basin sequence. The proposed marginal basin may have been floored by an older sialic basement and overlain by a basin-fill sequence consisting of a basal tholeiitic basalt, basic to intermediate volcanic or volcaniclastic rocks and carbonate sediments, a bimodal calc-alkaline volcanic sequence, and finally volcaniclastic, marine, and continental sediments. The presence of high-chlorine biotite and scapolite may indicate circulation of brine fluids or the presence of evaporite layers in the sequence. Abundant, stratabound magnetite deposits with a geologic setting very unlike that of cratonic, Proterozoic banded-iron formations are found throughout the proposed basin sequence. Associated with many of the magnetite deposits is unusual uranium and rare-earth element mineralization. It is proposed here that these deposits formed in an exhalative, volcanogenic, depositional environment within an extensional back-arc marginal basin. Such a tectonic setting is consistent with interpretations of protoliths in other portions of the Reading Prong, the Central Metasedimentary Belt of the Canadian Grenville Province, and recent interpretation of the origin of the Franklin lead-zinc deposits, suggesting a more cohesive evolving arc/back-arc tectonic model for the entire Proterozoic margin of the north-eastern portion of the North American craton. Published by Elsevier Ltd.

Depositional environments, sequence stratigraphy, and trap configuration of lower Wolfcampian clastics along eastern edge of Midland basin, west Texas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stewart, N.R.; Reuter, S.G.

1989-03-01

The Lower Permian (lower Wolfcampian) along the eastern edge of the Midland basin, west Texas, is characterized by ramp-type shelf margins. During eustatic lowstand, nearshore sedimentation shifted drastically to the west into a basinal setting below the Pennsylvanian (Canyon) shelf margin. Core descriptions demonstrate that lowstand systems tract (LST) and transgressive systems tract (TST) siliciclastics were deposited in deltaic and coastal-plain environments. Prodelta, delta-front, and stream-mouth bar facies are associated with the LST. Coastal-plain and distributary channels are preserved in the TST. The sequence stratigraphic framework indicates type 1 sequence boundaries at 287 Ma, 282 Ma, and 280 Ma inmore » the lower Wolfcampian clastics. This lower Wolfcampian package of sedimentary rocks overlies the Pennsylvanian and is capped by the 279-Ma middle Wolfcampian unconformity. All three sequence boundaries and associated systems tract deposits exhibit a prograding stacking pattern within the sequence stratigraphic framework. Basinally restricted prograding LST deltaic rocks are overlain by backstepping TST deltaics and highstand systems tract (HST) outer marine shales. Production in lower Wolfcampian clastic fields is associated with fine-grained quartzarenites up to 45 ft thick which were deposited in stream-mouth bars. Delta-front and prodelta low-permeability shales encase the reservoir facies, forming lateral permeability barriers. HST outer marine shales deposited over the stream-mouth-bar sandstones act as a top seal, creating a stratigraphic trap and providing source for the high-BTU gas and oil produced from these basinally restricted LST deltaics.« less

Cloning, expression, and characterization of a novel (S)-specific alcohol dehydrogenase from Lactobacillus kefir.

PubMed

Chen, Qilei; Hu, Youjia; Zhao, Wenjie; Zhu, Chunbao; Zhu, Baoquan

2010-01-01

A gene encoding a novel (S)-specific NADH-dependent alcohol dehydrogenase (LK-ADH) was isolated from the genomic DNA of Lactobacillus kefir DSM 20587 by thermal asymmetric interlaced-polymerase chain reaction. The nucleotide sequence of (S)-LK-ADH gene (adhS) was determined, which consists of an open reading frame of 1,044 bp, coding for 347 amino acids with a molecular mass of 37.065 kDa. After a BLAST similarity search in GenBank database, the amino acid sequence of (S)-LK-ADH showed some homologies to several zinc containing medium-chain alcohol dehydrogenases. This novel gene was deposited into GenBank with the accession number of EU877965. adhS gene was subcloned into plasmid pET-28a(+), and recombinant (S)-LK-ADH was successfully expressed in E. coli BL21(DE3) by isopropyl-beta-D-1-thiogalactopyranoside induction. Purified enzyme showed a high enantioselectivity in the reduction of acetophenone to (S)-phenylethanol with an ee value of 99.4%. The substrate specificity and cofactor preference of recombinant (S)-LK-ADH were also tested.

Upper Lower Cambrian depositional sequence in Avalonian New Brunswick

USGS Publications Warehouse

Landing, E.; Westrop, S.R.

1996-01-01

The Hanford Brook Formation (emended) is a thin (up to 42+ m), upper Lower Cambrian depositional sequence that is unconformably bounded by the lower Lower Cambrian (Random Formation) and the middle Middle Cambrian (Fossil Brook Member of the Chamberlain's Brook Formation). These stratigraphic relationships of the trilobite-bearing Hanford Brook Formation indicate deposition on the Avalonian marginal platform in the Saint John, New Brunswick, region and provide more evidence for a uniform, latest Precambrian-Cambrian epeirogenic history and cover sequence in Avalon. The Hanford Brook Formation is a deepening - shoaling sequence with (i) lower, transgressive sandstone deposited in episodically high-energy environments (St. Martins Member, new); (ii) highstand-regressive, dysaerobic mudstone - fine-grained sandstone with volcanic ashes (Somerset Street Member, new); and (iii) upper, regressive, planar and hummocky cross-stratified sandstone (Long Island Member, new). Trilobites are common in the distal Somerset Street Member, and ostracodes and brachiopods dominate the St. Martins and Long Island members. Condensation of the St. Martins Member and absence of the Long Island Member where the Random Formation and Fossil Brook Member are thinnest suggest onlap of the Hanford Brook and pronounced, sub-Middle Cambrian erosion across epeirogenically active blocks in southern New Brunswick.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.

PubMed

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-06

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an "extremophile collector" and may be a hot spot of novel extremophile biodiversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles

PubMed Central

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-01

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an “extremophile collector” and may be a hot spot of novel extremophile biodiversity. PMID:25565172

Seismic stratigraphy and late Quaternary shelf history, south-central Monterey Bay, California

USGS Publications Warehouse

Chin, J.L.; Clifton, H.E.; Mullins, H.T.

1988-01-01

The south-central Monterey Bay shelf is a high-energy, wave-dominated, tectonically active coastal region on the central California continental margin. A prominent feature of this shelf is a sediment lobe off the mouth of the Salinas River that has surface expression. High-resolution seismic-reflection profiles reveal that an angular unconformity (Quaternary?) underlies the entire shelf and separates undeformed strata above it from deformed strata below it. The Salinas River lobe is a convex bulge on the shelf covering an area of approximately 72 km2 in water depths from 10 to 90 m. It reaches a maximum thickness of 35 m about 2.5 km seaward of the river mouth and thins in all directions away from this point. Adjacent shelf areas are characterized by only a thin (2 to 5 m thick) and uniform veneer of sediment. Acoustic stratigraphy of the lobe is complex and is characterized by at least three unconformity-bounded depositional sequences. Acoustically, these sequences are relatively well bedded. Acoustic foresets occur within the intermediate sequence and dip seaward at 0.7?? to 2.0??. Comparison with sedimentary sequences in uplifted onshore Pleistocene marine-terrace deposits of the Monterey Bay area, which were presumably formed in a similar setting under similar processes, suggests that a general interpretation can be formulated for seismic stratigraphic patterns. Depositional sequences are interpreted to represent shallowing-upwards progradational sequences of marine to nonmarine coastal deposits formed during interglacial highstands and/or during early stages of falling sea level. Acoustic foresets within the intermediate sequence are evidence of seaward progradation. Acoustic unconformities that separate depositional sequences are interpreted as having formed largely by shoreface planation and may be the only record of the intervening transgressions. The internal stratigraphy of the Salinas River lobe thus suggests that at least several late Quaternary regressions and transgressions may be recorded under the present shelf. This record may represent the last major eustatic cycle of sea level, an interval not observed in uplifted onshore Pleistocene marine terraces. ?? 1988.

Upper Albian to Lower Turonian deposits and associated breccias along the Dahar cuestas (southeastern Tunisia): Origin and depositional environments

NASA Astrophysics Data System (ADS)

Krimi, Mabrouk; Ouaja, Mohamed; Zargouni, Fouad

2017-11-01

The carbonate Zebbag Formation of Upper Albian to Lower Turonian age which outcrops along the Dahar cuestas (south eastern Tunisia) includes several breccia intervals. The stratigraphic hierarchy of these breccia levels led to achieving a detailed sequential analysis within a spectrum of depositional environments extending from subtidal to inner to middle ramp settings. Six major transgressive/regressive sequences make up the stacking of the elementary sequences beginning with transgressive and/or storm wave breccias capped by desiccation and/or collapse breccias. The stratigraphic evolutionary history of the breccia facies are interpreted as the result of the interplay between eustatic and tectonic factors. This model is in accord with the tectonic activities common during Upper Albian-Lower Turonian responsible for the sequences onlapping.

Correcting names of bacteria deposited in National Microbial Repositories: an analysed sequence data necessary for taxonomic re-categorization of misclassified bacteria-ONE example, genus Lysinibacillus.

PubMed

Rekadwad, Bhagwan N; Gonzalez, Juan M

2017-08-01

A report on 16S rRNA gene sequence re-analysis and digitalization is presented using Lysinibacillus species (one example) deposited in National Microbial Repositories in India. Lysinibacillus species 16S rRNA gene sequences were digitalized to provide quick response (QR) codes, Chaose Game Representation (CGR) and Frequency of Chaose Game Representation (FCGR). GC percentage, phylogenetic analysis, and principal component analysis (PCA) are tools used for the differentiation and reclassification of the strains under investigation. The seven reasons supporting the statements made by us as misclassified Lysinibacillus species deposited in National Microbial Depositories are given in this paper. Based on seven reasons, bacteria deposited in National Microbial Repositories such as Lysinibacillus and many other needs reanalyses for their exact identity. Leaves of identity with type strains of related species shows difference 2 to 8 % suggesting that reclassification is needed to correctly assign species names to the analyzed Lysinibacillus strains available in National Microbial Repositories.

Metastable and equilibrium phase formation in sputter-deposited Ti/Al multilayer thin films

NASA Astrophysics Data System (ADS)

Lucadamo, G.; Barmak, K.; Lavoie, C.; Cabral, C., Jr.; Michaelsen, C.

2002-06-01

The sequence and kinetics of metastable and equilibrium phase formation in sputter deposited multilayer thin films was investigated by combining in situ synchrotron x-ray diffraction (XRD) with ex situ electron diffraction and differential scanning calorimetry (DSC). The sequence included both cubic and tetragonal modifications of the equilibrium TiAl3 crystal structure. Values for the formation activation energies of the various phases in the sequence were determined using the XRD and DSC data obtained here, as well as activation energy data reported in the literature.

Evolution Of Quaternary Stream Fan Deposits At The Confluences Of Turung Khola And Bembung Khola Of Middle Teesta Basin In Sikkim-Darjeeling Himalaya,India: A Tectonic - Climate Response

NASA Astrophysics Data System (ADS)

Lukram, I. M.

2007-12-01

Tributary fan deposits are well preserved on either side of the Teesta river in the non-glaciated middle part of the Himalayan valley lying in a tectonic region bounded by the MCT and MBT. The lithofacies characteristics and assemblage patterns of these deposits bear testimony to the effects of tectonic and climatic activities on the sedimentation process in the basin. Two tributary streams, with small catchments namely Turung Khola and Bembung Khola are important in this context. Three major fan lobes (F2, F1, and F0) are preserved at Turung Khola. In contrast, two fan lobes (F1,F0) are preserved at the confluence of the Bembung Khola. Terraces, floodplains, channel bars, chute bars are associated geomorphic features in this part of the Teesta basin. Landslides cover an area of 7% and 15% in the catchment of Turung Khola and Bembung Khola, respectively. Dense forest covers 24% and 12%; open forest covers 30% and 29 %; and scrubby vegetation covers 39% and 49% of the Turung Khola and Bembung Khola, respectively. The landslides mainly occur along the margins of the dense forest where they are active in every rainy season. Tributary longitudinal profiles and Hack profiles indicate a relationship between the knick points and high SL-Index values, where fault /thrust intersections are present. Active landslides and scarps are close to the major fault/thrust planes. Sediment characteristics of these fan deposits suggest that four types of depositional flows viz. debris flows, hyperconcentrated flows, sheet flows and channel flows laid down these sequences. The channel flow deposits are dominant (32%-54 %) in the fan sequence of the Turung Khola followed by sheet flow deposits (28.5%), hyperconcentrated flow deposits (26%) and debris flow deposits (12%), respectively. Hyperconcentrated flow deposits are dominant (44%) in the F1 sequence, whereas the active channel fanlobe is dominant (80%) in the channel flow deposits. The rest of the active channel sequence is composed of sheet flow deposits (20%). On the other hand, the major part (52%) of the F1 fanlobe of Bembung Khola is built up of debris flow deposits and F0 fanlobe is composed of channel flow deposits and flood sediment. From the above analysis, an evolutionary model of the deposition and incision at the tributary stream fan confluence is proposed. The insetting of the younger fan lobes into older fan lobe surfaces is an evidence of tectonic uplift in the region. The landform and their depositional pattern are a responds to link tectonic- climatic process systems; some depositional lithofacies assemblages are responses to climatic events.

Postimpact deposition in the Chesapeake Bay impact structure: Variations in eustasy, compaction, sediment supply, and passive-aggressive tectonism

USGS Publications Warehouse

Kulpecz, A.A.; Miller, K.G.; Browning, J.V.; Edwards, L.E.; Powars, D.S.; McLaughlin, P.P.; Harris, A.D.; Feigenson, M.D.

2009-01-01

The Eyreville and Exmore, Virginia, core holes were drilled in the inner basin and annular trough, respectively, of the Chesapeake Bay impact structure, and they allow us to evaluate sequence deposition in an impact crater. We provide new high-resolution geochronologic (<1 Ma) and sequence-stratigraphic interpretations of the Exmore core, identify 12 definite (and four possible) postimpact depositional sequences, and present comparisons with similar results from Eyreville and other mid- Atlantic core holes. The concurrence of increases in ??18O with Chesapeake Bay impact structure sequence boundaries indicates a primary glacioeustatic control on deposition. However, regional comparisons show the differential preservation of sequences across the mid-Atlantic margin. We explain this distribution by the compaction of impactites, regional sediment-supply changes, and the differential movement of basement structures. Upper Eocene strata are thin or missing updip and around the crater, but they thicken into the inner basin (and offshore to the southeast) due to rapid crater infilling and concurrent impactite compaction. Oligocene sequences are generally thin and highly dissected throughout the mid-Atlantic region due to sediment starvation and tectonism, except in southeastern New Jersey. Regional tectonic uplift of the Norfolk Arch coupled with a southward decrease in sediment supply resulted in: (1) largely absent Lower Miocene sections around the Chesapeake Bay impact structure compared to thick sections in New Jersey and Delaware; (2) thick Middle Miocene sequences across the Delmarva Peninsula that thin south of the Chesapeake Bay impact structure; and (3) upper Middle Miocene sections that pinch out just north of the Chesapeake Bay impact structure. Conversely, the Upper Miocene-Pliocene section is thick across Virginia, but it is poorly represented in New Jersey because of regional variations in relative subsidence. ?? 2009 The Geological Society of America.

Deposition and weathering of Asian dust in Korea

NASA Astrophysics Data System (ADS)

Jeong, G.

2013-12-01

Paleolithic stone artifacts in Korea typically occur in brown clay-silt (BCS) sequences. The origin and depositional environment of these sequences are important for reconstructing the paleoenvironment as well as for establishing chronologies of artifact-bearing stratigraphic units. We investigated four BCS-bearing sections in foothills and river and marine terraces in Korea by applying quantitative mineralogical, geochemical, microtextural, and K-Ar isotopic methods. In all four sections, the lower units are colluvial and fluvial deposits strongly influenced by diverse local lithology, whereas the upper units are characterized by BCS units. Mineralogical/geochemical compositions, grain sizes, and colors converge into common properties in the upper BCS units in all sections. These common properties are consistent with the eastward trends of increasing weathering degree and grain size fining throughout the loess-paleosol sections of the Chinese Loess Plateau (CLP). K-Ar detrital ages of the sections also converge upward into a narrow range similar to the age ranges of the loess and paleosols in the CLP. The top BCS unit in the Jeongok section, the thickest section, is underlain by an additionally weathered BCS unit, with strong red chroma indicating a change from warm to cold climate. We did not observe any clear evidence of climatic changes in other thinner sections, which may be due to a superposition of cold-stage accumulation and warm-stage deep weathering. The common properties of the BCSs in Korean sections and their relationship to the CLP loess and paleosols indicate widespread deposition of Asian dust and subsequent weathering in the late Quaternary, forming BCS sequences. In this respect, the BCS sequences investigated here are considered to be the additionally weathered equivalents of the CLP loess-paleosol sequences, having been exposed to the high annual precipitation of the Korean Peninsula. Given the wide distribution of BCS sequences at Paleolithic sites throughout the Peninsula, the findings of this study are important for the ongoing debate surrounding the depositional environments of the Paleolithic deposits, and provide a foundation for the establishment of the chronological framework of the Paleolithic artifact-bearing layers and lithic assemblages.

Deposition and weathering of Asian dust in Paleolithic sites, Korea

NASA Astrophysics Data System (ADS)

Jeong, Gi Young; Choi, Jeong-Heon; Lim, Hyoun Soo; Seong, Chuntaek; Yi, Seon Bok

2013-10-01

Paleolithic stone artifacts in Korea typically occur in brown clay-silt (BCS) sequences. The origin and depositional environment of these sequences are important for reconstructing the paleoenvironment as well as for establishing chronologies of artifact-bearing stratigraphic units. We investigated four BCS-bearing sections in foothills and river and marine terraces in Korea by applying quantitative mineralogical, geochemical, microtextural, and K-Ar isotopic methods. In all four sections, the lower units are colluvial and fluvial deposits strongly influenced by diverse local lithology, whereas the upper units are characterized by BCS units. Mineralogical/geochemical compositions, grain sizes, and colors converge into common properties in the upper BCS units in all sections. These common properties are consistent with the eastward trends of increasing weathering degree and grain size fining throughout the loess-paleosol sections of the Chinese Loess Plateau (CLP). K-Ar detrital ages of the sections also converge upward into a narrow range similar to the age ranges of the loess and paleosols in the CLP. The top BCS unit in the Jeongok section, the thickest section, is underlain by an additionally weathered BCS unit, with strong red chroma indicating a change from warm to cold climate. We did not observe any clear evidence of climatic changes in other thinner sections, which may be due to a superposition of cold-stage accumulation and warm-stage deep weathering. The common properties of the BCSs in Korean sections and their relationship to the CLP loess and paleosols indicate widespread deposition of Asian dust and subsequent weathering in the late Quaternary, forming BCS sequences. In this respect, the BCS sequences investigated here are considered to be the additionally weathered equivalents of the CLP loess-paleosol sequences, having been exposed to the high annual precipitation of the Korean Peninsula. Given the wide distribution of BCS sequences at Paleolithic sites throughout the Peninsula, the findings of this study are important for the ongoing debate surrounding the depositional environments of the Paleolithic deposits, and provide a foundation for the establishment of the chronological framework of the Paleolithic artifact-bearing layers and lithic assemblages.

The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

Treesearch

Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

2014-01-01

Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

Environmental, depositional and cultural changes in the upper Pleistocene and early Holocene; the Cinglera del Capello Sequence (Capellades, Spain)

USGS Publications Warehouse

Vaquero, Manuel; Allué, Ethel; Bischoff, James L.; Burjachs, Francesc; Vallverdú, Josep

2013-01-01

The correlation between environmental and cultural changes is one of the primary archeological and paleoanthropological research topics. Analysis of ice and marine cores has yielded a high-resolution record of millennial-scale changes during the Late Pleistocene and Holocene eras. However, cultural changes are documented in low-resolution continental deposits; thus, their correlation with the millennial-scale climatic sequence is often difficult. In this paper, we present a rare occurrence in which a thick archeological sequence is associated with a high-resolution environmental record. The Cinglera del Capello is a tufa-draped cliff located in the northeastern Iberian Peninsula, 50 km west of Barcelona. This cliff harbors several rock-shelters with Late Pleistocene and Early Holocene deposits. Together, the deposits of four rock-shelters span from 7000 to 70,000 years ago and provide a high-resolution record of the environmental and human dynamics during this timespan. This record allows the correlation of the cultural and environmental changes. The multiproxy approach to the Cinglera evidence indicates that the main cultural stages of the Late Pleistocene and Early Holocene (Middle Paleolithic, Upper Paleolithic and Mesolithic) are associated with significant changes in the environmental and depositional contexts.

Effects of the Laramide Structures on the Regional Distribution of Tight-Gas Sandstone in the Upper Mesaverde Group, Uinta Basin, Utah

NASA Astrophysics Data System (ADS)

Sitaula, R. P.; Aschoff, J.

2013-12-01

Regional-scale sequence stratigraphic correlation, well log analysis, syntectonic unconformity mapping, isopach maps, and depositional environment maps of the upper Mesaverde Group (UMG) in Uinta basin, Utah suggest higher accommodation in northeastern part (Natural Buttes area) and local development of lacustrine facies due to increased subsidence caused by uplift of San Rafael Swell (SRS) in southern and Uinta Uplift in northern parts. Recently discovered lacustrine facies in Natural Buttes area are completely different than the dominant fluvial facies in outcrops along Book Cliffs and could have implications for significant amount of tight-gas sand production from this area. Data used for sequence stratigraphic correlation, isopach maps and depositional environmental maps include > 100 well logs, 20 stratigraphic profiles, 35 sandstone thin sections and 10 outcrop-based gamma ray profiles. Seven 4th order depositional sequences (~0.5 my duration) are identified and correlated within UMG. Correlation was constructed using a combination of fluvial facies and stacking patterns in outcrops, chert-pebble conglomerates and tidally influenced strata. These surfaces were extrapolated into subsurface by matching GR profiles. GR well logs and core log of Natural Buttes area show intervals of coarsening upward patterns suggesting possible lacustrine intervals that might contain high TOC. Locally, younger sequences are completely truncated across SRS whereas older sequences are truncated and thinned toward SRS. The cycles of truncation and thinning represent phases of SRS uplift. Thinning possibly related with the Uinta Uplift is also observed in northwestern part. Paleocurrents are consistent with interpretation of periodic segmentation and deflection of sedimentation. Regional paleocurrents are generally E-NE-directed in Sequences 1-4, and N-directed in Sequences 5-7. From isopach maps and paleocurrent direction it can be interpreted that uplift of SRS changed route of sediment supply from west to southwest. Locally, paleocurrents are highly variable near SRS further suggesting UMG basin-fill was partitioned by uplift of SRS. Sandstone composition analysis also suggests the uplift of SRS causing the variation of source rocks in upper sequences than the lower sequences. In conclusion, we suggest that Uinta basin was episodically partitioned during the deposition of UMG due to uplift of Laramide structures in the basin and accommodation was localized in northeastern part. Understanding of structural controls on accommodation, sedimentation patterns and depositional environments will aid prediction of the best-producing gas reservoirs.

Ubiquiter circovirus sequences raise challenges in laboratory diagnosis: the case of honey bee and bee mite, reptiles, and free living amoebae.

PubMed

Marton, Szilvia; Ihász, Katalin; Lengyel, György; Farkas, Szilvia L; Dán, Ádám; Paulus, Petra; Bányai, Krisztián; Fehér, Enikő

2015-03-01

Circoviruses of pigs and birds are established pathogens, however, the exact role of other, recently described circoviruses and circovirus-like viruses remains to be elucidated. The aim of this study was the detection of circoviruses in neglected host species, including honey bees, exotic reptiles and free-living amoebae by widely used broad-spectrum polymerase chain reaction (PCR) assays specific for the replication initiation protein coding gene of these viruses. The majority of sequences obtained from honey bees were highly similar to canine and porcine circoviruses, or, were distantly related to dragonfly cycloviruses. Other rep sequences detected in some honey bees, reptiles and amoebae showed similarities to various rep sequences deposited in the GenBank. Back-to-back PCR primers designed for the amplification of whole viral genomes failed to work that suggested the existence of integrated rep-like elements in many samples. Rolling circle amplification and exonuclease treatment confirmed the absence of small circular DNA genomes in the specimens analysed. In case of honey bees Varroa mite DNA contamination might be a source of the identified endogenous rep-like elements. The reptile and amoebae rep-like sequences were nearly identical with each other and with sequences detected in chimpanzee feces raising the possibility that detection of novel or unusual rep-like elements in some host species might originate from the microbial community of the host. Our results indicate that attention is needed when broad-spectrum rep gene specific polymerase chain reaction is chosen for laboratory diagnosis of circovirus infections.

Ion-channel genosensor for the detection of specific DNA sequences derived from Plum Pox Virus in plant extracts.

PubMed

Malecka, Kamila; Michalczuk, Lech; Radecka, Hanna; Radecki, Jerzy

2014-10-09

A DNA biosensor for detection of specific oligonucleotides sequences of Plum Pox Virus (PPV) in plant extracts and buffer is proposed. The working principles of a genosensor are based on the ion-channel mechanism. The NH2-ssDNA probe was deposited onto a glassy carbon electrode surface to form an amide bond between the carboxyl group of oxidized electrode surface and amino group from ssDNA probe. The analytical signals generated as a result of hybridization were registered in Osteryoung square wave voltammetry in the presence of [Fe(CN)6]3-/4- as a redox marker. The 22-mer and 42-mer complementary ssDNA sequences derived from PPV and DNA samples from plants infected with PPV were used as targets. Similar detection limits of 2.4 pM (31.0 pg/mL) and 2.3 pM (29.5 pg/mL) in the concentration range 1-8 pM were observed in the presence of the 22-mer ssDNA and 42-mer complementary ssDNA sequences of PPV, respectively. The genosensor was capable of discriminating between samples consisting of extracts from healthy plants and leaf extracts from infected plants in the concentration range 10-50 pg/mL. The detection limit was 12.8 pg/mL. The genosensor displayed good selectivity and sensitivity. The 20-mer partially complementary DNA sequences with four complementary bases and DNA samples from healthy plants used as negative controls generated low signal.

Submarine fan facies of Upper Cretaceous Strata, Southern San Rafael Mountains, Santa Barbara County, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toyne, C.D.

1986-04-01

A 2900-m thick Campanian-Maestrichtian(.) turbidite sequence in Upper Mono Creek Canyon is interpreted to be a progradational submarine fan complex comprised of outer fan, middle fan, inner fan, and slope facies. The basal 600 m of the section consists of thinly bedded, laterally continuous fine sandstones, siltstones, and mudstones (mainly Mutti and Ricci Lucci facies D), interpreted to be outer fan interlobe and lobe-fringe deposits. These are punctuated by infrequent medium to very thickly bedded, flat-based, fine to coarse sandstones (facies C and B), which commonly coarsen and thicken upward, and are interpreted to be depositional lobes. Overlying these depositsmore » are approximately 1400 m of middle fan deposits composed of frequent lenticular, commonly channelized and amalgamated, thickly bedded, fine to very coarse sandstones (facies C and B) organized in fining- and thinning-upward sequences, interpreted to be braided-channel deposits. These alternate with less common nonchannelized coarsening- and thickening-upward sequences suggestive of lobe-apical cycles. These multistory sand deposits are nested within thick intervals of fine sandstones, siltstones, and mudstones (facies C and D), interpreted to be levee, crevasse-splay, and interchannel deposits. Interfingered with and overlying these deposits are approximately 500 m of fining- and thinning-upward or noncyclic, erosionally based, commonly amalgamated, very thickly bedded, medium to very coarse sandstones, pebbly sandstones, and conglomerates (facies A and B), interpreted to be inner fan deposits. Intercalated within this facies, infrequent, laterally discontinuous, thin to thickly bedded, fine to coarse sandstones, siltstones, and mudstones exist, interpreted to be interchannel, levee, and possibly channel-fill deposits.« less

The transitional depositional environment and sequence stratigraphy of Chasma Boreale

NASA Astrophysics Data System (ADS)

Brothers, S. C.; Kocurek, G.

2018-07-01

The depositional system within Chasma Boreale is unique in that it contains active aeolian environments, expressed as dune fields, and active cryosphere environments, present as layered ice deposits, as well as environments that transition between these. This work presents a new analysis of the Chasma Boreale sediment system that creates an interpretative framework addressing: (a) controls on the balance between aeolian and cryospheric processes in the modern depositional system, (b) the stratigraphic architecture of related sedimentary deposits, and (c) processes of sediment accumulation and preservation. Images from Context Camera (CTX; 6 m/pixel) are used to classify and map sedimentary environments, surfaces, and deposits on the reentrant floor, to refine the established geologic map of the reentrant, and to infer the stratigraphic record of the accumulation from Chasma Boreale's depositional system. A spectrum of sedimentary environments occurring between those dominated by aeolian and by cryospheric processes are identified. Through time, the boundaries of these sedimentary environments have shifted, resulting in complex lateral changes in the configuration of sedimentary environments on the reentrant's floor. Vertically, the stratigraphic record is characterized by the punctuation of sandy aeolian deposits by icy surfaces that indicate episodes of ice growth that preserve underlying deposits, resulting in accumulation. Stabilized icy surfaces occur at multiple vertical (temporal) scales and lateral extents, suggesting the influence of both regional climate change due to allogenic forcing, as well as autogenic dynamics within the transitional system. These observations demonstrate that the Chasma Boreale accumulation can be interpreted in an aeolian sequence stratigraphic framework. This work contributes the first detailed description of the processes forming polar aeolian sequences, with an emphasis on the competing and complementary dynamics between aeolian and cryospheric systems.

Late Holocene stratigraphy of the Tetimpa archaeological sites, northeast flank of Popocatepetl volcano, central Mexico

USGS Publications Warehouse

Panfil, M.S.; Gardner, T.W.; Hirth, K.G.

1999-01-01

Late Holocene (240 km2 on the east side of the volcano with >25 cm of tephra. Lavas from eruptive sequence I dammed drainage in the lowland area near the town of San Nicolas and caused local upstream deposition of as much as 30 m of lacustrine silts, clays, and sands. These lacustrine deposits record an eruptive hiatus for the Tetimpa area of about 750 14C yr: between ca. 2100 and ca. 1350 yr B.P., no major tephras were deposited in the Tetimpa area. In upland areas, this time period is represented by an unconformity and by Entisols formed in the top of pumice deposits and lavas from eruptive sequence I. Artifacts, agricultural furrows, and dwellings record human reoccupation of this surface. At the end of this hiatus, several lahars were deposited above the lacustrine sequence and locally above the Entisol in upland positions adjacent to streams. Between ca. 1350 and ca. 1200 yr B.P., tephras from eruptive sequence II buried these paleosols, occupation sites, lacustrine sediments, and lahars. Andesitic (~62% SiO2) pumice lapilli deposits in the Tetimpa area record three pumice-fall eruptions directed northeast and east of the crater. The first and smallest of these (maximum Tetimpa area thickness = 12 cm; >52 km2 covered by >25 cm) took place at ca. 1350 yr B.P. and was accompanied by pyroclastic surge events preserved in the Tetimpa area by charcoal, sand waves, and cross-stratified sand-sized tephra. At ca. 1200 yr B.P., the products of two Plinian-style events and additional pyroclastic surges reached the Tetimpa area. The largest of these tephra-fall events covered the Tetimpa area with 0.5-1 m of tephra and blanketed an area of >230 km2 with a thickness of >25 cm. The Tetimpa record confirms two of the four periods of explosive volcanism recognized by studies conducted around Popocatepetl in the past 30 yr. Eruptive sequence I corresponds to the explosive period between 2100 and 2500 yr B.P., and eruptive sequence II corresponds to the period between 900 and 1400 yr B.P. The archaeology and lacustrine stratigraphy of the Tetimpa area help constrain the timing of the Plinian phase of eruptive sequence I to ca. 2100 yr B.P. and suggest that the pumice-fall eruptions of eruptive sequence II took place in at least two intervals between ca. 1350 and ca. 1200 yr B.P.

Prediction of the aggregation propensity of proteins from the primary sequence: aggregation properties of proteomes.

PubMed

Castillo, Virginia; Graña-Montes, Ricardo; Sabate, Raimon; Ventura, Salvador

2011-06-01

In the cell, protein folding into stable globular conformations is in competition with aggregation into non-functional and usually toxic structures, since the biophysical properties that promote folding also tend to favor intermolecular contacts, leading to the formation of β-sheet-enriched insoluble assemblies. The formation of protein deposits is linked to at least 20 different human disorders, ranging from dementia to diabetes. Furthermore, protein deposition inside cells represents a major obstacle for the biotechnological production of polypeptides. Importantly, the aggregation behavior of polypeptides appears to be strongly influenced by the intrinsic properties encoded in their sequences and specifically by the presence of selective short regions with high aggregation propensity. This allows computational methods to be used to analyze the aggregation properties of proteins without the previous requirement for structural information. Applications range from the identification of individual amyloidogenic regions in disease-linked polypeptides to the analysis of the aggregation properties of complete proteomes. Herein, we review these theoretical approaches and illustrate how they have become important and useful tools in understanding the molecular mechanisms underlying protein aggregation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Depositional environments and sequence architecture of the Raha and Abu Qada formations (Cenomanian-Turonian), west central Sinai, Egypt

NASA Astrophysics Data System (ADS)

Anan, Tarek I.; El-Shahat, Adam; Genedi, Adel; Grammer, Michael

2013-06-01

Cenomanian-Turonian deposits are important reservoirs for many oil fields in the Western Desert and the Gulf of Suez region of Egypt. Study of the Raha and Abu Qada formations (Cenomanian-Turonian), from five dip-oriented outcrop locations in west central Sinai; indicates deposition of a mixed siliciclastic-carbonate system on a ramp setting. The inner ramp facies (bivalve and benthonic foraminiferal wackestone) grades northward to the mid ramp facies (echinoderm calcisphere packstone, and oyster floatstone), and outer ramp facies (planktonic foraminiferal wackestone and calcisphere wackestone). The two studied formations comprise one second-order depositional sequence (duration of approximately 10 Million years). This large scale sequence includes four third-order depositional sequences, three of which are observed in the Raha Formation, with the other one recorded in the Abu Qada Formation. Because west central Sinai was tectonically stable during the Cenomanian and Turonian, the main factor controlling the lateral and vertical distribution of facies tracts is likely due to changes in the relative sea level. The Cenomanian-Turonian boundary event is known as the largest oceanic anoxic event during the Cretaceous. This global event has been documented in three of the studied sections. The recorded δ13C excursions range from +3.04‰ to +5.24‰. These high positive excursions in δ13C are associated with highly negative values of δ18O (values range from -6.01‰ to -1.38‰).

Microscopic and Metallurgical Aspects of the Space Shuttle Columbia Accident Investigation and Reconstruction

NASA Technical Reports Server (NTRS)

McDaniels, Steven J.

2004-01-01

The Space Shuttle Columbia was descending for a landing at the Kennedy Space Center (KSC) on February 1, 2003. Approximately 20 minutes prior to touchdown, the Columbia began disintegrating over the western United States; the majority of debris eventually impacted in eastern Texas and western Louisiana. A monumental effort eventually recovered approximately 84,000 pieces of debris, approximately 38% of the Orbiter's original dry weight. The debris was transported to KSC, where the items were catalogued and evaluated. Critical areas of interest, such as the left and right leading edge surfaces and the underside of the ship, were placed upon a grid to aid in the reconstruction. Items of interest included metallic structures, reinforced carbon-carbon composites, and ceramic heat insulation tiles. Many of the leading edge elements had re-solidified metallic deposits spattered on them. These deposits became known as slag and were one of the main focuses of the investigation. In order to help determine the sequence of events inside the left wing during the accident, the slag's composition, layering order, and directionality of deposition were studied. A myriad of analytical tests were performed in an attempt to ascertain the compositional and depositional characteristics of selected slag deposits, including the ordering of deposited layers within each individual slag deposit harvested. Initially, Scanning Electron Microscopy and Energy Dispersive X-Ray Spectroscopy (SEM/EDX) were performed to quickly characterize the overall composition of individual slag deposits: SEM utilizes a narrowlyfocused high-energy electron beam impinging upon a specimen. The incident beam excites and liberates lower energy secondary electrons, which are detected and analyzed, providing a visual representation of the sample's surface topography. EDX also relies on an incident electron beam, except an EDX unit measures X-ray energies generated by the impinging beam. Each element generates a unique X-ray signature; the EDX detector measures these discreet energies. EDX actually penetrates approximately 2 microns into the bulk of the sample. However, random examination of various portions of slag, coupled with the semiquantitative nature of the SEM/EDX analysis, did not yield convincingly pertinent data. Therefore, X-ray dot mapping was conducted, which provided more understandable data, both in terms of slag layering and composition. An X-ray dot map is generated by performing numerous EDX scans for individual elements, then compiling the scans in a visual representation. Eventually, specimens consisting of not only the slag, but of the adjacent RCC substrate as well were cross-sectioned. X-Ray dot mapping of the materialographicallymounted and -polished cross- sections provided a visual representation of both the layering sequence and compositional characteristics of the slag. Contemporaneously, Electron Spectroscopy for Chemical Analysis/X-Ray Photoelectron Spectroscopy (ESCA/XPS) and powdered X-Ray Diffraction (XRD) were performed to further characterize the deposits and to attempt to identify what, if any, compounds were present. The ESCA/XPS analysis allowed the analyst to "sputter" into the sample with an electron gun, aiding in the identification of the layering sequence. XPS uses photons, rather than electrons, which impinge upon the surface of the sample. XPS measures the electrons emitted from within the first 5 nm of the sample's surface. The XRD measures the scatter angles of incident X-rays; the angle and intensity of scatter depend upon the crystalline structure of the pulverized sample. XRD is considered a qualitative rather than quantitative technique. ESCA/XPS revealed that the final layer to deposit was predominantly carbonaceous. XRD was successful in identifying specific compounds, such as Al 2O3, Al and/or Al3 21SiO47, mullite (3(Al2)O3 -SiO2), and nickel-aluminides. Eventually, Electron MicroProbe Analysis (EMPA) was conducted on the marialographically-prepared cross- sections of selected slag deposits. Microprobe combines SEM and Wavelength Dispersive X-Ray Spectroscopy (WDS), and, like EDX, uses a narrowly-focused high-energy electron beam impinging upon a specimen to elicit, in the case of EPMA, characteristic X-rays with specific wavelengths. This quantitative, analytical tool proved the most useful in determining depositional layering and composition of the slag deposits. This information was utilized in verifying the location of the breach in the left leading edge of the wing of the Columbia.

Sequence stratigraphy of the Lower Cenomanian Bahariya Formation, Bahariya Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Catuneanu, O.; Khalifa, M. A.; Wanas, H. A.

2006-08-01

The Lower Cenomanian Bahariya Formation corresponds to a second-order depositional sequence that formed within a continental shelf setting under relatively low-rate conditions of positive accommodation (< 200 m during 3-6 My). This overall trend of base-level rise was interrupted by three episodes of base-level fall that resulted in the formation of third-order sequence boundaries. These boundaries are represented by subaerial unconformities (replaced or not by younger transgressive wave ravinement surfaces), and subdivide the Bahariya Formation into four third-order depositional sequences. The construction of the sequence stratigraphic framework of the Bahariya Formation is based on the lateral and vertical changes between shelf, subtidal, coastal and fluvial facies, as well as on the nature of contacts that separate them. The internal (third-order) sequence boundaries are associated with incised valleys, which explain (1) significant lateral changes in the thickness of incised valley fill deposits, (2) the absence of third-order highstand and even transgressive systems tracts in particular areas, and (3) the abrupt facies shifts that may occur laterally over relatively short distances. Within each sequence, the concepts of lowstand, transgressive and highstand systems tracts are used to explain the observed lateral and vertical facies variability. This case study demonstrates the usefulness of sequence stratigraphic analysis in understanding the architecture and stacking patterns of the preserved rock record, and helps to identify 13 stages in the history of base-level changes that marked the evolution of the Bahariya Oasis region during the Early Cenomanian.

Effects of Different Materials Used for Internal Floating Electrode on the Photovoltaic Properties of Tandem Type Organic Solar Cell

NASA Astrophysics Data System (ADS)

Triyana, Kuwat; Yasuda, Takeshi; Fujita, Katsuhiko; Tsutsui, Tetsuo

2004-04-01

Three thin heterojunctions sandwiched between indium tin oxide (ITO) and the top electrode as triple-heterojunction organic solar cells have been fabricated. Each heterojunction cell consists of CuPc as a donor layer and perilene tetracrboxylic-bis-benzimidazole (PTCBI) as an acceptor layer. Ultra thin (1 nm average thickness) layers of Ag or Au have been inserted between two heterojunctions as an internal electrode. Ag and Au were chosen as materials both for internal floating and top electrodes. Influences of different deposition sequences of the organic layer in each heterojunction cell and different electrode materials were also investigated. The optimum devices were obtained when the same material was used both as an internal electrode and a top electrode. When the deposition sequence of the heterojunction is PTCBI/CuPc, the most suitable electrode is Au and the ITO is negative relative to the top electrode. Meanwhile, Ag is suitable for an electrode when the deposition sequence is CuPc/PTCBI. In this second deposition sequence, the ITO is positive relative to the top electrode. The open circuit voltage (Voc) of both optimum devices is on the order of 1.35-1.5 V. These values are approximately three times higher than that in single-heterojunction organic solar cells.

In situ monitoring of atomic layer controlled pore reduction in alumina tubular membranes using sequential surface reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berland, B.S.; Gartland, I.P.; Ott, A.W.

1998-12-01

The pore diameter in alumina tubular membranes with an initial diameter of 50 {angstrom} was systematically reduced using the atomic layer controlled deposition of Al{sub 2}O{sub 3}. The Al{sub 2}O{sub 3} was deposited using sequential exposures of Al(CH{sub 3}){sub 3} (trimethylaluminum, TMA) and H{sub 2}O in an ABAB... binary reaction sequence. The pore diameter reduction was monitored using in situ N{sub 2} and Ar conductance measurements. The conductance, C = Q/{Delta}P, was measured using a mass flow controller to define a constant gas throughput, Q, and a pair of capacitance manometers to monitor the transmembrane pressure drop, {Delta}P. Conductance measurementsmore » were periodically obtained at 298 K as a function of AB binary reaction cycles. These conductance measurements were consistent with a pore diameter reduction from 50 {angstrom} to {approximately}5--10 {angstrom} at a rate of {approximately}2.5 {angstrom} for each AB cycle. Conductance measurements were also performed during the Al{sub 2}O{sub 3} deposition at 500 K after each half-reaction in the binary reaction sequence. These in situ conductance measurements demonstrate that the pore diameters in mesoporous membranes can be reduced to molecular dimensions with atomic layer control using sequential surface reactions. Poe diameters can be tailored for specific applications by varying the number of AB cycles and changing the nature of the terminating surface functional groups.« less

Development of highly sensitive electrochemical genosensor based on multiwalled carbon nanotubes-chitosan-bismuth and lead sulfide nanoparticles for the detection of pathogenic Aeromonas.

PubMed

Fernandes, António Maximiano; Abdalhai, Mandour H; Ji, Jian; Xi, Bing-Wen; Xie, Jun; Sun, Jiadi; Noeline, Rasoamandrary; Lee, Byong H; Sun, Xiulan

2015-01-15

In this paper, we reported the construction of new high sensitive electrochemical genosensor based on multiwalled carbon nanotubes-chitosan-bismuth complex (MWCNT-Chi-Bi) and lead sulfide nanoparticles for the detection of pathogenic Aeromonas. Lead sulfide nanoparticles capped with 5'-(NH2) oligonucleotides thought amide bond was used as signalizing probe DNA (sz-DNA) and thiol-modified oligonucleotides sequence was used as fixing probe DNA (fDNA). The two probes hybridize with target Aeromonas DNA (tDNA) sequence (fDNA-tDNA-szDNA). The signal of hybridization is detected by differential pulse voltammetry (DPV) after electrodeposition of released lead nanoparticles (PbS) from sz-DNA on the surface of glass carbon electrode decorated with MWCNT-Chi-Bi, which improves the deposition and traducing electrical signal. The optimization of incubation time, hybridization temperature, deposition potential, deposition time and the specificity of the probes were investigated. Our results showed the highest sensibility to detect the target gene when compared with related biosensors and polymerase chain reaction (PCR). The detection limit for this biosensor was 1.0×10(-14) M. We could detect lower than 10(2) CFU mL(-1) of Aeromonas in spiked tap water. This method is rapid and sensitive for the detection of pathogenic bacteria and would become a potential application in biomedical diagnosis, food safety and environmental monitoring. Copyright © 2014 Elsevier B.V. All rights reserved.

Intraspecific variation between the ITS sequences of Toxocara canis, Toxocara cati and Toxascaris leonina from different host species in south-western Poland.

PubMed

Fogt-Wyrwas, R; Mizgajska-Wiktor, H; Pacoń, J; Jarosz, W

2013-12-01

Some parasitic nematodes can inhabit different definitive hosts, which raises the question of the intraspecific variability of the nematode genotype affecting their preferences to choose particular species as hosts. Additionally, the issue of a possible intraspecific DNA microheterogeneity in specimens from different parts of the world seems to be interesting, especially from the evolutionary point of view. The problem was analysed in three related species - Toxocara canis, Toxocara cati and Toxascaris leonina - specimens originating from Central Europe (Poland). Using specific primers for species identification, internal transcribed spacer (ITS)-1 and ITS-2 regions were amplified and then sequenced. The sequences obtained were compared with sequences previously described for specimens originating from other geographical locations. No differences in nucleotide sequences were established in T. canis isolated from two different hosts (dogs and foxes). A comparison of ITS sequences of T. canis from Poland with sequences deposited in GenBank showed that the scope of intraspecific variability of the species did not exceed 0.4%, while in T. cati the differences did not exceed 2%. Significant differences were found in T. leonina, where ITS-1 differed by 3% and ITS-2 by as much as 7.4% in specimens collected from foxes in Poland and dogs in Australia. Such scope of differences in the nucleotide sequence seems to exceed the intraspecific variation of the species.

Molecular analysis of the human faecal archaea in a southern Indian population.

PubMed

Rani, Sandya B; Balamurugan, Ramadass; Ramakrishna, Balakrishnan S

2017-03-01

Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea in an Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschool children, school-going children, adolescents, adults and elderly) of a southern Indian population, and from a tribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified from pooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequences in the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequences were deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 - KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% in neonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacter accounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Other genera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibacter smithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can be found in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominant faecal archeon in all age groups, with other genera being found at the extremes of age.

TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.

PubMed Central

Wallace, A. C.; Borkakoti, N.; Thornton, J. M.

1997-01-01

It is well established that sequence templates such as those in the PROSITE and PRINTS databases are powerful tools for predicting the biological function and tertiary structure for newly derived protein sequences. The number of X-ray and NMR protein structures is increasing rapidly and it is apparent that a 3D equivalent of the sequence templates is needed. Here, we describe an algorithm called TESS that automatically derives 3D templates from structures deposited in the Brookhaven Protein Data Bank. While a new sequence can be searched for sequence patterns, a new structure can be scanned against these 3D templates to identify functional sites. As examples, 3D templates are derived for enzymes with an O-His-O "catalytic triad" and for the ribonucleases and lysozymes. When these 3D templates are applied to a large data set of nonidentical proteins, several interesting hits are located. This suggests that the development of a 3D template database may help to identify the function of new protein structures, if unknown, as well as to design proteins with specific functions. PMID:9385633

The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera.

PubMed

Sargent, D J; Rys, A; Nier, S; Simpson, D W; Tobutt, K R

2007-01-01

We have developed 46 primer pairs from exon sequences flanking polymorphic introns of 23 Fragaria gene sequences and one Malus sequence deposited in the EMBL database. Sequencing of a set of the PCR products amplified with the novel primer pairs in diploid Fragaria showed the products to be homologous to the sequences from which the primers were originally designed. By scoring the segregation of the 24 genes in two diploid Fragaria progenies FV x FN (F. vesca x F. nubicola F(2)) and 815 x 903BC (F. vesca x F. viridis BC(1)) 29 genetic loci at discrete positions on the seven linkage groups previously characterised could be mapped, bringing to 35 the total number of known function genes mapped in Fragaria. Twenty primer pairs, representing 14 genes, amplified a product of the expected size in both Malus and Prunus. To demonstrate the applicability of these gene-specific loci to comparative mapping in Rosaceae, five markers that displayed clear polymorphism between the parents of a Malus and a Prunus mapping population were selected. The markers were then scored and mapped in at least one of the two additional progenies.

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

PubMed

Falk, Marni J; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T; Stassen, Alphons P M; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G; Brilhante, Virginia; Ralph, David; DaRe, Jeana T; Shelton, Robert; Terry, Sharon F; Zhang, Zhe; Copeland, William C; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2015-03-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial diseases. Copyright © 2014 Elsevier Inc. All rights reserved.

Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

PubMed Central

Falk, Marni J.; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T.; Stassen, Alphons P.M.; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G.; Brilhante, Virginia; Ralph, David; DaRe, Jeana T.; Shelton, Robert; Terry, Sharon; Zhang, Zhe; Copeland, William C.; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C.; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2014-01-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The “Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium” is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1,300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial disease. PMID:25542617

Lateral trends and vertical sequences in estuarine sediments, Willapa Bay, Washington

USGS Publications Warehouse

Clifton, H. Edward; Phillips, L.

1980-01-01

Willapa Bay is a sizable estuary on the southern coast of Washington- Relatively unmodified in a geologic sense by human activity the bay provides an excellent example of modern depositional facies in an estuarine setting. Studies of these deposits indicate that consistent lateral trends exist in sediment texture and sedimentary structures. The texture changes from sandy at the mouth of the bay to muddy in its upper parts. In any part of the bay , sediment is coarsest in the channel bottoms, where lag deposits accumulate. The sediment tends to fine in an upslope direction and is finest in supratidal flat deposits of silt and clay. The nature of sedimentary structures depends on the combination of physical and biological processes and sediment textures. Bedforms exist wherever the bed is sandy. In the main tidal channels sandwaves and dunes up to 4 meters high occur. In tributary channels and at the margins of the main channel, at shallower depths and under less intense currents , the structures are generally less than a meter high. Current ripples occur in t he sandy bed of all of the tidal channels and in runoff channels cross the tidal flat. Symmetric long-crested ripples are produced by wave action over the sandy intertidal flat. Internal structures in the bay's sediment depend not only on the nature of the bedform but also on the rate of bioturbation relative to physical processes. Under fields of large sandwaves or dunes, medium- to large-scale tabular and trough crossbedding predominates. This crossbedding generally is unidirectional, reflecting the locally dominant current (ebb or flood). Ripple bedding predominates elsewhere in sandy sediment within the channels. Where sand transport is diminished, as on the floor of the upper tributary channels, bioturbation exceeds the rate of production of physical structures and bedding is destroyed. The depositional banks in such areas tend to be sites of rapid sediment accumulation and bedding in the form of interlayered sand (commonly ripple bedded) and mud persists. On intertidal flats the sediment accumulates slowly and bioturbation erases nearly all physical structures. Bedding is preserved only where deposition is locally rapid , as in topographic depressions or on the depositional banks of runoff channels, or where faunal activity is inhibited, as beneath mounds of blue-green algae. The rate of sedimentation is slower still on the supratidal flats, but the general paucity of faunal activity allows the preservation of thin alternations of fine sand , silt or clay. The lateral migration of the tidal channels produces vertical sequences in which topographically higher facies are superposed on one another. Near the mouth of the estuary the upward sequence: lag deposit — crossbedded sand — ripple or planar-bedded sand is typical. The crossbedding shows a general upward decrease in thickness and a progression from trough to tabular units. In the main tidal channel - in the central estuary and in sandy tributary channels, the typical vertical sequence resembles that near the mouth , with the exception that the sequence is capped by bioturbated sandy or muddy tide flat deposits. In the upper estuary , where muddy sediment predominates, a typical sequence shows the progression-. bioturbated lag deposit — gently dipping interlaminated sand and mud layers of the accretionary bank — bioturbated mud flat deposits — thinly laminated fine supratidal deposits.

Paleogeographic implications of an erosional remnant of Paleogene rocks southwest of the Sur-Nacimiento Fault Zone, southern Coast Ranges, California

USGS Publications Warehouse

Vedder, J.G.; McLean, H.; Stanley, R.G.; Wiley, T.J.

1991-01-01

A small tract of heretofore-unrecognized Paleogene rocks lies about 30 km northeast of Santa Maria and 1 km southwest of the Sur-Nacimiento fault zone near upper Pine Creek. This poorly exposed assemblage of rocks is less than 50 m thick, lies unconformably on regionally distributed Upper Cretaceous submarine-fan deposits, and consists of three units: fossiliferous lower Eocene mudstone, Oligocene(?) conglomerate, and basaltic andesite that has a radiometric age of 26.6 ?? 0.5 Ma. Both the sedimentary and igneous constituents in the Paleogene sequence are unlike those of known sequences on either side of the Sur-Nacimiento fault zone. The Paleogene sedimentary rocks near upper Pine Creek presumably are remnants of formerly widespread early Eocene bathyal deposits and locally distributed Oligocene(?) fluvial deposits southwest of the fault zone. The 26.6 Ma basaltic andesite, however, may not have extended much beyond its present outcrops. An episode of Oligocene(?) displacement is required by the contrast in thicknesses, depositional patterns, and paleobathymetry of the juxtaposed rock sequences. -from Authors

Ichnology applied to sequence stratigraphic analysis of Siluro-Devonian mud-dominated shelf deposits, Paraná Basin, Brazil

NASA Astrophysics Data System (ADS)

Sedorko, Daniel; Netto, Renata G.; Savrda, Charles E.

2018-04-01

Previous studies of the Paraná Supersequence (Furnas and Ponta Grossa formations) of the Paraná Basin in southern Brazil have yielded disparate sequence stratigraphic interpretations. An integrated sedimentological, paleontological, and ichnological model was created to establish a refined sequence stratigraphic framework for this succession, focusing on the Ponta Grossa Formation. Twenty-nine ichnotaxa are recognized in the Ponta Grossa Formation, recurring assemblages of which define five trace fossil suites that represent various expressions of the Skolithos, Glossifungites and Cruziana ichnofacies. Physical sedimentologic characteristics and associated softground ichnofacies provide the basis for recognizing seven facies that reflect a passive relationship to bathymetric gradients from shallow marine (shoreface) to offshore deposition. The vertical distribution of facies provides the basis for dividing the Ponta Grossa Formation into three major (3rd-order) depositional sequences- Siluro-Devonian and Devonian I and II-each containing a record of three to seven higher-order relative sea-level cycles. Major sequence boundaries, commonly coinciding with hiatuses recognized from previously published biostratigraphic data, are locally marked by firmground Glossifungites Ichnofacies associated with submarine erosion. Maximum transgressive horizons are prominently marked by unbioturbated or weakly bioturbated black shales. By integrating observations of the Ponta Grossa Formation with those recently made on the underlying marginal- to shallow-marine Furnas Formation, the entire Paraná Supersequence can be divided into four disconformity-bound sequences: a Lower Silurian (Llandovery-Wenlock) sequence, corresponding to lower and middle units of the Furnas; a Siluro-Devonian sequence (?Pridoli-Early Emsian), and Devonian sequences I (Late Emsian-Late Eifelian) and II (Late Eifelian-Early Givetian). Stratigraphic positions of sequence boundaries generally coincide with regressive phases on established global sea-level curves for the Silurian-Devonian.

A note on coarse-grained gravity-flow deposits within proterozoic lacustrine sedimentary rocks, Transvaal sequence, South Africa

NASA Astrophysics Data System (ADS)

Eriksson, P. G.

A widely developed, thin, coarse-matrix conglomerate occurs within early Proterozoic lacustrine mudrocks in the Transvaal Sequence, South Africa. The poorly sorted tabular chert clasts, alternation of a planar clast fabric with disorientated zones, plus normal and inverse grading in the former rock type suggest deposition by density-modified grain-flow and high density turbidity currents. The lower fan-delta slope palæenvironment inferred for the conglomerate is consistent with the lacustrine interpretation for the enclosing mudrock facies. This intracratonic setting contrasts with the marine environment generally associated with density-modified grain-flow deposits.

Geochemical signatures of tsunami deposits - what do they tell us?

NASA Astrophysics Data System (ADS)

Chague-Goff, Catherine; Goff, James R.

2010-05-01

In the last two and half decades, but even more since the 2004 Indian Ocean Tsunami (IOT), there has been a significant increase in the amount of literature dealing with recent, historical and palaeotsunamis. Much has been written and debated about the diagnostic criteria of historical and palaeotsunami deposits. Most of the diagnostic criteria or proxies used reflect the expertise of the researchers involved and thus tend to be biased towards sedimentology, stratigraphy and micropalaeontology, with some reference to geomorphology, archaeology, anthropology and palynology. It should however be noted that all criteria have never been reported from one site, and neither are they all found in one single deposit. Thus, the lack of one or more proxies should not be taken as unique evidence to refute the tsunamigenic origin of a specific deposit. Although geochemical signatures have long been used as indicators for palaeosalinity in sedimentary sequences, there appears to have been some reluctance to use them to help in the identification of historical and palaeotsunami deposits. Like other proxies, geochemistry alone may not provide a definite answer to the origin of a deposit. Furthermore, poor preservation due to environmental conditions or as a result of post-diagenetic processes, might complicate the interpretation of geochemical signatures left by tsunami inundation. Similar taphonomic problems are also faced for microfossil proxies. However, geochemistry provides another piece to the puzzle, and together with other proxies, it can help identify palaeotsunami deposits. Geochemical signatures can also provide clues about the landward limit of runup of a tsunami, beyond the area of sediment deposition. This was recently documented following the 2004 IOT and the 2009 South Pacific tsunami. A summary of examples of geochemical signatures recorded in interstitial water and sediment of recent, historical and palaeotsunami deposits is presented.

The Late Holocene Stratigraphy of an Inlet-Dominated Barrier Island, Pea Island, North Carolina.

NASA Astrophysics Data System (ADS)

Smith, C. G.; Ames, D.; Corbett, D. R.; Culver, S.; Mallinson, D.; Riggs, S. R.; Vance, D.

2002-12-01

Sedimentological, foraminiferal, geochemical, and geophysical data sets as well as aerial photographs have been used to investigate the natural processes (inlet dynamics, ocean/estuarine washover, and sea-level change) responsible for the late Holocene units preserved in the barrier island subsurface at Pea Island National Wildlife Refuge. Historic nautical charts indicate that three inlets characterized Pea Island between early European exploration (1590) and the late 19th century; aerial photographs show New Inlet open in 1932 and 1940. Vibracores (up to 5.5 m) collected along three transects across Pea Island extend our knowledge of the geological evolution of this region to pre-historic times. The section in the longest core (PI01S6) consists of four fining-upwards depositional sequences. The basal unit of each sequence is a bedded, medium to fine, clean quartz sand with increasing concentrations of organic matter (3-4 % detrital and 5-7 % in situ Spartina alterniflora roots) or irregular mud clasts (2-5 cm) to spherical mud balls (1-2 cm) up core. The clean sand units have so far proven to be barren of foraminifera except for a shelly unit at ca. 220 cm below MSL. The foraminiferal assemblage in this unit is of open shelf character (Elphidium excavatum, Hanzawaia strattoni, and Buccella inusitata). A 14C age on a disarticulated Chione cancellata valve from this unit is cal. 930+/-60 BP. The sand grades into a gray, tight mud in the first two sequences and into an inter-laminated mud and in situ peat in the third sequence. The peat contains leaf fragments and rhizomes of the marsh plants Juncus roemarianus, Spartina cynosuroides, and/or Phragmites spp. The peat and muddy sand units contain marsh foraminifera (Trochammina spp., Miliammina fusca, Arenoparrella mexicana), which are also found in modern marsh deposits. A peat sample from the third fining upward sequence (the only one to grade into a true peat) has a 14C age of cal. 395+/-35 BP, cal. 295+/-35 BP, or cal 180+/-40 BP. The four fining-upwards sequences have sharp erosional basal contacts. These deposits appear to reflect back-barrier processes including sequential deposition of flood-tide delta sands and/or sound sands adjacent to marshes. The shelly sands, containing open shelf foraminiferal assemblages, represent oceanic overwash, inlet deposits, or open embayment sands deposited behind a laterally extensive breach in the barrier island. The sequences are capped by the deposits of modern environments that include algal flats, tidal creeks, high and low marshes, back-barrier berms, overwash fans, and aeolian dunes. Several of the modern environments became covered with marsh vegetation after the construction of barrier dune ridges in the late 1930?s.

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacMillan, Colleen P.; Birke, Hannah; Chuah, Aaron

Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a ‘typical’ lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.

Application of TIMS data in stratigraphic analysis

NASA Technical Reports Server (NTRS)

Lang, H. R.

1986-01-01

An in-progress study demonstrates the utility of Thermal Infrared Multispectral Scanner (TIMS) data for unraveling the stratigraphic sequence of a western interior, North American foreland basin. The TIMS data can be used to determine the stratigraphic distribution of minerals that are diagnostic of specific depositional distribution. The thematic mapper (TM) and TIMS data were acquired in the Wind River/Bighorn area of central Wyoming in November 1982, and July 1983, respectively. Combined image processing, photogeologic, and spectral analysis methods were used to: map strata; construct stratigraphic columns; correlate data; and identify mineralogical facies.

Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls

DOE PAGES

MacMillan, Colleen P.; Birke, Hannah; Chuah, Aaron; ...

2017-07-18

Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a ‘typical’ lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre.

Sedimentary record of erg migration

NASA Astrophysics Data System (ADS)

Porter, M. L.

1986-06-01

The sedimentary record of erg (eolian sand sea) migration consists of an idealized threefold division of sand-sea facies sequences. The basal division, here termed the fore-erg, is composed of a hierarchy of eolian sand bodies contained within sediments of the flanking depositional environment. These sand bodies consist of eolian strata deposited by small dune complexes, zibars, and sand sheets. The fore-erg represents the downwind, leading edge of the erg and records the onset of eolian sedimentation. Basin subsidence coupled with erg migration places the medial division, termed the central erg, over the fore-erg strata. The central erg, represented by a thick accumulation of large-scale, cross-stratified sandstone, is the product of large draa complexes. Eolian influence on regional sedimentation patterns is greatest in the central erg, and most of the sand transported and deposited in the erg is contained within this region. Reduction in sand supply and continued erg migration will cover the central-erg deposits with a veneer of back-erg deposits. This upper division of the erg facies sequence resembles closely the fore-erg region. Similar types of eolian strata are present and organized in sand bodies encased in sediments of the upwind flanking depositional environment(s). Back-erg deposits may be thin due to limited eolian influence on sedimentation or incomplete erg migration, or they may be completely absent because of great susceptibility to postdepositional erosion. Tectonic, climatic, and eustatic influences on sand-sea deposition will produce distinctive variations or modifications of the idealized erg facies sequence. The resulting variants in the sedimentary record of erg migration are illustrated with ancient examples from western North America, Europe, southern Africa, and South America.

Depositional environments and paleogeography of the Upper Miocene Wassuk Group, west-central Nevada

USGS Publications Warehouse

Golia, R.T.; Stewart, John H.

1984-01-01

Fluvial and lacustrine deposits of the Miocene Wassuk Group, exposed in Coal Valley, west-central Nevada, are divided into five lithofacies: (1) diatomite, claystone, siltstone, and carbonaceous siltstone deposited in a lake with paludal conditions at the margin; (2) upward-coarsening sequences of sandstone deposited on a delta and fan-delta; (3) channel-form sandstone deposited on a distal braided alluvial plain; (4) clast-supported conglomerate deposited on a proxial braided alluvial plain or distal alluvial fan; and (5) matrix-supported conglomerate deposited on a distal to middle alluvial fan. Petrographic analysis records an upsection change from a predominantly andesitic to a predominantly plutonic provenance. This change, combined with the overall upward-coarsening of the Wassuk Group and the great thickness (2400 m) of the sequence, suggests active uplift and rapid subsidence during deposition of the group. Facies relationships and paleocurrent directions indicate source areas to the south, southeast and west of Coal Valley. The Miocene Wassuk Group was deposited in an intra-arc basin with penecontemporaneous volcanism and tectonic activity. Syndepositional faulting at the southern margin of Coal Valley between 13 and 11 m.y. ago suggests an early episode of northeast-southwest extension prior to the onset of east-west basin and range extension. ?? 1984.

Seismic analysis of clinoform depositional sequences and shelf-margin trajectories in Lower Cretaceous (Albian) strata, Alaska North Slope

USGS Publications Warehouse

Houseknecht, D.W.; Bird, K.J.; Schenk, C.J.

2009-01-01

Lower Cretaceous strata beneath the Alaska North Slope include clinoform depositional sequences that filled the western Colville foreland basin and overstepped the Beaufort rift shoulder. Analysis of Albian clinoform sequences with two-dimensional (2D) seismic data resulted in the recognition of seismic facies inferred to represent lowstand, transgressive and highstand systems tracts. These are stacked to produce shelf-margin trajectories that appear in low-resolution seismic data to alternate between aggradational and progradational. Higher-resolution seismic data reveal shelf-margin trajectories that are more complex, particularly in net-aggradational areas, where three patterns commonly are observed: (1) a negative (downward) step across the sequence boundary followed by mostly aggradation in the lowstand systems tract (LST), (2) a positive (upward) step across the sequence boundary followed by mostly progradation in the LST and (3) an upward backstep across a mass-failure d??collement. These different shelf-margin trajectories are interpreted as (1) fall of relative sea level below the shelf edge, (2) fall of relative sea level to above the shelf edge and (3) mass-failure removal of shelf-margin sediment. Lowstand shelf margins mapped using these criteria are oriented north-south in the foreland basin, indicating longitudinal filling from west to east. The shelf margins turn westward in the north, where the clinoform depositional system overstepped the rift shoulder, and turn eastward in the south, suggesting progradation of depositional systems from the ancestral Brooks Range into the foredeep. Lowstand shelf-margin orientations are consistently perpendicular to clinoform-foreset-dip directions. Although the Albian clinoform sequences of the Alaska North Slope are generally similar in stratal geometry to clinoform sequences elsewhere, they are significantly thicker. Clinoform-sequence thickness ranges from 600-1000 m in the north to 1700-2000 m in the south, reflecting increased accommodation from the rift shoulder into the foredeep. The unusually thick clinoform sequences suggest significant subsidence followed by rapid sediment influx. No claim to original US government works. Journal Compilation ?? Blackwell Publishing Ltd, European Association of Geoscientists & Engineers and International Association of Sedimentologists.

Significance of a near-source tephra-stratigraphic sequence to the eruptive history of Hayes Volcano, south-central Alaska

USGS Publications Warehouse

Wallace, Kristi; Coombs, Michelle L.; Hayden, Leslie A.; Waythomas, Christopher F.

2014-01-01

Bluffs along the Hayes River valley, 31 km northeast and 40 km downstream from Hayes Volcano, reveal volcanic deposits that shed new light on its eruptive history. Three thick (>10 cm) and five thin (<10 cm) tephra-fall deposits are dacitic in whole rock composition and contain high proportions of amphibole to pyroxene and minor biotite and broadly correlate to Hayes tephra set H defined by earlier investigators. Two basal ages for the tephra-fall sequence of 3,690±30 and 3,750±30 14C yr B.P. are also consistent with the Hayes tephra set H timeframe. Distinguishing among Hayes tephra set H units is critical because the set is an important time-stratigraphic marker in south-central Alaska and this section provides a new reference section for Hayes tephra set H. Analysis of Fe-Ti oxide grains in the tephras shows promise for identifying individual Hayes deposits. Beneath the dacitic tephra sequence lies an older, poorly sorted tephra (tephra A) that contains dacite and rhyolite lapilli and whose basal age is 4,450±30 14C yr B.P. Immediately below the tephra-fall sequence (Unit III) lies a series of mass-flow deposits that are rich in rhyodacitic clasts (Unit II). Below Unit II and possibly coeval with it, is a 20–30 m thick pumiceous pyroclastic-flow deposit (Unit I) that extends to the valley floor. Here informally named the Hayes River ignimbrite, this deposit contains pumice clasts of rhyolite with quartz, sanidine, plagioclase, and biotite phenocrysts, an assemblage that is unique among known Quaternary volcanic products of Hayes and other Alaskan volcanoes. Units I, II, and tephra A of Unit III represent at least two previously unrecognized eruptions of Hayes Volcano that occurred prior to ~3,700 yr B.P. No compositionally equivalent distal tephra deposits correlative with Hayes Volcano rhyodacites or rhyolites have yet been identified, perhaps indicating that some of these deposits are pre-Holocene, and were largely removed by glacial ice during the last ice age. More field and analytical work is needed to further refine the eruptive history of Hayes Volcano.

Earliest accumulation history of the north polar layered deposits, Mars from SHARAD

NASA Astrophysics Data System (ADS)

Nerozzi, Stefano; Holt, John W.

2018-07-01

The approximately 2 km thick north polar layered deposits (NPLD) are often considered to contain the most complete and detailed stratigraphic records of recent climate of Mars. Exposures of the dense layering within troughs and scarps allowed detailed reconstructions of the latest accumulation history of these water ice deposits, but we lack knowledge of their initial emplacement. The Shallow Radar (SHARAD) onboard Mars Reconnaissance Orbiter (MRO) penetrates the NPLD to their base and detects their internal layering, overcoming the limitation of scarce and scattered visible outcrops of the lowermost sequences. In this study, we map reflectors in SHARAD data that result from discrete stratigraphic horizons in order to delineate the three-dimensional stratigraphy of the lowermost ∼500 m NPLD sequence and reconstruct their accumulation history. We confirm the large-scale lateral continuity and thickness uniformity of the deposits previously detected within the lowermost NPLD. However, stratigraphic complexity-in the form of pinch-outs and significant thickness variations-arises when we examine single radar units. We find evidence of an initially limited geographic stability of water ice within two deposits that are centered at the North Pole and present-day Gemina Lingula. A period of lateral ice sheet growth followed, interrupted only once by a retreat episode. Lower net accumulation is observed on pre-existing slopes, suggesting a reduction of water ice stability due to increased solar radiation incidence and/or transport by katabatic winds. Lateral transport of water ice by wind is also suggested by thickness undulations toward the top of the sequence, resembling cyclic steps. Water ice accumulation models based on orbital forcing predict a sequence of deposition and retreat events that is generally compatible with our reconstructed accumulation history. Therefore, we interpret the stratigraphic complexity that we observe as regional and, possibly global, climate change induced by orbital forcing. We also find that at least two units are completely buried within the NPLD and do not outcrop, and that NPLD deposition in some places was contemporaneous with deposition of the stratigraphically underlying cavi unit in other places. Both of these findings show that radar reflector mapping is a necessary complement to any stratigraphic reconstruction based on visible exposures.

Sequence-Stratigraphic Analysis of the Regional Observation Monitoring Program (ROMP) 29A Test Corehole and Its Relation to Carbonate Porosity and Regional Transmissivity in the Floridan Aquifer System, Highlands County, Florida

USGS Publications Warehouse

Ward, W. C.; Cunningham, K.J.; Renken, R.A.; Wacker, M.A.; Carlson, J.I.

2003-01-01

An analysis was made to describe and interpret the lithology of a part of the Upper Floridan aquifer penetrated by the Regional Observation Monitoring Program (ROMP) 29A test corehole in Highlands County, Florida. This information was integrated into a one-dimensional hydrostratigraphic model that delineates candidate flow zones and confining units in the context of sequence stratigraphy. Results from this test corehole will serve as a starting point to build a robust three-dimensional sequence-stratigraphic framework of the Floridan aquifer system. The ROMP 29A test corehole penetrated the Avon Park Formation, Ocala Limestone, Suwannee Limestone, and Hawthorn Group of middle Eocene to Pliocene age. The part of the Avon Park Formation penetrated in the ROMP 29A test corehole contains two composite depositional sequences. A transgressive systems tract and a highstand systems tract were interpreted for the upper composite sequence; however, only a highstand systems tract was interpreted for the lower composite sequence of the deeper Avon Park stratigraphic section. The composite depositional sequences are composed of at least five high-frequency depositional sequences. These sequences contain high-frequency cycle sets that are an amalgamation of vertically stacked high-frequency cycles. Three types of high-frequency cycles have been identified in the Avon Park Formation: peritidal, shallow subtidal, and deeper subtidal high-frequency cycles. The vertical distribution of carbonate-rock diffuse flow zones within the Avon Park Formation is heterogeneous. Porous vuggy intervals are less than 10 feet, and most are much thinner. The volumetric arrangement of the diffuse flow zones shows that most occur in the highstand systems tract of the lower composite sequence of the Avon Park Formation as compared to the upper composite sequence, which contains both a backstepping transgressive systems tract and a prograding highstand systems tract. Although the porous and permeable layers are not thick, some intervals may exhibit lateral continuity because of their deposition on a broad low-relief ramp. A thick interval of thin vuggy zones and open faults forms thin conduit flow zones mixed with relatively thicker carbonate-rock diffuse flow zones between a depth of 1,070 and 1,244 feet below land surface (bottom of the test corehole). This interval is the most transmissive part of the Avon Park Formation penetrated in the ROMP 29A test corehole and is included in the highstand systems tract of the lower composite sequence. The Ocala Limestone is considered to be a semiconfining unit and contains three depositional sequences penetrated by the ROMP 29A test corehole. Deposited within deeper subtidal depositional cycles, no zones of enhanced porosity and permeability are expected in the Ocala Limestone. A thin erosional remnant of the shallow marine Suwannee Limestone overlies the Ocala Limestone, and permeability seems to be comparatively low because moldic porosity is poorly connected. Rocks that comprise the lower Hawthorn Group, Suwannee Limestone, and Ocala Limestone form a permeable upper zone of the Upper Floridan aquifer, and rocks of the lower Ocala Limestone and Avon Park Formation form a permeable lower zone of the Upper Floridan aquifer. On the basis of a preliminary analysis of transmissivity estimates for wells located north of Lake Okeechobee, spatial relations among groups of relatively high and low transmissivity values within the upper zone are evident. Upper zone transmissivity is generally less than 10,000 feet squared per day in areas located south of a line that extends through Charlotte, Sarasota, DeSoto, Highlands, Polk, Osceola, Okeechobee, and St. Lucie Counties. Transmissivity patterns within the lower zone of the Avon Park Formation cannot be regionally assessed because insufficient data over a wide areal extent have not been compiled.

[Morphological and molecular characterization of isolates of Macrophomina phaseolina associated with sugarcane in Mexico].

PubMed

Leyva-Mir, Santos G; Velázquez-Martínez, Guadalupe C; Tlapal-Bolaños, Bertha; Tovar-Pedraza, Juan M; Rosas-Saito, Greta H; Alvarado-Gómez, Omar G

2015-01-01

Charcoal rot caused by Macrophomina phaseolina is an important disease of sugarcane in Mexico. This study was carried out to characterize isolates of M. phaseolina obtained from sugarcane by the combination of morphological and molecular analyses. The morphological characterization of 10 isolates was performed using scanning electron microscopy and light microscopy. To confirm the morphological identification, rDNA from two representative isolates was extracted, and the internal transcribed spacer (ITS) region was amplified by polymerase chain reaction and sequenced using specific primers MpKF1 and MpKR1. Based on their morphological characteristics, all isolates were identified as M. phaseolina. Moreover, the analysis of two ITS sequences showed 100% similarity with the M. phaseolina sequences deposited in the GenBank. To our knowledge, this is the first study in the world aimed at characterizing isolates of M. phaseolina obtained from sugarcane. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

The Olympic Dam copper-uranium-gold deposit, Roxby Downs, South Australia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, D.E.; Hudson, G.R.T.

1983-08-01

The Olympic Dam copper-uranium-gold deposit appears to be a new type of strata-bound sediment-hosted ore deposit. It is located 650 km north-northwest of Adelaide in South Australia and was discovered in 1975. It has an areal extent exceeding 20 km/sup 2/ with vertical thicknesses of mineralization up to 350 m. The deposit is estimated to contain in excess of 2,000 million metric tons of mineralized material with an average grade of 1.6 percent copper, 0.06 percent uranium oxide, and 0.6 g/metric ton gold. The deposit occurs in the basement beneath 350 m of unmineralized, flat-lying Adelaidean (late Proterozoic) to Cambrianmore » sediments in the Stuart shelf region of South Australia. The host rocks of the deposit are unmetamorphosed and are probably younger than 1,580 m.y. The deposit is spatially related to coincident gravity and magnetic anomalies and the intersection of west-northwest- and north-northwest-trending lineaments. The Proterozoic sediments comprising the local basement sequence are predominantly sedimentary breccias ranging from matrix-poor granite breccias to matrix-rich polymict breccias containing clasts of a variety of rock types. This sequence is over 1 km thick and has been divided into two main units--the Olympic Dam Formation and the Greenfield Formation. The Olympic Dam Formation has five members, three of which are matrix rich. The Greenfield Formation has three members, the lower two being very hematite rich while the upper has a significant volcanic component. Pervasive hematite, chlorite, and sericite alteration of varying intensity affects all the basement sequence.« less

Glacial origin for cave rhythmite during MIS 5d-c in a glaciokarst landscape, Picos de Europa (Spain)

NASA Astrophysics Data System (ADS)

Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; Giralt, Santiago; DeFelipe, Irene; García-Sansegundo, Joaquín

2017-06-01

Laminated slackwater deposits have been identified in many karst caves related to fluvial and lacustrine sedimentation. However, sedimentological evidence rarely supports a glacial origin for these deposits, which was proposed by previous studies. The Torca La Texa shaft is located in a glaciokarst area that comprises numerous slackwater-type deposits, piled up in fining-upward sequences. A basal sandy erosive layer and millimeter-sized laminated rhythmite with interbedded flowstone characterize these sequences. Fining-upward layers of carbonate silt, clay, and minor quartz sand deposited in flooded conduits define the rhythmite lamination. The presence of allochthonous minerals indicates that the rhythmite sediment comes from the glacial erosion of nearby carbonate mountains. Two 234U/230Th radiometric ages dated the rhythmite deposits around 109 and 95 ka, coinciding with relative cold periods included in the MIS 5d-c. These cold periods were marked by a high annual seasonality, immediately after the glacial local maximum extension, in agreement with a varve-type deposit. The combination of these sedimentological mineralogical, geomorphological and paleoclimate information indicates that the rhythmite should be introduced into the studied cave during the summer melting of the glaciers, which produced the recharge of the karst aquifer, triggering cave floods. In addition, punctual glacier collapses would also have their imprint in the slackwater sequences with thicker, coarser and erosive sand deposits and the spring blocking by glaciers may have promoted floods inside the cave. Therefore, the studied rhythmite can be interpreted as glacial varves decanted during the relatively cold climate conditions.

Sodium inversion recovery MRI of the knee joint in vivo at 7T

NASA Astrophysics Data System (ADS)

Madelin, Guillaume; Lee, Jae-Seung; Inati, Souheil; Jerschow, Alexej; Regatte, Ravinder R.

2010-11-01

The loss of proteoglycans (PG) in the articular cartilage is an early signature of osteoarthritis (OA). The ensuing changes in the fixed charge density in the cartilage can be directly linked to sodium concentration via charge balance. Sodium ions in the knee joint appear in two pools: in the synovial fluids or joint effusion where the ions are in free motion and bound within the cartilage tissue where the Na+ ions have a restricted motion. The ions in these two compartments have therefore different T1 and T2 relaxation times. The purpose of this study is to demonstrate the feasibility of a fluid-suppressed 3D ultrashort TE radial sodium sequence by implementing an inversion recovery (IR) preparation of the magnetization at 7T. This method could allow a more accurate and more sensitive quantification of loss of PG in patients with OA. It is shown that adiabatic pulses offer significantly improved performance in terms of robustness to B1 and B0 inhomogeneities when compared to the hard pulse sequence. Power deposition considerations further pose a limit to the RF inversion power, and we demonstrate in simulations and experiments how a practical compromise can be struck between clean suppression of fluid signals and power deposition levels. Two IR sequences with different types of inversion pulses (a rectangular pulse and an adiabatic pulse) were tested on a liquid phantom, ex vivo on a human knee cadaver and then in vivo on five healthy volunteers, with a (Nyquist) resolution of ∼3.6 mm and a signal-to-noise ratio of ∼30 in cartilage without IR and ∼20 with IR. Due to specific absorption rate limitations, the total acquisition time was ∼17 min for the 3D radial sequence without inversion or with the rectangular IR, and 24:30 min for the adiabatic IR sequence. It is shown that the adiabatic IR sequence generates a more uniform fluid suppression over the whole sample than the rectangular IR sequence.

Sodium inversion recovery MRI of the knee joint in vivo at 7T.

PubMed

Madelin, Guillaume; Lee, Jae-Seung; Inati, Souheil; Jerschow, Alexej; Regatte, Ravinder R

2010-11-01

The loss of proteoglycans (PG) in the articular cartilage is an early signature of osteoarthritis (OA). The ensuing changes in the fixed charge density in the cartilage can be directly linked to sodium concentration via charge balance. Sodium ions in the knee joint appear in two pools: in the synovial fluids or joint effusion where the ions are in free motion and bound within the cartilage tissue where the Na(+) ions have a restricted motion. The ions in these two compartments have therefore different T₁ and T₂ relaxation times. The purpose of this study is to demonstrate the feasibility of a fluid-suppressed 3D ultrashort TE radial sodium sequence by implementing an inversion recovery (IR) preparation of the magnetization at 7T. This method could allow a more accurate and more sensitive quantification of loss of PG in patients with OA. It is shown that adiabatic pulses offer significantly improved performance in terms of robustness to B₁ and B₀ inhomogeneities when compared to the hard pulse sequence. Power deposition considerations further pose a limit to the RF inversion power, and we demonstrate in simulations and experiments how a practical compromise can be struck between clean suppression of fluid signals and power deposition levels. Two IR sequences with different types of inversion pulses (a rectangular pulse and an adiabatic pulse) were tested on a liquid phantom, ex vivo on a human knee cadaver and then in vivo on five healthy volunteers, with a (Nyquist) resolution of ∼3.6 mm and a signal-to-noise ratio of ∼30 in cartilage without IR and ∼20 with IR. Due to specific absorption rate limitations, the total acquisition time was ∼17 min for the 3D radial sequence without inversion or with the rectangular IR, and 24:30 min for the adiabatic IR sequence. It is shown that the adiabatic IR sequence generates a more uniform fluid suppression over the whole sample than the rectangular IR sequence. Copyright © 2010 Elsevier Inc. All rights reserved.

Sedimentology and geochemistry of lacustrine sequences of the upper Pleistocene and holocene in intertropical area (Lake Magadi and Green crater lake): paleoclimatic implications

NASA Astrophysics Data System (ADS)

Damnati, B.

1993-05-01

Sedimentological and geochemical analyses have been carried out on lacustrine deposits of East Africa, at Lake Magadi (2°S, 36°E, Kenya) and at Green Crater Lake (0°S, 36°E, Kenya), to determine the parameters controlling climatic and environmental dynamics during late Pleistocene and Holocene. These sedimentary sequences were collected with a stationary piston corer. At Lake Magadi (Fig. 1), sedimentary and geochemical control show three phases of lake level variation which corresponds to climatic change occurring during the last 40 thousand years. These phases were defined by three lithostratigraphic units. Laminated deposits of Lake Magadi were formed during a wet period. Analysis of these laminae define two microfacies: a dark lamina, characterised by lacustrine organic matter and a light lamina enriched in detritus, carbonates (CaCO 3) and magadiite (NaSi 7O 13(OH) 3, 3H 2O). The formation and preservation of each couplet was favoured by climatic contrast, lake stratification and various origin of the sediments (autochthon and allochthon) in the drainage basin. Therefore a relative chronology can be derived from laminae counting and the duration of deposition of each couplet. Spectral analysis applied on variation of the laminae thickness, shows the existence of three main periods, 4-7 years, 8-14 years and 18-30 years, respectively (Fig. 2). These cyclicites of the lacustrine environment precise former determinations established on more recent lacustrine sequences from East Africa. They are related to the global climatic cycle (quasi-biannual oscillations, El Nino Southern Oscillations and the sun spot cycles). At Green Crater Lake, the study of the sedimentary sequence was completed by physico-chemical analysis of the waters and interface sediments which demonstrate the carbonate, sodium, bicarbonate composition and the thermal and chemical stratification of the modern lake. The sedimentary sequence is characterized by volcanic deposits overlain by physico-chemical analysis of the lake waters and interface sediments which demonstrate the carbonate, sodium, bicarbonate composition and the thermal and chemical stratification of the modern lake. The sedimentary sequence is characterized by volcanic deposits overlain by silt and clays deposited before 7400 years B.P., followed by loweing of the lake level at 3000 years B. P. Results from lake Magadi document the occurrence of a wet period starting at about 12,000 years B. P. The methodology applied on modern Green Crater lake provides base of interpretative models for other Holocene sequence lacustrine systems of intertropical zones.

Geology, ore facies and sulfur isotopes geochemistry of the Nudeh Besshi-type volcanogenic massive sulfide deposit, southwest Sabzevar basin, Iran

NASA Astrophysics Data System (ADS)

Maghfouri, Sajjad; Rastad, Ebrahim; Mousivand, Fardin; Lin, Ye; Zaw, Khin

2016-08-01

The southwest Sabzevar basin is placed in the southwestern part of a crustal domain known as the Sabzevar zone, at the north of Central Iranian microcontinent. This basin hosts abundant mineral deposits; particularly of the Mn exhalative and Cu-Zn volcanogenic massive sulfide (VMS) types. The evolution of this basin is governed by the Neo-tethys oceanic crust subduction beneath the Central Iranian microcontinent and by the resulting continental arc (Sanandaj-Sirjan) and back-arc (Sabzevar-Naien). This evolution followed two major sequences: (I) Lower Late Cretaceous Volcano-Sedimentary Sequence (LLCVSS), which is indicated by fine-grained siliciclastic sediments, gray basic coarse-grained different pyroclastic rocks and bimodal volcanism. During this stage, tuff-hosted stratiform, exhalative Mn deposits (Nudeh, Benesbourd, Ferizy and Goft), oxide Cu deposits (Garab and Ferizy) and Cu-Zn VMS (Nudeh, Chun and Lala) deposits formed. (II) Upper Late Cretaceous Sedimentary Dominated Sequence (ULCSS), including pelagic limestone, marly tuff, silty limestone and marl with minor andesitic tuff rocks. The economically most important Mn (Zakeri and Cheshmeh-sefid) deposits of Sabzevar zone occur within the marly tuff of this sequence. The Nudeh Cu-Zn volcanogenic massive sulfide (VMS) deposit is situated in the LLCVSS. The host-rock of deposits consists of alkali olivine basalt flow and tuffaceous silty sandstone. Mineralization occurs as stratiform blanket-like and tabular orebodies. Based on ore body structure, mineralogy, and ore fabric, we recognize three different ore facies in the Nudeh deposit: (1) a stringer zone, consisting of a discordant mineralization of sulfides forming a stockwork of sulfide-bearing quartz veins cutting the footwall volcano-sedimentary rocks; (2) a massive ore, consisting of massive replacement pyrite, chalcopyrite, sphalerite and Friedrichite with magnetite; (3) bedded ore, with laminated to disseminated pyrite, and chalcopyrite. Chloritization, silicification, sericitization and epidotization are the main wall-rock alterations; alteration intensity increases towards the stringer zone. The δ34S composition of the sulfides ranges from -1.5‰ to +3.69‰ with a general increase of δ34S ratios of massive ore facies to stockwork zone. The heavier values indicate that some of the sulfur was derived from seawater sulfate that was ultimately thermochemically reduced in deep hydrothermal reaction zones. Sulfur isotopes, along with sedimentological, textural, petrological, mineralogical, and geochemical evidences, suggest that this deposit should be classified as a Besshi-type VMS ore deposit.

Early Miocene sequence development across the New Jersey margin

USGS Publications Warehouse

Monteverde, D.H.; Mountain, Gregory S.; Miller, K.G.

2008-01-01

Sequence stratigraphy provides an understanding of the interplay between eustasy, sediment supply and accommodation in the sedimentary construction of passive margins. We used this approach to follow the early to middle Miocene growth of the New Jersey margin and analyse the connection between relative changes of sea level and variable sediment supply. Eleven candidate sequence boundaries were traced in high-resolution multi-channel seismic profiles across the inner margin and matched to geophysical log signatures and lithologic changes in ODP Leg 150X onshore coreholes. Chronologies at these drill sites were then used to assign ages to the intervening seismic sequences. We conclude that the regional and global correlation of early Miocene sequences suggests a dominant role of global sea-level change but margin progradation was controlled by localized sediment contribution and that local conditions played a large role in sequence formation and preservation. Lowstand deposits were regionally restricted and their locations point to both single and multiple sediment sources. The distribution of highstand deposits, by contrast, documents redistribution by along shelf currents. We find no evidence that sea level fell below the elevation of the clinoform rollover, and the existence of extensive lowstand deposits seaward of this inflection point indicates efficient cross-shelf sediment transport mechanisms despite the apparent lack of well-developed fluvial drainage. ?? 2008 The Authors. Journal compilation ?? 2008 Blackwell Publishing.

Stratigraphic evolution of the Late Jurassic Hanifa Formation along the Tuwaiq Escarpment, Saudi Arabia: Evidence for a carbonate ramp system

NASA Astrophysics Data System (ADS)

Fallatah, Mohammed I.; Kerans, Charles

2018-01-01

A sequence stratigraphic framework of the Late Jurassic (Oxfordian) Hanifa Formation at its exposure in Central Arabia is presented for the first time. This study offers the first high-resolution stratigraphic framework of the Hanifa along the Tuwaiq Escarpment by measuring 15 sections ( 770 m total thickness) over an oblique-to-dip distance of 260 km and collecting 295 samples for petrographic analysis. On the basis of these data, the Hanifa Formation can be subdivided into eight facies; 1) tabular cross-bedded quartz-peloidal-skeletal grainstone, 2) cross-bedded skeletal-peloidal grainstone, 3) bioturbated foraminiferal wackestone/mud-dominated packstone, 4) oncolitic rudstone, 5) stromatoporoid-coral biostrome/bioherm, 6) peloidal/composite-grain grain-dominated packstone/grainstone, 7) bioturbated spiculitic wackestone/mud-dominated packstone, and 8) thinly-bedded argillaceous mudstone/wackestone. The vertical and lateral distributions of these facies along the exposure define their sequence setting using the principals of sequence stratigraphy. By recognizing erosional surfaces, facies offset, and changes in facies proportions, five third-order sequences, with an average duration of 1.1 Myr, are interpreted for the Hanifa Formation. The correlation of the sequences across the study area shows that only four sequences are preserved in the north where shallow-water deposits are well-developed. Facies trends within these sequences are further illustrated in depositional models representing the highstand systems tracts (HST) and the transgressive systems tracts (TST) of the Hanifa Formation. These proposed models represent depositional settings of a carbonate ramp with normal open-marine conditions. The HST depositional model is characterized by a high-energy shoreline and depicts the presence of an offshore, structurally controlled skeletal-peloidal shoal body described here for the first time at the Hanifa exposure in the Hozwa area. This work provides a predictive framework and outcrop analog for applications in hydrocarbon exploration and development. Furthermore, a basinal setting predicted to the south of the study area is a potential site for unconventional plays.

Anatomy of major coal successions: Facies analysis and sequence architecture of a brown coal-bearing valley fill to lacustrine tract (Upper Valdarno Basin, Northern Apennines, Italy)

NASA Astrophysics Data System (ADS)

Ielpi, Alessandro

2012-07-01

A late Pliocene incised valley fill to lacustrine succession, which contains an interbedded brown coal seam (< 20 m thick), is examined in terms of facies analysis, physical stratigraphy and sequence architecture. The succession (< 50 m thick) constitutes the first depositional event of the Castelnuovo Synthem, which is the oldest unconformity bounded stratigraphic unit of the nonmarine Upper Valdarno Basin, Northern Apennines (Italy). The integration of field surveys and borehole logs identified the following event sequence: first valley filling stages by coarse alluvial fan and channelised streams; the progressive setting of low gradient floodbasins with shallow floodplain lakes; subsequent major waterlogging and extensive peat mire development; and system drowning and establishment of permanent lacustrine conditions. The deposits are grouped in a set of nested valley fills and are arranged as high-frequency depositional sequences. The sequences are bounded by minor erosive truncations and have distinctive upward trends: lowstand system tract thinning; transgressive system tract thickening; highstand system tract thinning and eventual non-deposition; and the smoothing of along-sequence boundary sub-aerial incisions. Such features fit in with the notion of an idealised model where second-order (high-frequency) fluctuations, modulated by first-order (low-frequency) base-level rising, have short-lived standing + falling phases and prolonged transgressions, respectively. Furthermore, the general sequence architecture reveals how a mixed palustrine-siliciclastic system differs substantially from a purely siliciclastic one. In the transgressive phases, terrigenous starvation induces prevailing peat accumulation, generating abnormally thick transgressive system tracts that eventually come to occupy much of the same transgression-generated accommodation space. In the highstand phases, the development of thick highstand system tracts is then prevented by sediment upstream trapping due to retrogressive fluvial aggradations, probably coupled with low-accommodation settings inherited from the transgressive phases.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

PubMed Central

Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

2009-01-01

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

Apparatus and process for freeform fabrication of composite reinforcement preforms

NASA Technical Reports Server (NTRS)

Yang, Junsheng (Inventor); Wu, Liangwei (Inventor); Liu, Junhai (Inventor); Jang, Bor Z. (Inventor)

2001-01-01

A solid freeform fabrication process and apparatus for making a three-dimensional reinforcement shape. The process comprises the steps of (1) operating a multiple-channel material deposition device for dispensing a liquid adhesive composition and selected reinforcement materials at predetermined proportions onto a work surface; (2) during the material deposition process, moving the deposition device and the work surface relative to each other in an X-Y plane defined by first and second directions and in a Z direction orthogonal to the X-Y plane so that the materials are deposited to form a first layer of the shape; (3) repeating these steps to deposit multiple layers for forming a three-dimensional preform shape; and (4) periodically hardening the adhesive to rigidize individual layers of the preform. These steps are preferably executed under the control of a computer system by taking additional steps of (5) creating a geometry of the shape on the computer with the geometry including a plurality of segments defining the preform shape and each segment being preferably coded with a reinforcement composition defining a specific proportion of different reinforcement materials; (6) generating programmed signals corresponding to each of the segments in a predetermined sequence; and (7) moving the deposition device and the work surface relative to each other in response to these programmed signals. Preferably, the system is also operated to generate a support structure for any un-supported feature of the 3-D preform shape.

Molecular analysis of carbon monoxide-oxidizing bacteria associated with recent Hawaiian volcanic deposits.

PubMed

Dunfield, Kari E; King, Gary M

2004-07-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.

Facies analysis and sequence stratigraphy of neoproterozoic Platform deposits in Adrar of Mauritania, Taoudeni basin, West Africa

NASA Astrophysics Data System (ADS)

Benan, C. A. A.; Deynoux, M.

The Neoproterozoic and Palaeozoic Taoudeni basin forms the flat-lying and unmetamorphosed sedimentary cover of the West African Craton. In the western part of this basin, the Char Group and the lower part of the Atar Group make up a 400-m-thick Neoproterozoic siliciclastic succession which rests on the Palaeoproterozoic metamorphic and granitic basement. Five erosional bounding surfaces of regional extent have been identified in this succession. These surfaces separate five stratigraphic units with lithofacies associations ranging from fluvial to coastal and fluvial-, tide-, or wave-dominated shallow marine deposits. Owing to their regional extent and their position within the succession, the erosive bounding surfaces correspond to relative sea-level falls, and accordingly the five stratigraphic units they bound represent allocyclic transgressive-regressive depositional sequences (S1-S5). Changes in the nature of the deposits forming the transgressive-regressive cycles reflect landward or seaward shifts of the stacked sequences. These successive relative sea-level changes are related to the reactivation of basement faults and tilting during rifting of the Pan-Afro-Brasiliano supercontinent 1000 m.y. ago. The stromatolite bearing carbonate-shale sequences which form the rest of the Atar Group mark the onset of a quiet period of homogeneous subsidence contemporaneous with the Pan-African I oceanization 800-700 m.y. ago.

Sequence stratigraphy of the Lower Triassic Sinbad Formation, San Rafael Swell, east-central, Utah

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodspeed, T.H.; Elrick, M.; Lucas, S.G.

1993-04-01

The Lower Triassic Sinbad Fm (20--30 m thick) in the San Rafael Swell of east-central Utah is high energy carbonate deposits that conformably overlie tidal flat/fluvial channel deposits of the Black Dragon Fm. The Torrey Fm conformably overlies the Sinbad Fm and consists primarily of siliciclastic tidal flat and fluvial deposits. Five facies (in ascending order) are characteristic of the Sinbad Fm: (1) bioturbated calcisiltite with calcite-replaced evaporite nodules and ripple laminations, (2) skeletal-oolitic-intraclastic packstone and grainstone, (3) slightly bioturbated, mechanically laminated, pelletal calcisiltite (5) trough cross-bedded, peloidal to oolitic grainstone, and (5) thin-bedded, skeletal-pelletal-oolitic grainstone with mud to wackestonemore » drapes. Regional facies relationships of the Sinbad Fm indicate initial deepening followed by shallowing. The skeletal-intraclastic packstone and grainstone facies represents maximum flooding. This facies thickens to the northwest and contains an open marine molluscan fauna of ammonites, bivalves, gastropods and scaphopods. The ammonites are indicative of the Tardus Zone of late Smithian age. Deposits above the maximum flooding zone (MFZ) are restricted foreshoal, pelletal calcisiltite, oolitic shoal, and backshoal skeletal-oolitic (with a restricted fauna of molluscs and ostracods) deposits. This shallowing-upward sequence represents the early HST. The Sinbad Fm represents the MFZ and early HST of a 150-m-thick depositional sequence of rocks with the Black Dragon FM representing the TST, and the Torrey Fm representing the late HST.« less

Eruptive history of the Ubehebe Crater cluster, Death Valley, California

NASA Astrophysics Data System (ADS)

Fierstein, Judy; Hildreth, Wes

2017-04-01

A sequence of late Holocene eruptions from the Ubehebe Crater cluster in Death Valley was short-lived, emplacing several phreatomagmatic and magmatic deposits. Seven craters form the main group, which erupted along a north-south alignment 1.5 km long. At least five more make a 500-m east-west alignment west of the main crater group. One more is an isolated shallow crater 400 m south of that alignment. All erupted through Miocene fanglomerate and sandstone, which are now distributed as comminuted matrix and lithic clasts in all Ubehebe deposits. Stratigraphic evidence showing that all Ubehebe strata were emplaced within a short time interval includes: (1) deposits from the many Ubehebe vents make a multi-package sequence that conformably drapes paleo-basement topography with no erosive gullying between emplacement units; (2) several crater rims that formed early in the eruptive sequence are draped smoothly by subsequent deposits; and (3) tack-welded to agglutinated spatter and bombs that erupted at various times through the sequence remained hot enough to oxidize the overlying youngest emplacement package. In addition, all deposits sufficiently consolidated to be drilled yield reliable paleomagnetic directions, with site mean directions showing no evidence of geomagnetic secular variation. Chemical analyses of juvenile components representing every eruptive package yield a narrow range in major elements [SiO2 (48.65-50.11); MgO (4.98-6.23); K2O (2.24-2.39)] and trace elements [Rb (28-33); Sr (1513-1588); Zr (373-404)]. Despite lithologic similarities, individual fall units can be traced outward from vent by recording layer thicknesses, maximum scoria and lithic sizes, and juvenile clast textural variations. This permits reconstruction of the eruptive sequence, which produced a variety of eruptive styles. The largest and northernmost of the craters, Ubehebe Crater, is the youngest of the group. Its largely phreatomagmatic deposits drape all of the others, thicken in paleogullies and thin over several newly created crater rims. Evidence in-hand virtually requires that the Ubehebe cluster of craters erupted over a brief time interval, not protracted over centuries.

Sequence stratigraphy of the siliciclastic East Puolanka Group, the Palaeoproterozoic Kainuu Belt, Finland

NASA Astrophysics Data System (ADS)

Strand, Kari

2005-04-01

The 2300-2600 m thick Palaeoproterozoic East Puolanka Group within the central Fennoscandian Shield records four major transgressions on the cratonic margin within the approximate time period 2.25-2.10 Ga. Stacking of siliciclastic facies in parasequences and parasequence sets provides data to evaluate oscillation of relative sea-level and subsidence on different temporal scales. The lowermost part of the passive margin prism is characterized by alluvial plain to shallow marine sediments deposited in incised valleys. The succeeding highstand period is recorded by ca. 250 m of progradational parasequence sets of predominantly rippled and horizontally laminated sandstones, representing stacked wave-dominated shoreline units in sequence 1, capped by a hiatus or, in some places, by a subaerial lava. As relative sea-level rose again, sand-rich barrier-beach complexes developed with microtidal lagoons and inlets, corresponding to a retrogradational parasequence set. This was followed by a highstand period, with aggradation and progradation of alluvial plain and coastal sediments grading up into wave-tide influenced shoreline deposits in sequence 2. In sequence 3, the succeeding mudstones represent tidal flat deposits in a back-barrier region. With continued transgression, the parasequences stacked retrogradationally, each flooding episode being recorded by increasingly deeper water deposits above low-angle cross-bedded sandstones of the swash zones. The succeeding highstand progradation is represented by alluvial plain deposits. The next transgressive systems tract, overlying an inferred erosional ravinement surface, is recorded by a retrogradational parasequence set dominated by low-angle cross-stratified swash zone deposits in sequence 4. The large-scale trough cross-bed sets in these parasequences represent sand shoals and sheets of the inner shelf system. The overall major transgression recorded in the lowermost part of the Palaeoproterozoic cratonic margin succession was related to first- to second-order sea-level changes, probably due to increasing regional thermal subsidence of the lithosphere following partial continental breakup. The stratigraphic evolution can be related to changes of relative sea-level with a frequency of ca. 25 million years, probably propagated by episodic thermal subsidence. The parasequences identified here are related to high-frequency cycles of relative sea-level change due to low-magnitude eustatic oscillations.

Palaeoclimate characteristics in interior Siberia of MIS 6-2: first insights from the Batagay permafrost mega-thaw slump in the Yana Highlands

NASA Astrophysics Data System (ADS)

Ashastina, Kseniia; Schirrmeister, Lutz; Fuchs, Margret; Kienast, Frank

2017-07-01

Syngenetic permafrost deposits formed extensively on and around the arising Beringian subcontinent during the Late Pleistocene sea level lowstands. Syngenetic deposition implies that all material, both mineral and organic, freezes parallel to sedimentation and remains frozen until degradation of the permafrost. Permafrost is therefore a unique archive of Late Pleistocene palaeoclimate. Most studied permafrost outcrops are situated in the coastal lowlands of northeastern Siberia; inland sections are, however, scarcely available. Here, we describe the stratigraphical, cryolithological, and geochronological characteristics of a permafrost sequence near Batagay in the Siberian Yana Highlands, the interior of the Sakha Republic (Yakutia), Russia, with focus on the Late Pleistocene Yedoma ice complex (YIC). The recently formed Batagay mega-thaw slump exposes permafrost deposits to a depth of up to 80 m and gives insight into a climate record close to Verkhoyansk, which has the most severe continental climate in the Northern Hemisphere. Geochronological dating (optically stimulated luminescence, OSL, and 14C ages) and stratigraphic implications delivered a temporal frame from the Middle Pleistocene to the Holocene for our sedimentological interpretations and also revealed interruptions in the deposition. The sequence of lithological units indicates a succession of several distinct climate phases: a Middle Pleistocene ice complex indicates cold stage climate. Then, ice wedge growth stopped due to highly increased sedimentation rates and eventually a rise in temperature. Full interglacial climate conditions existed during accumulation of an organic-rich layer - plant macrofossils reflected open forest vegetation existing under dry conditions during Marine Isotope Stage (MIS) 5e. The Late Pleistocene YIC (MIS 4-MIS 2) suggests severe cold-stage climate conditions. No alas deposits, potentially indicating thermokarst processes, were detected at the site. A detailed comparison of the permafrost deposits exposed in the Batagay thaw slump with well-studied permafrost sequences, both coastal and inland, is made to highlight common features and differences in their formation processes and palaeoclimatic histories. Fluvial and lacustrine influence is temporarily common in the majority of permafrost exposures, but has to be excluded for the Batagay sequence. We interpret the characteristics of permafrost deposits at this location as a result of various climatically induced processes that are partly seasonally controlled. Nival deposition might have been dominant during winter time, whereas proluvial and aeolian deposition could have prevailed during the snowmelt period and the dry summer season.

Stratigraphic, Granulometric and Geochemical Studies of a Major Plinian Eruption on Dominica, Lesser Antilles

NASA Astrophysics Data System (ADS)

Smith, A. L.; Daly, G.; Killingsworth, N.; Deuerling, K.; Schneider, S.; Fryxell, J. E.

2008-12-01

The island of Dominica, located in the center of the Lesser Antilles island arc has witnessed, probably within the last 100,000 years, three large volume Plinian eruptions. One of these, associated with the Morne Diablotins center, forms the Grande Savane pyroclastic flow fan, that extends off shore as a distinctive submarine feature for a distance of at least 14 km. Stratigraphical studies of road cuts and well-exposed sea cliffs indicate the fan is composed of an older unit composed of reworked deposits at the base followed by at least four sequences, based on the presence of paleosols, of block and ash flow deposits. The upper unit of block and ash flows is overlain, with no evidence of an intervening paleosol, by a sequence of ignimbrites and pumiceous surges (representing the Plinian eruption). There is no evidence of an initial Plinian fall deposit, so the lowest bed in the succession is an ignimbrite with a highly irregular base that cuts into the underlying block and ash flow deposits, the upper parts of which are colored red due to thermal effects. This lowest ignimbrite is welded (minimum porosity of 15%) throughout its thickness (maximum thickness of greater than 21 m), although a few outcrops near the margins show a thin (20-30 cm) non-welded but lithified zone beneath the welded zone. The remainder of the sequence is composed of lithified ignimbrite that can be subdivided into three units separated by pumiceous surge layers. The ignimbrite succession is overlain, with no obvious break, by a thin fall deposit containing accretionary lapilli and gas cavities, followed by three pumiceous surge deposits (lower and upper show planar stratification and the middle surge shows massive bedding); towards the north the upper two surge deposits are separated by thin pumiceous lapilli fall and ash fall deposits. This surge sequence extends laterally outside of the main area of ignimbrite deposition. The pumice clasts from the ignimbrites are andesitic in composition and show essentially no variation up stratigraphy. In contrast, the surges are more variable in composition, ranging from andesite to dacite. Modeling of these data will provide information on the dynamics of this major Plinian eruption including the effects of water/magma interaction.

A Deep Insight Into the Sialotranscriptome of the Chagas Disease Vector, Panstrongylus megistus (Hemiptera: Heteroptera)

PubMed Central

Ribeiro, José M. C.; Schwarz, Alexandra; Francischetti, Ivo M. B.

2015-01-01

Saliva of blood-sucking arthropods contains a complex cocktail of pharmacologically active compounds that assists feeding by counteracting their hosts’ hemostatic and inflammatory reactions. Panstrongylus megistus (Burmeister) is an important vector of Chagas disease in South America, but despite its importance there is only one salivary protein sequence publicly deposited in GenBank. In the present work, we used Illumina technology to disclose and publicly deposit 3,703 coding sequences obtained from the assembly of >70 million reads. These sequences should assist proteomic experiments aimed at identifying pharmacologically active proteins and immunological markers of vector exposure. A supplemental file of the transcriptome and deducted protein sequences can be obtained from http://exon.niaid.nih.gov/transcriptome/P_megistus/Pmeg-web.xlsx. PMID:26334808

Architectures and criteria for the design of high efficiency organic photovoltaic cells

DOEpatents

Rand, Barry; Forrest, Stephen R; Pendergrast Burk, Diane

2015-03-31

A method for fabricating an organic photovoltaic cell includes providing a first electrode; depositing a series of at least seven layers onto the first electrode, each layer consisting essentially of a different organic semiconductor material, the organic semiconductor material of at least an intermediate layer of the sequence being a photoconductive material; and depositing a second electrode onto the sequence of at least seven layers. One of the first electrode and the second electrode is an anode and the other is a cathode. The organic semiconductor materials of the series of at least seven layers are arranged to provide a sequence of decreasing lowest unoccupied molecular orbitals (LUMOs) and a sequence of decreasing highest occupied molecular orbitals (HOMOs) across the series from the anode to the cathode.

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. PMID:22180823

An exploratory drilling exhaustion sequence plot program

USGS Publications Warehouse

Schuenemeyer, J.H.; Drew, L.J.

1977-01-01

The exhaustion sequence plot program computes the conditional area of influence for wells in a specified rectangular region with respect to a fixed-size deposit. The deposit is represented by an ellipse whose size is chosen by the user. The area of influence may be displayed on computer printer plots consisting of a maximum of 10,000 grid points. At each point, a symbol is presented that indicates the probability of that point being exhausted by nearby wells with respect to a fixed-size ellipse. This output gives a pictorial view of the manner in which oil fields are exhausted. In addition, the exhaustion data may be used to estimate the number of deposits remaining in a basin. ?? 1977.

Complete Genome Sequences of Two Vesicular Stomatitis Virus Isolates Collected in Mexico.

PubMed

Velazquez-Salinas, Lauro; Isa, Pavel; Pauszek, Steven J; Rodriguez, Luis L

2017-09-14

We report two full-genome sequences of vesicular stomatitis New Jersey virus (VSNJV) obtained by Illumina next-generation sequencing of RNA isolated from epithelial suspensions of cattle naturally infected in Mexico. These genomes represent the first full-genome sequences of vesicular stomatitis New Jersey viruses circulating in Mexico deposited in the GenBank database.

Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents.

PubMed

Benson, Courtney A; Bizzoco, Richard W; Lipson, David A; Kelley, Scott T

2011-04-01

Fumaroles, commonly called steam vents, are ubiquitous features of geothermal habitats. Recent studies have discovered microorganisms in condensed fumarole steam, but fumarole deposits have proven refractory to DNA isolation. In this study, we report the development of novel DNA isolation approaches for fumarole deposit microbial community analysis. Deposit samples were collected from steam vents and caves in Hawaii Volcanoes National Park, Yellowstone National Park and Lassen Volcanic National Park. Samples were analyzed by X-ray microanalysis and classified as nonsulfur, sulfur or iron-dominated steam deposits. We experienced considerable difficulty in obtaining high-yield, high-quality DNA for cloning: only half of all the samples ultimately yielded sequences. Analysis of archaeal 16S rRNA gene sequences showed that sulfur steam deposits were dominated by Sulfolobus and Acidianus, while nonsulfur deposits contained mainly unknown Crenarchaeota. Several of these novel Crenarchaeota lineages were related to chemoautotrophic ammonia oxidizers, indicating that fumaroles represent a putative habitat for ammonia-oxidizing Archaea. We also generated archaeal and bacterial enrichment cultures from the majority of the deposits and isolated members of the Sulfolobales. Our results provide the first evidence of Archaea in geothermal steam deposits and show that fumaroles harbor diverse and novel microbial lineages. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Depositional environments and cyclicity of the Early Ordovician carbonate ramp in the western Tarim Basin (NW China)

NASA Astrophysics Data System (ADS)

Guo, Chuan; Chen, Daizhao; Song, Yafang; Zhou, Xiqiang; Ding, Yi; Zhang, Gongjing

2018-06-01

During the Early Ordovician, the Tarim Basin (NW China) was mainly occupied by an extensive shallow-water carbonate platform, on which a carbonate ramp system was developed in the Bachu-Keping area of the western part of the basin. Three well-exposed typical outcrop sections of the Lower Ordovician Penglaiba Formation were investigated in order to identify the depositional facies and to clarify origins of meter-scale cycles and depositional sequences, thereby the platform evolution. Thirteen lithofacies are identified and further grouped into three depositional facies (associations): peritidal, restricted and open-marine subtidal facies. These lithofacies are vertically stacked into meter-scale, shallowing-upward peritidal and subtidal cycles. The peritidal cycles are mainly distributed in the lower and uppermost parts of the Penglaiba Formation deposited in the inner-middle ramp, and commonly start with shallow subtidal to intertidal facies followed by inter- to supratidal facies. In contrast, the subtidal cycles occur throughout the formation mostly in the middle-outer ramp and are dominated by shallow to relatively deep (i.e., intermediate) subtidal facies. The dominance of asymmetrical and incomplete cycles suggests a dominant control of Earth's orbital forcing on the cyclic deposition on the platform. On the basis of vertical facies and cycle stacking patterns, and accommodation changes illustrated by the Fischer plots from all studied sections, five third-order depositional sequences are recognized in the Penglaiba Formation. Individual sequences comprise a lower transgressive part and an upper regressive one. In shallow-water depositional environments, the transgressive packages are dominated by thicker-than-average subtidal cycles, indicating an increase in accommodation space, whereas regressive parts are mainly represented by thinner-than-average peritidal and subtidal cycles, denoting a decrease in accommodation space. In contrast, in intermediate to deep subtidal environments, transgressive and regressive packages display an opposite trend in accommodation space changes. Sequence boundaries (except the basal and top boundaries of the Penglaiba Formation) are usually represented by laterally traceable, transitional boundary zones without apparent subaerial exposure features. Good correlation of the long-term changes in accommodation space (or sea-level) inferred from vertical stacking patterns of facies and cycles suggests an overriding eustatic control on the formation of meter-scale cycles and third-order depositional sequences as well as platform evolution superimposed with local and/or regional tectonic influence during the Early Ordovician. This study would help understand the controls on the tempo-spatial facies distribution, stratal cyclicity and carbonate platform evolution in the western Tarim Basin during the Early Ordovician, facilitating prediction for favorable subsurface carbonate reservoirs and future hydrocarbon exploration and production in the Penglaiba Formation.

Genetic and grade and tonnage models for sandstone-hosted roll-type uranium deposits, Texas Coastal Plain, USA

USGS Publications Warehouse

Hall, Susan M.; Mihalasky, Mark J.; Tureck, Kathleen; Hammarstrom, Jane M.; Hannon, Mark

2017-01-01

The coincidence of a number of geologic and climatic factors combined to create conditions favorable for the development of mineable concentrations of uranium hosted by Eocene through Pliocene sandstones in the Texas Coastal Plain. Here 254 uranium occurrences, including 169 deposits, 73 prospects, 6 showings and 4 anomalies, have been identified. About 80 million pounds of U3O8 have been produced and about 60 million pounds of identified producible U3O8 remain in place. The development of economic roll-type uranium deposits requires a source, large-scale transport of uranium in groundwater, and deposition in reducing zones within a sedimentary sequence. The weight of the evidence supports a source from thick sequences of volcanic ash and volcaniclastic sediment derived mostly from the Trans-Pecos volcanic field and Sierra Madre Occidental that lie west of the region. The thickest accumulations of source material were deposited and preserved south and west of the San Marcos arch in the Catahoula Formation. By the early Oligocene, a formerly uniformly subtropical climate along the Gulf Coast transitioned to a zoned climate in which the southwestern portion of Texas Coastal Plain was dry, and the eastern portion humid. The more arid climate in the southwestern area supported weathering of volcanic ash source rocks during pedogenesis and early diagenesis, concentration of uranium in groundwater and movement through host sediments. During the middle Tertiary Era, abundant clastic sediments were deposited in thick sequences by bed-load dominated fluvial systems in long-lived channel complexes that provided transmissive conduits favoring transport of uranium-rich groundwater. Groundwater transported uranium through permeable sandstones that were hydrologically connected with source rocks, commonly across formation boundaries driven by isostatic loading and eustatic sea level changes. Uranium roll fronts formed as a result of the interaction of uranium-rich groundwater with either (1) organic-rich debris adjacent to large long-lived fluvial channels and barrier–bar sequences or (2) extrinsic reductants entrained in formation water or discrete gas that migrated into host units via faults and along the flanks of salt domes and shale diapirs. The southwestern portion of the region, the Rio Grande embayment, contains all the necessary factors required for roll-type uranium deposits. However, the eastern portion of the region, the Houston embayment, is challenged by a humid environment and a lack of source rock and transmissive units, which may combine to preclude the deposition of economic deposits. A grade and tonnage model for the Texas Coastal Plain shows that the Texas deposits represent a lower tonnage subset of roll-type deposits that occur around the world, and required aggregation of production centers into deposits based on geologic interpretation for the purpose of conducting a quantitative mineral resource assessment.

Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes

PubMed Central

2012-01-01

Background The feline genome is valuable to the veterinary and model organism genomics communities because the cat is an obligate carnivore and a model for endangered felids. The initial public release of the Felis catus genome assembly provided a framework for investigating the genomic basis of feline biology. However, the entire set of protein coding genes has not been elucidated. Results We identified and characterized 1227 protein coding feline sequences, of which 913 map to public sequences and 314 are novel. These sequences have been deposited into NCBI's genbank database and complement public genomic resources by providing additional protein coding sequences that fill in some of the gaps in the feline genome assembly. Through functional and comparative genomic analyses, we gained an understanding of the role of these sequences in feline development, nutrition and health. Specifically, we identified 104 orthologs of human genes associated with Mendelian disorders. We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions. We detected relatively less negative selection on protein sequences encoding extracellular networks, apoptotic pathways and mitochondrial gene ontology annotations. Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes. Together, this analysis provides an overview of the value of our cDNA sequences and enhances our understanding of how the feline genome is similar to, and different from other mammalian genomes. Conclusions The cDNA sequences reported here expand existing feline genomic resources by providing high-quality sequences annotated with comparative genomic information providing functional, clinical, nutritional and orthologous gene information. PMID:22257742

Late Devonian shale deposition based on known and predicted occurrence of Foerstia in Michigan basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matthews, R.D.

The fossil Foerstia (Protosalvinia) marks a time zone within Late Devonian shale sequences in the eastern US. Its recent discovery in Michigan has led to more accurate correlations among the three large eastern basins. Subdivisions of the Devonian-Mississippi shale sequence in Michigan based on gamma-ray correlations reveal an idealized black shale geometry common to other eastern black shales, such as the Sunbury of Michigan and Ohio, the Clegg Creek of Indiana, the Dunkirk of Pennsylvania and New York, and the lower Huron of Ohio and West Virginia. In Michigan, Foerstia occurs at a stratigraphic position postulated to mark a majormore » change in depositional conditions and source areas. This position strengthens the physical and paleontologic evidence for a formal division of the Antrim. Isopach maps of the shale sequence above and below Foerstia show a relatively uniform and continuous black shale deposit (units 1A, 1B, and 1C) below Foerstia. This deposit is unlike the wedge of sediment found above Foerstia, which is composed of a western facies (Ellsworth) and an eastern facies (upper Antrim) that should be combined in a single stratigraphic unit conforming to Forgotson's concept of a format.« less

Glacial morphology and depositional sequences of the Antarctic Continental Shelf

USGS Publications Warehouse

ten Brink, Uri S.; Schneider, Christopher

1995-01-01

Proposes a simple model for the unusual depositional sequences and morphology of the Antarctic continental shelf. It considers the regional stratal geometry and the reversed morphology to be principally the results of time-integrated effects of glacial erosion and sedimentation related to the location of the ice grounding line. The model offers several guidelines for stratigraphic interpretation of the Antarctic shelf and a Northern Hemisphere shelf, both of which were subject to many glacial advances and retreats. -Authors

Banded iron-formations of late Proterozoic age in the central eastern desert, Egypt: geology and tectonic setting.

USGS Publications Warehouse

Sims, P.K.; James, H.L.

1984-01-01

Iron-formation occurs as stratigraphic units within a layered andesite-basalt sequence. The sequence is metamorphosed to greenschist facies, intruded by syntectonic granodiorite and post-tectonic granite, and complexly deformed and grossly fragmented; the rocks are allochthonous along thrust faults. The iron deposits are chemical precipitates, accumulated during lulls in volcanism, apparently in an intraoceanic island-arc environment. The deposits are of the Algoma type of iron-formation.-G.J.N.

Sedimentary manganese metallogenesis in response to the evolution of the Earth system

NASA Astrophysics Data System (ADS)

Roy, Supriya

2006-08-01

The concentration of manganese in solution and its precipitation in inorganic systems are primarily redox-controlled, guided by several Earth processes most of which were tectonically induced. The Early Archean atmosphere-hydrosphere system was extremely O 2-deficient. Thus, the very high mantle heat flux producing superplumes, severe outgassing and high-temperature hydrothermal activity introduced substantial Mn 2+ in anoxic oceans but prevented its precipitation. During the Late Archean, centered at ca. 2.75 Ga, the introduction of Photosystem II and decrease of the oxygen sinks led to a limited buildup of surface O 2-content locally, initiating modest deposition of manganese in shallow basin-margin oxygenated niches (e.g., deposits in India and Brazil). Rapid burial of organic matter, decline of reduced gases from a progressively oxygenated mantle and a net increase in photosynthetic oxygen marked the Archean-Proterozoic transition. Concurrently, a massive drawdown of atmospheric CO 2 owing to increased weathering rates on the tectonically expanded freeboard of the assembled supercontinents caused Paleoproterozoic glaciations (2.45-2.22 Ga). The spectacular sedimentary manganese deposits (at ca. 2.4 Ga) of Transvaal Supergroup, South Africa, were formed by oxidation of hydrothermally derived Mn 2+ transferred from a stratified ocean to the continental shelf by transgression. Episodes of increased burial rate of organic matter during ca. 2.4 and 2.06 Ga are correlatable to ocean stratification and further rise of oxygen in the atmosphere. Black shale-hosted Mn carbonate deposits in the Birimian sequence (ca. 2.3-2.0 Ga), West Africa, its equivalents in South America and those in the Francevillian sequence (ca. 2.2-2.1 Ga), Gabon are correlatable to this period. Tectonically forced doming-up, attenuation and substantial increase in freeboard areas prompted increased silicate weathering and atmospheric CO 2 drawdown causing glaciation on the Neoproterozoic Rodinia supercontinent. Tectonic rifting and mantle outgassing led to deglaciation. Dissolved Mn 2+ and Fe 2+ concentrated earlier in highly saline stagnant seawater below the ice cover were exported to shallow shelves by transgression during deglaciation. During the Sturtian glacial-interglacial event (ca. 750-700 Ma), interstratified Mn oxide and BIF deposits of Damara sequence, Namibia, was formed. The Varangian (≡ Marinoan; ca. 600 Ma) cryogenic event produced Mn oxide and BIF deposits at Urucum, Jacadigo Group, Brazil. The Datangpo interglacial sequence, South China (Liantuo-Nantuo ≡ Varangian event) contains black shale-hosted Mn carbonate deposits. The Early Paleozoic witnessed several glacioeustatic sea level changes producing small Mn carbonate deposits of Tiantaishan (Early Cambrian) and Taojiang (Mid-Ordovician) in black shale sequences, China, and the major Mn oxide-carbonate deposits of Karadzhal-type, Central Kazakhstan (Late Devonian). The Mesozoic period of intense plate movements and volcanism produced greenhouse climate and stratified oceans. During the Early Jurassic OAE, organic-rich sediments host many Mn carbonate deposits in Europe (e.g., Úrkút, Hungary) in black shale sequences. The Late Jurassic giant Mn Carbonate deposit at Molango, Mexico, was also genetically related to sea level change. Mn carbonates were always derived from Mn oxyhydroxides during early diagenesis. Large Mn oxide deposits of Cretaceous age at Groote Eylandt, Australia and Imini-Tasdremt, Morocco, were also formed during transgression-regression in greenhouse climate. The Early Oligocene giant Mn oxide-carbonate deposit of Chiatura (Georgia) and Nikopol (Ukraine) were developed in a similar situation. Thereafter, manganese sedimentation was entirely shifted to the deep seafloor and since ca. 15 Ma B.P. was climatically controlled (glaciation-deglaciation) assisted by oxygenated polar bottom currents (AABW, NADW). The changes in climate and the sea level were mainly tectonically forced.

The Binding Database: data management and interface design.

PubMed

Chen, Xi; Lin, Yuhmei; Liu, Ming; Gilson, Michael K

2002-01-01

The large and growing body of experimental data on biomolecular binding is of enormous value in developing a deeper understanding of molecular biology, in developing new therapeutics, and in various molecular design applications. However, most of these data are found only in the published literature and are therefore difficult to access and use. No existing public database has focused on measured binding affinities and has provided query capabilities that include chemical structure and sequence homology searches. We have created Binding DataBase (BindingDB), a public, web-accessible database of measured binding affinities. BindingDB is based upon a relational data specification for describing binding measurements via Isothermal Titration Calorimetry (ITC) and enzyme inhibition. A corresponding XML Document Type Definition (DTD) is used to create and parse intermediate files during the on-line deposition process and will also be used for data interchange, including collection of data from other sources. The on-line query interface, which is constructed with Java Servlet technology, supports standard SQL queries as well as searches for molecules by chemical structure and sequence homology. The on-line deposition interface uses Java Server Pages and JavaBean objects to generate dynamic HTML and to store intermediate results. The resulting data resource provides a range of functionality with brisk response-times, and lends itself well to continued development and enhancement.

Petrogenesis and depositional history of felsic pyroclastic rocks from the Melka Wakena archaeological site-complex in South central Ethiopia

NASA Astrophysics Data System (ADS)

Resom, Angesom; Asrat, Asfawossen; Gossa, Tegenu; Hovers, Erella

2018-06-01

The Melka Wakena archaeological site-complex is located at the eastern rift margin of the central sector of the Main Ethiopian Rift (MER), in south central Ethiopia. This wide, gently sloping rift shoulder, locally called the "Gadeb plain" is underlain by a succession of primary pyroclastic deposits and intercalated fluvial sediments as well as reworked volcaniclastic rocks, the top part of which is exposed by the Wabe River in the Melka Wakena area. Recent archaeological survey and excavations at this site revealed important paleoanthropological records. An integrated stratigraphic, petrological, and major and trace element geochemical study has been conducted to constrain the petrogenesis of the primary pyroclastic deposits and the depositional history of the sequence. The results revealed that the Melka Wakena pyroclastic deposits are a suite of mildly alkaline, rhyolitic pantellerites (ash falls, pumiceous ash falls and ignimbrites) and slightly dacitic ash flows. These rocks were deposited by episodic volcanic eruptions during early to middle Pleistocene from large calderas along the Wonji Fault Belt (WFB) in the central sector of the MER and from large silicic volcanic centers at the eastern rift shoulder. The rhyolitic ash falls, pumiceous ash falls and ignimbrites have been generated by fractional crystallization of a differentiating basaltic magma while the petrogenesis of the slightly dacitic ash flows involved some crustal contamination and assimilation during fractionation. Contemporaneous fluvial activities in the geomorphologically active Gadeb plain deposited overbank sedimentary sequences (archaeology bearing conglomerates and sands) along meandering river courses while a dense network of channels and streams have subsequently down-cut through the older volcanic and sedimentary sequences, redepositing the reworked volcaniclastic sediments further downstream.

Sediment budget as affected by construction of a sequence of dams in the lower Red River, Viet Nam

NASA Astrophysics Data System (ADS)

Lu, Xi Xi; Oeurng, Chantha; Le, Thi Phuong Quynh; Thuy, Duong Thi

2015-11-01

Dam construction is one of the main factors resulting in riverine sediment changes, which in turn cause river degradation or aggradation downstream. The main objective of this work is to examine the sediment budget affected by a sequence of dams constructed upstream in the lower reach of the Red River. The study is based on the longer-term annual data (1960-2010) with a complementary daily water and sediment data set (2008-2010). The results showed that the stretch of the river changed from sediment surplus (suggesting possible deposition processes) into sediment deficit (possible erosion processes) after the first dam (Thac Ba Dam) was constructed in 1972 and changed back to deposition after the second dam (Hoa Binh Dam) was constructed in 1985. The annual sediment deposition varied between 1.9 Mt/y and 46.7 Mt/y with an annual mean value of 22.9 Mt/y (1985-2010). The sediment deposition at the lower reach of the Red River would accelerate river aggradation which would change river channel capacity in the downstream of the Red River. The depositional processes could be sustained or changed back to erosional processes after more dams (the amount of sediment deposit was much less after the latest two dams Tuyen Quang Dam in 2009 and Sonla Dam in 2010) are constructed, depending on the water and sediment dynamics. This study revealed that the erosional and depositional processes could be shifted for the same stretch of river as affected by a sequence of dams and provides useful insights in river management in order to reduce flood frequency along the lower reach of the Red River.

Hidden Ice Worlds - Pleistocene glacigenic deposits in Essex, England. Application of the novel systematic approach to thin-section description.

NASA Astrophysics Data System (ADS)

Leszczynska, Karolina; Boreham, Julie; Boreham, Steve

2013-04-01

In the 'Hidden Ice Worlds' research project a novel systematic approach for thin-section description (Leszczynska et al., 2011) is applied to analyse the internal structure of 8 m thick periglacially disturbed sequence from the Royal Oak Pit - a small disused quarry in East Anglia, Essex, east of Chelmsford, near Danbury. Danbury Hill is situated on the south-eastern margin of the Elsterian (Anglian) till sheet. This area was glaciated only once, during the Pleistocene, Elsterian (Anglian) glaciation (480-420 ka BP), however two local ice-sheet margin fluctuations are envisaged (inter alia Turner, 1970 and others). The stratigraphical sequence of the Royal Oak Pit comprises: massive gravel, arranged in sheets, overlain by fine silty-clay and silty-sand with ripple marks and planar cross beds, overlain by a 50 cm thick unit of massive gravel gradually changing into periglacially disturbed silty-clayey-gravel with the bottom 50 cm of fine laminated silty clay. This sequence is situated on the lee side of Danbury Hill, at over 50 m OD. This is an atypical location for the periglacially disturbed deposits of such a substantial thickness (up to 8 m), which usually occur in the lower areas. The deposits at this site were investigated at a macro-scale using field-section logging, ground penetrating radar survey, clast lithology, clay mineralogy analysis and loss-on-ignition and at a micro-scale using thin-section analysis. There are two main aims of the project presented: • To describe the genesis and to discern the main processes associated with the formation of the unusually thick periglacially disturbed unit at the Danbury Hill slope and • To test the novel, tree-based, systematic approach as a guiding tool for thin for thin-section description of Quaternary deposits (Leszczynska et al., 2011). The results of the micromorphological analyses of the deposits from the Royal Oak Pit allow a new hypothesis for the origin of the sequence to be put forward. The main process responsible for the evolution of the deposits consist of multiple phases of freezing and thawing of the deposit and associated physical reworking, subsequent to Elsterian (Anglian). Inversion of the topography is proposed as a necessary condition for the formation and preservation of the periglacially disturbed sequence on hill slope at such elevated location. The novel systematic approach proved to be a useful tool in guiding the thin-section description, regardless of the type of the deposit and the aim of the research. Reference: Leszczynska, K., Boreham, J. and Boreham, S., 2011. A novel methodological approach for thin-section description and its application to periglacially disturbed Pleistocene deposits from Danbury, Essex, UK. Netherlands Journal of Geosciences 90: 271-291. Turner, C., 1970. Middle Pleistocene deposits at Marks Tey, Essex. Philosophical Transactions of the Royal Society of London, series B 257: 373-440.

Stratigraphy and paleogeographic significance of a Late Pennsylvanian to Early Permian channeled slope sequence in the Darwin Basin, southern Darwin Hills, east-central California

USGS Publications Warehouse

Stevens, Calvin H.; Stone, Paul; Magginetti, Robert T.; Ritter, Scott M.

2015-01-01

The complex stratigraphy of late Paleozoic rocks in the southern Darwin Hills consists of regionally extensive Mississippian and Early to Middle Pennsylvanian rocks overlain by latest Pennsylvanian to Early Permian rocks, herein called the Darwin Hills sequence. Deposition of this latter sequence marked the beginning of the Darwin Basin. In Mississippian time, a carbonate platform prograded westward over slightly older slope deposits. In the Late Mississippian this platform was exposed to erosion and siliciclastic sediments were deposited. In Early to Middle Pennsylvanian time the area subsided, forming a west-facing ramp that was subjected to deformation and erosion in Middle or early Late Pennsylvanian time. Later this area was tilted westward and deep-water sediments were deposited on this slope. In latest Pennsylvanian to earliest Permian time, a major channel was cut through the older Pennsylvanian rocks and into the Upper Mississippian strata. This channel was gradually filled with increasingly finer grained, deep-water sediment as the area evolved into a basin floor by Early Permian (Sakmarian) time. Expansion of the Darwin Basin in Artinskian time led to a second phase of deposition represented by strata of the regionally extensive Darwin Canyon Formation. The geology in this small area thus documents tectonic events occurring during the early development of the Darwin Basin.

Using palynology to re-assess the Dead Sea laminated sediments - Indeed varves?

NASA Astrophysics Data System (ADS)

Bookman, Revital; Lopez-Merino, Lourdes; Belmaker, Reuven; Eshel, Amram; Epshtein Epshtein, Valentina; Leroy, Suzanne

2017-04-01

Lacustrine laminated sediments are often varves representing annual rhythmic deposition. The Dead Sea high-stand laminated sections consist of mm-scale alternating detrital and authigenic aragonite laminae. Previous studies assumed these laminae were varves; detritus deposition during the winter and aragonite in the summer. These sequences were used for varve counting and chronology, however this assumption has never been robustly validated. Here, we report an examination of the seasonal deposition of detrital and aragonite couplets from two well-known Late Holocene laminated sections at the Ze'elim fan-delta using palynology and grain-size distribution analyses. These analyses are complemented by the study of contemporary flash-flood samples and multivariate statistical analysis. Because transport affects the pollen preservation state, well-preserved (mostly) air-borne transported pollen was analysed separately from badly-preserved pollen and fungal spores, which are more indicative of water transport and reworking from soils. Our results indicate that (i) both detrital and aragonite laminae were deposited during the rainy season; (ii) aragonite laminae have significantly lower reworked pollen and fungal spore concentrations than detrital and flash-flood samples; and (iii) detrital laminae are composed of recycling of local and distal sources, with coarser particles that were initially deposited in the Dead Sea watershed and later transported via run-off to the lake. The conclusions suggest that detrital and aragonite couplets in the Dead Sea laminated sediments are most likely not varves and that the laminae deposition is related to the occurrence of flash-flood events. Consequently, at least for the Holocene sequences, laminated sediments cannot be considered as varves and Quaternary laminated sequences should be re-evaluated. The Dead Sea Basin laminated sequences (as the ICDP Dead Sea Deep Drilling Project record) should be used for the reconstruction of palaeo-flash flood records that will have a significant impact on understanding the palaeo-hydrology of the DSB and its implication to high-resolution climatic interpretation.

Quantitative Susceptibility Mapping as a Possible Tool to Radiographically Diagnose Sentinel Headache Associated with Intracranial Aneurysm: Case Report.

PubMed

Nakagawa, Daichi; Cushing, Cameron; Nagahama, Yasunori; Allan, Lauren; Hasan, David

2017-07-01

Sentinel headache (SH) occurs before aneurysm rupture in an estimated 15%-60% of cases of aneurysmal subarachnoid hemorrhage (aSAH). By definition, noncontrast computed tomography (CT) scan of the brain and lumbar puncture are both negative in patients presenting with SH. One of the theories explaining this phenomenon is that microhemorrhage (MH) from the aneurysm wall contribute to iron deposition in the interface between the aneurysm wall and brain parenchyma. Quantitative susceptibility mapping (QSM) is a recently introduced magnetic resonance imaging (MRI) technique that has proven capable of localizing the deposition of paramagnetic metals, particularly ferric iron. Thus, the QSM sequence may be able to detect iron deposition secondary to MH. A 76-year-old male presented with the "worst headache of my life." Noncontrast head CT scan and lumbar puncture were negative. Magnetic resonance angiography (MRA) of the brain revealed an anterior communicating artery (A-com) aneurysm measuring 7 mm with a large bleb. T1-weighted imaging (WI), T2-WI, MRA, T2 star-weighted angiography (SWAN), and QSM sequences were obtained. T2-WI, SWAN, and QSM revealed isointense, hypointense, and hyperintense signals, respectively, at the interface of the aneurysm wall and brain tissue. These findings were consistent with deposition of ferric iron at this interface. The A-com aneurysm was treated with coil embolization, and the patient exhibited no postoperative deficits. The MRI QSM sequence can localize iron deposition resulting from MH within an aneurysmal wall. This sequence may be a promising imaging tool for screening patients presenting with SH. Copyright © 2017 Elsevier Inc. All rights reserved.

Deposition of a saline giant in the Mississippian Windsor Group, Nova Scotia, and the nascent Late Paleozoic Ice Age

NASA Astrophysics Data System (ADS)

MacNeil, Laura A.; Pufahl, Peir K.; James, Noel P.

2018-01-01

Saline giants are vast marine evaporite deposits that currently have no modern analogues and remain one of the most enigmatic of chemical sedimentary rocks. The Mississippian Windsor Group (ca. 345 Ma), Maritimes Basin, Atlantic Canada is a saline giant that consists of two evaporite-rich sedimentary sequences that are subdivided into five subzones. Sequence 1 is composed almost entirely of thick halite belonging to Subzone A (Osagean). Sequence 2 is in unconformable contact and comprised of stacked carbonate-evaporite peritidal cycles of Subzones B through E (Meramecian). Subzone B, the focus of research herein, documents the transition from wholly evaporitic to open marine conditions and thus, preserves an exceptional window into the processes forming saline giants. Lithofacies stacking patterns in Subzone B reveal that higher-order fluctuations in relative sea level produced nine stacked parasequences interpreted to reflect high frequency glacioeustatic oscillations during the onset of the Late Paleozoic Ice Age. Each parasequence reflects progradation of intertidal and sabkha sediments over subtidal carbonate and evaporite deposits. Dissimilarities in cycle composition between sub-basins imply the development of contrasting brine chemistries from differing recharge rates with the open ocean. What the Windsor Group shows is that evaporite type is ostensibly linked to the amplitude and frequency of sea level rise and fall during deposition. True saline giants, like the basinwide evaporites of Sequence 1, apparently require low amplitude, long frequency changes in sea level to promote the development of stable brine pools that are only periodically recharged with seawater. By contrast, the high amplitude, short frequency glacioeustatic variability in sea level that controlled the accumulation of peritidal evaporites in Subzone B produce smaller, subeconomic deposits with more complex facies relationships.

The stratigraphy of the southern Pab Range, Pakistan

NASA Astrophysics Data System (ADS)

White, H. J.

The Cretaceous strata exposed in the southern Pab Range, southeast Baluchistan, Pakistan is investigated. It records the precollision deposition history of the Indo-Pakistani continental shelf. The strata comprise two depositional successions, namely, The Early to Late Cretaceous Sembar-Goru-Parh sequence and the Maestrichtian Mughal Kot-Pab sequence. The former began with deposition of black shales on the continental slope (Sembar Formation), succeeded by calcareous shale, marl and micstone of outer shelf origin (Goru Formation), and ended with inner shelf platform carbonates (Parh Limestone). These deep to shallow water lithofacies prograted westward over the continental shelf of the north-advancing Subcontinent. The Mughal Kot-Pab propagation contains the first significant influx of terrigenous sand reaching the western portion of the continental shelf. Deposition environments in the Mughal Kot Formation include inner shelf, prodelta, delta front and distributary channel. A thick succession of shoreface cycles comprises the Pab sandstone.

SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets.

PubMed

Jones, Darryl R; Thomas, Dallas; Alger, Nicholas; Ghavidel, Ata; Inglis, G Douglas; Abbott, D Wade

2018-01-01

Deposition of new genetic sequences in online databases is expanding at an unprecedented rate. As a result, sequence identification continues to outpace functional characterization of carbohydrate active enzymes (CAZymes). In this paradigm, the discovery of enzymes with novel functions is often hindered by high volumes of uncharacterized sequences particularly when the enzyme sequence belongs to a family that exhibits diverse functional specificities (i.e., polyspecificity). Therefore, to direct sequence-based discovery and characterization of new enzyme activities we have developed an automated in silico pipeline entitled: Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity (SACCHARIS). This pipeline streamlines the selection of uncharacterized sequences for discovery of new CAZyme or CBM specificity from families currently maintained on the CAZy website or within user-defined datasets. SACCHARIS was used to generate a phylogenetic tree of a GH43, a CAZyme family with defined subfamily designations. This analysis confirmed that large datasets can be organized into sequence clusters of manageable sizes that possess related functions. Seeding this tree with a GH43 sequence from Bacteroides dorei DSM 17855 (BdGH43b, revealed it partitioned as a single sequence within the tree. This pattern was consistent with it possessing a unique enzyme activity for GH43 as BdGH43b is the first described α-glucanase described for this family. The capacity of SACCHARIS to extract and cluster characterized carbohydrate binding module sequences was demonstrated using family 6 CBMs (i.e., CBM6s). This CBM family displays a polyspecific ligand binding profile and contains many structurally determined members. Using SACCHARIS to identify a cluster of divergent sequences, a CBM6 sequence from a unique clade was demonstrated to bind yeast mannan, which represents the first description of an α-mannan binding CBM. Additionally, we have performed a CAZome analysis of an in-house sequenced bacterial genome and a comparative analysis of B. thetaiotaomicron VPI-5482 and B. thetaiotaomicron 7330, to demonstrate that SACCHARIS can generate "CAZome fingerprints", which differentiate between the saccharolytic potential of two related strains in silico. Establishing sequence-function and sequence-structure relationships in polyspecific CAZyme families are promising approaches for streamlining enzyme discovery. SACCHARIS facilitates this process by embedding CAZyme and CBM family trees generated from biochemically to structurally characterized sequences, with protein sequences that have unknown functions. In addition, these trees can be integrated with user-defined datasets (e.g., genomics, metagenomics, and transcriptomics) to inform experimental characterization of new CAZymes or CBMs not currently curated, and for researchers to compare differential sequence patterns between entire CAZomes. In this light, SACCHARIS provides an in silico tool that can be tailored for enzyme bioprospecting in datasets of increasing complexity and for diverse applications in glycobiotechnology.

The Orosirian-Statherian banded iron formation-bearing sequences of the southern border of the Espinhaço Range, Southeast Brazil

NASA Astrophysics Data System (ADS)

Rolim, Vassily Khoury; Rosière, Carlos A.; Santos, João Orestes Schneider; McNaughton, Neal J.

2016-01-01

The Serra da Serpentina and the Serra de São José groups are two distinct banded iron formation-bearing metasedimentary sequences along the eastern border of the southern Espinhaço Range that were deposited on the boundary between the Orosirian and Statherian periods. The Serra da Serpentina Group (SSG) has an Orosirian maximum depositional age (youngest detrital zircon grain age = 1990 ± 16 Ma) and consists of fine clastic metasediments at the base and chemical sediments, including banded iron formations (BIFs), on the top, corresponding to the Meloso and Serra do Sapo formations, respectively, and correlating with the pre-Espinhaço Costa Sena Group. The SSG represents sedimentary deposition on an epicontinental-epeiric, slow downwarping sag basin with little tectonic activity. The younger Serra de São José Group (SJG) is separated from the older SSG by an erosional unconformity and was deposited in a tectonically active continental rift-basin in the early stages of the opening of the Espinhaço Trough. The Serra do São José sediments stretch along the north-south axis of the rift and comprise a complete cycle of transgressive sedimentary deposits, which were subdivided, from base to top, into the Lapão, Itapanhoacanga, Jacém and Canjica formations. The Itapanhoacanga Formation has a maximum depositional age of 1666 ± 32 Ma (Statherian), which coincides with the maximum depositional age (i.e., 1683 ± 11 Ma) of the São João da Chapada Formation, one of the Espinhaço Supergroup's basal units. The Serra de São José Rift and the Espinhaço Rift likely represent the same system, with basal units that are facies variations of the same sequence. The supracrustal rocks have undergone two stages of deformation during the west-verging Brasiliano orogeny that affected the eastern margin of the São Francisco Craton and generated a regional-scale, foreland N-S trending fold-thrust belt, which partially involved the crystalline basement. Thrust faults have segmented the terrain into a large number of tectonic blocks, where the stratigraphic sequence was nevertheless well preserved.

Complete Genome Sequences of Two Vesicular Stomatitis Virus Isolates Collected in Mexico

PubMed Central

Isa, Pavel; Pauszek, Steven J.; Rodriguez, Luis L.

2017-01-01

ABSTRACT We report two full-genome sequences of vesicular stomatitis New Jersey virus (VSNJV) obtained by Illumina next-generation sequencing of RNA isolated from epithelial suspensions of cattle naturally infected in Mexico. These genomes represent the first full-genome sequences of vesicular stomatitis New Jersey viruses circulating in Mexico deposited in the GenBank database. PMID:28912331

Genetic diversity of Histoplasma and Sporothrix complexes based on sequences of their ITS1-5.8S-ITS2 regions from the BOLD System.

PubMed

Estrada-Bárcenas, Daniel Alfonso; Vite-Garín, Tania; Navarro-Barranco, Hortensia; de la Torre-Arciniega, Raúl; Pérez-Mejía, Amelia; Rodríguez-Arellanes, Gabriela; Ramirez, Jose Antonio; Humberto Sahaza, Jorge; Taylor, Maria Lucia; Toriello, Conchita

2014-01-01

High sensitivity and specificity of molecular biology techniques have proven usefulness for the detection, identification and typing of different pathogens. The ITS (Internal Transcribed Spacer) regions of the ribosomal DNA are highly conserved non-coding regions, and have been widely used in different studies including the determination of the genetic diversity of human fungal pathogens. This article wants to contribute to the understanding of the intra- and interspecific genetic diversity of isolates of the Histoplasma capsulatum and Sporothrix schenckii species complexes by an analysis of the available sequences of the ITS regions from different sequence databases. ITS1-5.8S-ITS2 sequences of each fungus, either deposited in GenBank, or from our research groups (registered in the Fungi Barcode of Life Database), were analyzed using the maximum likelihood (ML) method. ML analysis of the ITS sequences discriminated isolates from distant geographic origins and particular wild hosts, depending on the fungal species analyzed. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Barcode Identifiers as a Practical Tool for Reliable Species Assignment of Medically Important Black Yeast Species

PubMed Central

Heinrichs, Guido; de Hoog, G. Sybren

2012-01-01

Herpotrichiellaceous black yeasts and relatives comprise severe pathogens flanked by nonpathogenic environmental siblings. Reliable identification by conventional methods is notoriously difficult. Molecular identification is hampered by the sequence variability in the internal transcribed spacer (ITS) domain caused by difficult-to-sequence homopolymeric regions and by poor taxonomic attribution of sequences deposited in GenBank. Here, we present a potential solution using short barcode identifiers (27 to 50 bp) based on ITS2 ribosomal DNA (rDNA), which allows unambiguous definition of species-specific fragments. Starting from proven sequences of ex-type and authentic strains, we were able to describe 103 identifiers. Multiple BLAST searches of these proposed barcode identifiers in GenBank revealed uniqueness for 100 taxonomic entities, whereas the three remaining identifiers each matched with two entities, but the species of these identifiers could easily be discriminated by differences in the remaining ITS regions. Using the proposed barcode identifiers, a 4.1-fold increase of 100% matches in GenBank was achieved in comparison to the classical approach using the complete ITS sequences. The proposed barcode identifiers will be made accessible for the diagnostic laboratory in a permanently updated online database, thereby providing a highly practical, reliable, and cost-effective tool for identification of clinically important black yeasts and relatives. PMID:22785187

Stratigraphy and depositional environments of Fox Hills Formation in Williston basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, D.J.

The Fox Hills Formation (Maestrichtian), representing part of a regressive wedge deposited during the withdrawal of the sea from the Western Interior at the close of the Cretaceous, consists of marginal marine strata transitional between the offshore deposits of the underlying Pierre Shale and the terrestrial deltaic and coastal deposits of the overlying Hell Creek Formation. An investigation of outcrops of the Fox Hills Formation along the western and southern flanks of the Williston basin and study of over 300 oil and gas well logs from the central part of the basin indicate that the formation can be divided bothmore » stratigraphically and areally. Stratigraphically, the Fox Hills can be divided into lower and upper sequences; the lower includes the Trail City and Timber Lake Members, and the upper sequence includes the Colgate Member in the west and the Iron Lightning and Linton Members in the east. Areally, the formation can be divided into a northeastern and western part, where the strata are 30-45 m thick and are dominated by the lower sequence, and into a southeastern area where both the lower and upper sequences are well developed in a section 80-130 m thick. Typically, the lower Fox Hills consists of upward-coarsening shoreface or delta-front sequences containing hummocky bedding and a limited suite of trace fossils, most notably Ophiomorpha. In the southeast, however, these strata are dominated by bar complexes, oriented northeast-southwest, composed of cross-bedded medium to very fine-grained sand with abundant trace and body fossils. The upper Fox Hills represents a variety of shoreface, deltaic, and channel environments. The strata of the Fox Hills Formation exhibit facies similar to those reported for Upper Cretaceous gas reservoirs in the northern Great Plains.« less

Identification of third-order (approx. 10{sup 6} yrs) and fourth-order (approx. 10{sup 5}/10{sup 4} yrs) stratigraphic cycles in the South Addition, West Cameron Lease Area, Louisiana offshore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowrie, A.; Meeks, P.; Hoffman, K.

In the highly explored South Addition of the West Cameron Lease Area, Louisiana offshore, interpretation of a six-mile ({approx}10 km) seismic section across a single intraslope basin yielded 20 sediment packages. Several interpretive tools were necessary. Seismic stratigraphy indicated that the shallower zone was an outer shelf marked by 8 major sea level oscillations. In the portion between 1 and 3 seconds, seismic stratigraphy and paleontology led to the interpretation of depositional environments such as upper slope, and paleobathymetrically deeper intervals with descent through the section. The intraslope basin, while small, may be viewed as a micro-continental margin. Each seamore » level oscillation cycle apparently made a distinct progradational unit, decipherable in the seismic data. Fourth order cycles have been provisionally interpreted, throughout most of the entire 3.7 second section. Such precision is possible only in explored basins with excellent seismic data. The sequence thickness showed a seven-fold variability, from 0.08 to 0.58 seconds. The shallower section, deposited along an outer shelf, has an average individual sequence thickness of 0.13 seconds. Individual seismic sequences in the deeper section, interpreted to have been deposited on an upper slope, have average thicknesses of 0.25 seconds. The thinner sequences of the shallower section are compatible with the notion that the outer shelf was a bypass zone during a glacial epoch. The thicker sequences of the deeper section are the result of deposition onto an aggrading upper slope within an intraslope basin during a highstand.« less

Low-Temperature Molecular Layer Deposition Using Monofunctional Aromatic Precursors and Ozone-Based Ring-Opening Reactions.

PubMed

Svärd, Laura; Putkonen, Matti; Kenttä, Eija; Sajavaara, Timo; Krahl, Fabian; Karppinen, Maarit; Van de Kerckhove, Kevin; Detavernier, Christophe; Simell, Pekka

2017-09-26

Molecular layer deposition (MLD) is an increasingly used deposition technique for producing thin coatings consisting of purely organic or hybrid inorganic-organic materials. When organic materials are prepared, low deposition temperatures are often required to avoid decomposition, thus causing problems with low vapor pressure precursors. Monofunctional compounds have higher vapor pressures than traditional bi- or trifunctional MLD precursors, but do not offer the required functional groups for continuing the MLD growth in subsequent deposition cycles. In this study, we have used high vapor pressure monofunctional aromatic precursors in combination with ozone-triggered ring-opening reactions to achieve sustained sequential growth. MLD depositions were carried out by using three different aromatic precursors in an ABC sequence, namely with TMA + phenol + O 3 , TMA + 3-(trifluoromethyl)phenol + O 3 , and TMA + 2-fluoro-4-(trifluoromethyl)benzaldehyde + O 3 . Furthermore, the effect of hydrogen peroxide as a fourth step was evaluated for all studied processes resulting in a four-precursor ABCD sequence. According to the characterization results by ellipsometry, infrared spectroscopy, and X-ray reflectivity, self-limiting MLD processes could be obtained between 75 and 150 °C with each of the three aromatic precursors. In all cases, the GPC (growth per cycle) decreased with increasing temperature. In situ infrared spectroscopy indicated that ring-opening reactions occurred in each ABC sequence. Compositional analysis using time-of-flight elastic recoil detection indicated that fluorine could be incorporated into the film when 3-(trifluoromethyl)phenol and 2-fluoro-4-(trifluoromethyl)benzaldehyde were used as precursors.

Sedimentology of the lower part of the Upper Triassic Chinle Formation and its relationship to uranium deposits, White Canyon area, southeastern Utah

USGS Publications Warehouse

Dubiel, Russell F.

1983-01-01

Closely spaced measured stratigraphic sections of the lower part of the Late Triassic Chinle Formation in the White Canyon area of southeastern Utah depict a fluvial-deltaic-lacustrine depositional sequence that hosts uranium deposits in basal fluvial sandstones. The basal Shinarump Member consists of predominantly trough-crossbedded, coarse-grained sandstone and minor gray, carbonaceous mudstone and is interpreted as a valley-fill sequence overlain by deposits of a braided stream system. The overlying Monitor Butte Member is composed of cyclic- and foreset-bedded siltstone, sandstone, and mudstone and is interpreted as a succession of low-energy fluvial, deltaic and orqanicrich, lacustrine-marsh sediments. The overlying Moss Back Member is composed of a laterally extensive, coarse- to medium-grained, conglomeratic sandstone and is interpreted as a braided-stream system that flowed north to northwest. The entire sequence was deposited in response to changes in local base level associated with a large lake that lay to the west. Isopachs of lithofacies indicate distinct lacustrine basins and a correspondence between these facies and modern structural synclines. Facies changes and coincidence of isopach thicks suggest that structural synclines were active in the Late Triassic and influenced the pattern of sediment distribution within the basins. Uranium mineralization appears to be related to certain low-energy depositional environments in that uranium is localized in fluvial sandstones that lie beneath organic-rich lacustrine-marsh mudstones and carbonaceous delta-front sediments. The reducing environment preserved in these facies may have played an important role in the localization of uranium.

Mass Dependent Fractionation of Hg Isotopes in Source Rocks, Mineral Deposits and Spring Waters of the California Coast Ranges, USA

NASA Astrophysics Data System (ADS)

Smith, C. N.; Kesler, S. E.; Blum, J. D.; Rytuba, J. J.

2007-12-01

We present here the first study of the isotopic composition of Hg in rocks, ore deposits, and active hydrothermal systems from the California Coast Ranges, one of Earth's largest Hg-depositing systems. The Franciscan Complex and Great Valley Sequence, which form the bedrock in the California Coast Ranges, are intruded and overlain by Tertiary volcanic rocks including the Clear Lake Volcanic Sequence. These rocks contain two types of Hg deposits, hot-spring deposits that form at shallow depths (<300 m) and silica-carbonate deposits that extend to greater depths (200 to 1000 m), as well as active springs and geothermal systems that release Hg to the present surface. The Franciscan Complex and Great Valley Sequence contain clastic sedimentary rocks with higher concentrations of Hg than volcanic rocks of the Clear Lake Volcanic Field. Mean Hg isotope compositions for all three rock units are similar, although the range of values in Franciscan Complex rocks is greater than in either Great Valley or Clear Lake rocks. Hot spring and silica-carbonate Hg deposits have similar average isotopic compositions that are indistinguishable from averages for the three rock units, although δ202Hg values for the Hg deposits have a greater variance than the country rocks. Precipitates from dilute spring and saline thermal waters in the area have similarly large variance and a mean δ202Hg value that is significantly lower than the ore deposits and rocks. These observations indicate there is little or no isotopic fractionation during release of Hg from its source rocks into hydrothermal solutions. Isotopic fractionation does appear to take place during transport and concentration of Hg in deposits, especially in their uppermost parts. Boiling of hydrothermal fluids is likely the most important process causing of the observed Hg isotope fractionation. This should result in the release of Hg with low δ202Hg values into the atmosphere from the top of these hydrothermal systems and a consequent enrichment in heavy Hg isotopes in the upper crust through time.

Tracing Marine Cryptotephras in the North Atlantic during the Last Glacial Period

NASA Astrophysics Data System (ADS)

Abbott, Peter; Davies, Siwan; Griggs, Adam; Bourne, Anna

2017-04-01

Tephrochronology is a powerful technique that can be utilised for the independent correlation and synchronisation of disparate palaeoclimatic records from different depositional environments. There is a high potential to utilise this technique to integrate ice, marine and terrestrial records to study climatic phasing within the North Atlantic region due to the high eruptive frequency of Icelandic volcanic systems. However, until now North Atlantic marine records have been relatively understudied. Here we report on investigations to define a tephra framework integrating new studies of cryptotephra horizons within a wide network of North Atlantic marine cores with horizons identified in prior work. This framework has the potential to underpin the correlation of the marine records to the Greenland ice-core records and European terrestrial sequences. Tephrochronological investigations were conducted on 13 marine sequences from a range of locations and depositional settings using cryptotephra extraction techniques, including density and magnetic separation, to gain high resolution glass shard concentration profiles and rigorous single-shard major element geochemical analysis to characterise identified deposits. Cryptotephras with an Icelandic source were identified in many records and displayed diversity in shard concentration profiles and the geochemical homo/heterogeneity of shards within the deposits. These differences reflect spatial and temporal variability in the operation of a range of transport processes, e.g. airfall, sea-ice and iceberg rafting, and post-depositional processes, e.g. bioturbation and secondary redeposition. The operation of these processes within the marine environment can potentially impart a temporal delay on tephra deposition and hamper the placement of the isochron, therefore, it is crucial to assess their influence. To aid this assessment a range of deposit types with common transport and depositional histories have been defined. Spatial patterns in the occurrence of these deposit types have been detected, the dominant controls at different sites explored and key regions of the North Atlantic with a greater likelihood for preserving isochronous deposits identified. Overall, these investigations have allowed a framework of isochronous marine cryptotephras to be defined for the last glacial period. The most widespread deposit is the rhyolitic phase of North Atlantic Ash Zone II, identified in 9 of the marine sequences and providing a direct tie-line to the Greenland ice-cores records. The framework is dominated by horizons with a basaltic composition, predominantly sourced from the Icelandic Grímsvötn volcanic system but horizons with Katla, Hekla, Kverkfjöll, Veidivötn and Vestmannaeyjar like compositions have also been isolated. Correlations to horizons in the Greenland ice-core tephra framework are being explored, however, this is a challenging process due to the large number of horizons with similar geochemical signatures in the records and the difference in temporal resolution and stratigraphic control between the ice and marine sequences.

Hemocyanin with phenoloxidase activity in the chitin matrix of the crayfish gastrolith.

PubMed

Glazer, Lilah; Tom, Moshe; Weil, Simy; Roth, Ziv; Khalaila, Isam; Mittelman, Binyamin; Sagi, Amir

2013-05-15

Gastroliths are transient extracellular calcium deposits formed by the crayfish Cherax quadricarinatus von Martens on both sides of the stomach wall during pre-molt. Gastroliths are made of a rigid chitinous organic matrix, constructed as sclerotized chitin-protein microfibrils within which calcium carbonate is deposited. Although gastroliths share many characteristics with the exoskeleton, they are simpler in structure and relatively homogeneous in composition, making them an excellent cuticle-like model for the study of cuticular proteins. In searching for molt-related proteins involved in gastrolith formation, two integrated approaches were employed, namely the isolation and mass spectrometric analysis of proteins from the gastrolith matrix, and 454-sequencing of mRNAs from both the gastrolith-forming and sub-cuticular epithelia. SDS-PAGE separation of gastrolith proteins revealed a set of bands at apparent molecular masses of 75-85 kDa; mass spectrometry data matched peptide sequences from the deduced amino acid sequences of seven hemocyanin transcripts. This assignment was then examined by immunoblot analysis using anti-hemocyanin antibodies, also used to determine the spatial distribution of the proteins in situ. Apart from contributing to oxygen transport, crustacean hemocyanins were previously suggested to be involved in several aspects of the molt cycle, including hardening of the new post-molt exoskeleton via phenoloxidation. The phenoloxidase activity of gastrolith hemocyanins was demonstrated. It was also noted that hemocyanin transcript expression during pre-molt was specific to the hepatopancreas. Our results thus reflect a set of functionally versatile proteins, expressed in a remote metabolic tissue and dispersed via the hemolymph to perform different roles in various organs and structures.

3D Micro-tomography on Aggregates from the 2014- 2015 Eruption of Hunga Tonga-Hunga Ha'apai Volcano

NASA Astrophysics Data System (ADS)

Colombier, M.; Scheu, B.; Cronin, S. J.; Tost, M.; Dobson, K. J.; Dingwell, D. B.

2016-12-01

In December 2014- January 2015, a surtseyan eruption at Hunga Tonga-Hunga Ha'apai volcano (Tonga) formed a new island. Three main eruptive phases were distinguished by observation and deposits: (i) mound and cone construction, involving collapse of 300-600 m-high wet tephra jets, grain flows, slope-remobilisation and energetic surges, with little or no convective plume (ii) The upper cone-building phase with lower jets (mainly <300 m) but greater ash production (weak, steam-rich plumes to 6 km) and weak surges, and (iii) final phase with weak surge, fall and ballistic deposits with more vesicular pyroclasts producing proximal capping deposits. Most sampled deposits contain ash, lapilli and bombs, and lapilli-sized aggregates are ubiquitous. We used high-resolution 3D X-ray microcomputed tomography (XCT) to quantify the grain size distribution (GSD) and porosity by sampling multiple stratigraphic units within the main eruptive sequences. We visualized and quantified the internal structure of the aggregates to understand the evolution of this surtseyan eruption. We present here an overview of the textural information: porosity, vesicle size distribution and morphology as well as the variability of the aggregation features. Aggregates from the fall deposits of the early wet phase are mostly loosely packed, poorly-structured ash clusters. Aggregates from the early surge sequence and the main cone building phase dominantly exhibit a central particle coated by ash cluster material. Vesicles in the particles from the early fall deposits tend to be smaller and more isolated than in the particles from the surge sequence and the main cone building phase. The GSD of aggregates obtained by XCT is highly valuable to correct the total GSD of volcaniclastic deposits. The strong variations in the aggregation features across the eruption suggest a range of different formation and deposition mechanisms related to varying degrees of magma-water-interaction, which changed the morphology and textural properties of the individual particles.

Comparison of Paleogene paleogeography: Southern Coast Ranges and western Transverse Ranges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schussler, S.A.

1991-02-01

The paleogene stratigraphic sequence exposed in the southwestern San Rafael Mountains at the southern terminus of the Coast Ranges, consists of up to 850 m (2,800 ft) of the marine limestone, sandstone, and mudstone that lies with a unique depositional contact upon Franciscan Complex rocks. Lithofacies identified represent four sedimentary environments: (1) foreslope talus deposits of a neritic algal bank (Sierra Blanca limestone), (2) bathyal basin plain and outer submarine fan deposits (Juncal/Anita Formation and Cozy Dell Shale), (3) suprafan lobe deposits of a bathyal submarine fan (lower Mitilija Sandstone), and (4) sublittoral shelf deposits (upper Matilija Sandstone). Similarities betweenmore » paleogene rocks in the southwest San Rafael mountains and the western Santa Ynez Mountains of the Transverse Ranges, approximately 60 km (40 mi) to the west, suggest deposition in a similar paleogeographic setting. Paleomagnetic data suggests post-Paleogene clockwise rotations of the western Transverse Ranges of 90{degree}+. Counterclockwise rotation of the western Transverse Ranges by this amount aligns the similar depositional sequences of the western Transverse Ranges with the northwest-trending Paleogene forearc basin of the southern Coast Ranges and eliminates the necessity for an east-west-oriented Paleogene basin at the site of the present western Transverse Ranges.« less

Major controls on architecture, sequence stratigraphy and paleosols of middle Pleistocene continental sediments ("Qc Unit"), eastern central Italy

NASA Astrophysics Data System (ADS)

Di Celma, Claudio; Pieruccini, Pierluigi; Farabollini, Piero

2015-05-01

Middle Pleistocene continental sediments in central Italy ("Qc Unit") record the oldest fluvial accumulation along the uplifting margin of the Peri-Adriatic basin. The architecture of the sediment body can be divided into two unconformity-bounded, fining-upward cycles interpreted as genetically related depositional sequences. These sequences highlight the systematic adjustment of the fluvial system to changes in the ratio between accommodation space and sediment supply (A/S ratio) and, from base to top, comprise the following surfaces and stratal components: (i) a regionally correlative sequence boundary resulting from an A/S ratio ≤ 0; (ii) a low-accommodation systems tract characterized by conglomerate-rich, amalgamated channel fills and recording an A/S ratio < 1; (iii) an expansion surface marking the turnaround point from low-accommodation systems tract to high-accommodation systems tract deposits; (iv) a high-accommodation systems tract dominated by floodplain fines encasing lens-like, fluvial channel deposits and denoting an A/S ratio > 1; and (v) a mature red argillic paleosol. To constrain the climatic signal for paleosols formation, the two sequence-capping mature paleosols have been investigated. The results of these studies suggest that they were developed under humid and warm climatic conditions associated with interglacial phases, which have been correlatively attributed to Marine Oxygen Isotope Stages 11 and 9.

The Cretaceous glauconitic sandstones of Abu Tartur, Egypt

NASA Astrophysics Data System (ADS)

Pestitschek, Brigitte; Gier, Susanne; Essa, Mahmoud; Kurzweil, Johannes

2010-05-01

The Abu Tartur mine is located in the Western Desert of Egypt, 50 km west of El Kharga City. Geologically, the Abu Tartur plateau is built by a sequence of Upper Cretaceous (Campanian - Maastrichtian) phosphorites, black shales and glauconitic sandstones. The phosphate deposits are of great economic importance and have been mined since their discovery in 1967. Outcrop sections were measured, sampled, sedimentologically characterized and described. One specific glaucony layer was investigated mineralogically and chemically in detail and compared to a subsurface sample from the mine. Two depositional regimes can be interpreted based on sedimentary architecture and structures: 1) a deeper-water hemipelagic environment, where phosphorites and organic carbon-rich shales were deposited and 2) a shallower, prograding higher energy shelf environment with glauconies. From a sequence stratigraphic perspective 1) was deposited during the transgressive systems tract and the early highstand while 2) was deposited during the remaining highstand and a lowstand prograding wedge (Glenn & Arthur, 1990). Petrographic and SEM investigations show that the glaucony grains are of authochtonous origin. XRF, EMPA and thin-section analyses show that the glaucony grains from the outcrop differ significantly in their chemical composition, morphology and color from the grains of the mine sample. The fresh glauconies are enriched in Fe2O3 and K2O compared to the surface samples. XRD analyses of the clay fraction of the six outcrop samples and the mine sample show that the grains consist of illite(glauconite)/smectite mixed-layers, with more illite layers (80 %) in the mine sample. The charge distribution diagram muscovite-pyrophyllite-celadonite shows a clear trend from smectitic glaucony to illitic glaucony, the mine sample plots exactly in the field for glauconites. All these features indicate that the surface samples are strongly altered by weathering and that glauconite progressively transforms into iron-rich illte/smectite mixed layers and then into smectites. For any chemical and mineralogical characterization of glauconites at surface, these weathering effects have to be taken into consideration. GLENN, C. R. & ARTHUR, M. A. (1990): Anatomy and origin of a Cretaceous phosphorites-greensand giant, Egypt. Sedimentology, 37, 123-154.

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania.

PubMed

Coman, Cristian; Chiriac, Cecilia M; Robeson, Michael S; Ionescu, Corina; Dragos, Nicolae; Barbu-Tudoran, Lucian; Andrei, Adrian-Ştefan; Banciu, Horia L; Sicora, Cosmin; Podar, Mircea

2015-01-01

Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients.

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

PubMed Central

Coman, Cristian; Chiriac, Cecilia M.; Robeson, Michael S.; Ionescu, Corina; Dragos, Nicolae; Barbu-Tudoran, Lucian; Andrei, Adrian-Ştefan; Banciu, Horia L.; Sicora, Cosmin; Podar, Mircea

2015-01-01

Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients. PMID:25870594

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

DOE PAGES

Coman, Cristian; Chiriac, Cecilia M.; Robeson, Michael S.; ...

2015-03-30

Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbialmore » mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (<0.5%) but increased significantly at 65°C (36%). The bacterial diversity was either similar to other microbialites described in literature (the 32°C sample) or displayed a specific combination of phyla and classes (the 49°C and 65°C samples). Bacterial taxa were distributed among 39 phyla, out of which 14 had inferred abundances >1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Lastly, several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients.« less

Effect of Sequence Blockiness on the Morphologies of Surface-grafted Elastin-like Polypeptides

NASA Astrophysics Data System (ADS)

Albert, Julie; Sintavanon, Kornkanok; Mays, Robin; MacEwan, Sarah; Chilkoti, Ashutosh; Genzer, Jan

2014-03-01

The inter- and intra- molecular interactions among monomeric units of copolymers and polypeptides depend strongly on monomer sequence distribution and dictate the phase behavior of these species both in solution and on surfaces. To study the relationship between sequence and phase behavior, we have designed a series of elastin-like polypeptides (ELPs) with controlled monomer sequences that mimic copolymers with various co-monomer sequence distributions and attached them covalently to silicon substrates from buffer solutions at temperatures below and above the bulk ELPs' lower critical solution temperatures (LCSTs). The dependence of ELP grafting density on solution temperature was examined by ellipsometry and the resultant surface morphologies were examined in air and under water with atomic force microscopy. Depositions performed above the LCST resulted in higher grafting densities and greater surface roughness of ELPs relative to depositions carried out below the LCST. In addition, we are using gradient substrates to examine the effect of ELP grafting density on temperature responsiveness.

Sequence stratigraphic control on prolific HC reservoir development, Southwest Iran

USGS Publications Warehouse

Lasemi, Y.; Kondroud, K.N.

2008-01-01

An important carbonate formation in the Persian Gulf and the onshore oil fields of Southwest Iran is the Lowermost Cretaceous Fahliyan formation. The formation in Darkhowain field consists of unconformity-bounded depositional sequences containing prolific hydrocarbon reservoirs of contrasting origin. Located in the high stand systems tract (HST) of the lower sequence encompassing over 200m of oil column are the most prolific reservoir. Another reservoir is over 80m thick consisting of shallowing-upward cycles that are best developed within the transgressive systems tract of the upper sequence. Vertical facies distribution and their paleobathymetry and geophysical log signatures of the Fahliyan formation in the Darkhowain platform reveal the presence of two unconformity-bounded depositional sequences in Vail et al., Van Wagoner et al., and Sarg. The Fahliyan formation mainly consists of platform carbonates composed of restricted bioclastic lime mudstone to packstone of the platform interior, Lithocodium boundstone or ooid-intraclast-bioclast grainstone of the high energy platform margin and the bioclast packstone to lime mudstone related to the off-platform setting.

Lithofacies and sequence stratigraphic description of the upper part of the Avon Park Formation and the Arcadia Formation in U.S. Geological Survey G–2984 test corehole, Broward County, Florida

USGS Publications Warehouse

Cunningham, Kevin J.; Robinson, Edward

2017-07-18

Rock core and sediment from U.S. Geological Survey test corehole G–2984 completed in 2011 in Broward County, Florida, provide an opportunity to improve the understanding of the lithostratigraphic, sequence stratigraphic, and hydrogeologic framework of the intermediate confining unit and Floridan aquifer system in southeastern Florida. A multidisciplinary approach including characterization of sequence stratigraphy, lithofacies, ichnology, foraminiferal paleontology, depositional environments, porosity, and permeability was used to describe the geologic samples from this test corehole. This information has produced a detailed characterization of the lithofacies and sequence stratigraphy of the upper part of the middle Eocene Avon Park Formation and Oligocene to middle Miocene Arcadia Formation. This enhancement of the knowledge of the sequence stratigraphic framework is especially important, because subaerial karst unconformities at the upper boundary of depositional cycles at various hierarchical scales are commonly associated with secondary porosity and enhanced permeability in the Floridan aquifer system.

Effect of Thermal Budget on the Electrical Characterization of Atomic Layer Deposited HfSiO/TiN Gate Stack MOSCAP Structure

PubMed Central

Khan, Z. N.; Ahmed, S.; Ali, M.

2016-01-01

Metal Oxide Semiconductor (MOS) capacitors (MOSCAP) have been instrumental in making CMOS nano-electronics realized for back-to-back technology nodes. High-k gate stacks including the desirable metal gate processing and its integration into CMOS technology remain an active research area projecting the solution to address the requirements of technology roadmaps. Screening, selection and deposition of high-k gate dielectrics, post-deposition thermal processing, choice of metal gate structure and its post-metal deposition annealing are important parameters to optimize the process and possibly address the energy efficiency of CMOS electronics at nano scales. Atomic layer deposition technique is used throughout this work because of its known deposition kinetics resulting in excellent electrical properties and conformal structure of the device. The dynamics of annealing greatly influence the electrical properties of the gate stack and consequently the reliability of the process as well as manufacturable device. Again, the choice of the annealing technique (migration of thermal flux into the layer), time-temperature cycle and sequence are key parameters influencing the device’s output characteristics. This work presents a careful selection of annealing process parameters to provide sufficient thermal budget to Si MOSCAP with atomic layer deposited HfSiO high-k gate dielectric and TiN gate metal. The post-process annealing temperatures in the range of 600°C -1000°C with rapid dwell time provide a better trade-off between the desirable performance of Capacitance-Voltage hysteresis and the leakage current. The defect dynamics is thought to be responsible for the evolution of electrical characteristics in this Si MOSCAP structure specifically designed to tune the trade-off at low frequency for device application. PMID:27571412

Stratigraphy and depositional environments of Jurassic Gypsum Spring and Sundance Formations, Sheep Mountain anticline area, Big Horn County, Wyoming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doyle, A.B.

1986-08-01

The Sheep Mountain anticlinal complex between Lovell and Greybull, Wyoming, in the Bighorn basin provides exposure suitable for three-dimensional stratigraphic studies of Mesozoic rocks. The lower unit of the Gypsum Spring Formation is interbedded shale and gypsum. The middle unit is a cyclic sequence of variegated shales, mudstones, and wackestones. The upper unit is red shale. The contact between the underlying Upper Triassic Chugwater Group and the Gypsum Spring Formation is unconformable, as evidenced by an erosional surface. The Sundance Formation is divided into Sundance A and Sundance B, based on fossil data. Sundance A is predominantly green shale withmore » some limestone-shale interbeds. Sundance B lithology is similar to Sundance A with belemnoid guards. Toward the top of Sundance B are beds of glauconitic sandstones that grade upward into fossiliferous limestone. The contact between the Gypsum Spring, Sundance, and Morrison Formations appears to be gradational. The Western Interior sedimentary basin experienced four major transgressions during the Jurassic, resulting in the deposition of the Gypsum Spring and Sundance. Gypsum Spring deposition was influenced by paleohighs, specifically the Belt Island and Sheridan arch, and a warm, arid climate with rare storms. The lower Gypsum Spring unit was deposited in a restricted basin, with the middle and upper units reflecting subsequent deepening and freshening of the Jurassic sea. Most of the Sundance Formation was deposited in a relatively quiet, open-marine environment. Individual units represent shoaling conditions during minor regressions. Storms cut channels into sand bars, which were filled with coquinoid deposits.« less

Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling

Treesearch

D.J. Glass; N. Takebayashi; L. Olson; D.L. Taylor

2013-01-01

The number of sequences from both formally described taxa and uncultured environmental DNA deposited in the International Nucleotide Sequence Databases has increased substantially over the last two decades. Although the majority of these sequences represent authentic gene copies, there is evidence of DNA artifacts in these databases as well. These include lab artifacts...

Draft Genome Sequence of Ideonella sp. Strain A 288, Isolated from an Iron-Precipitating Biofilm

PubMed Central

Künzel, Sven; Szewzyk, Ulrich

2017-01-01

ABSTRACT Here, we report the draft genome sequence of the betaproteobacterium Ideonella sp. strain A_228. This isolate, obtained from a bog iron ore-containing floodplain area in Germany, provides valuable information about the genetic diversity of neutrophilic iron-depositing bacteria. The Illumina NextSeq technique was used to sequence the draft genome sequence of the strain. PMID:28818902

Constraints on the depositional age and tectonometamorphic evolution of marbles from the Biharia Nappe System (Apuseni Mountains, Romania)

NASA Astrophysics Data System (ADS)

Reiser, Martin Kaspar; Schuster, Ralf; Tropper, Peter; Fügenschuh, Bernhard

2017-04-01

Basement rocks from the Biharia Nappe System in the Apuseni Mountains comprise several dolomite and calcite marble sequences or lenses which experienced deformation and metamorphic overprint during the Alpine orogeny. New Sr, O and C-isotope data in combination with considerations from the lithological sequences indicate Middle to Late Triassic deposition of calcite marbles from the Vulturese-Belioara Series (Biharia Nappe s.str.). Ductile deformation and large-scale folding of the siliciclastic and carbonatic lithologies is attributed to NW-directed nappe stacking during late Early Cretaceous times (D2). The studied marble sequences experienced a metamorphic overprint under lower greenschist- facies conditions (316-370 °C based on calcite - dolomite geothermometry) during this tectonic event. Other marble sequences from the Biharia Nappe System (i.e. Vidolm and Baia de Arieș nappes) show similarities in the stratigraphic sequence and their isotope signature, together with a comparable structural position close to nappe contact. However, the dataset is not concise enough to allow for a definitive attribution of a Mesozoic origin to other marble sequences than the Vulturese-Belioara Series.

NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

PubMed Central

Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

2015-01-01

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits. PMID:22517761

Sequence stratigraphy, sedimentary systems and petroleum plays in a low-accommodation basin: Middle to upper members of the Lower Jurassic Sangonghe Formation, Central Junggar Basin, Northwestern China

NASA Astrophysics Data System (ADS)

Feng, Youliang; Jiang, Shu; Wang, Chunfang

2015-06-01

The Lower Jurassic Junggar Basin is a low-accommodation basin in northwestern China. Because of low subsidence rates and a warm, wet climate, deposits of the Central subbasin of the Junggar Basin formed from fluvial, deltaic, shallow lake facies. Sequence stratigraphy and sedimentary systems of the Lower Jurassic members of the Sangonghe Formation (J1s) were evaluated by observing cores, interpreting wireline logs and examining seismic profiles. Two third-order sequences were recognized in the strata. The distribution of the sedimentary systems in the systems tracts shows that tectonic movement, paleorelief, paleoclimate and changes in lake level controlled the architecture of individual sequences. During the development of the lowstand systems tract (LST), the intense structural movement of the basin resulted in a significant fall in the water level in the lake, accompanied by rapid accommodation decrease. Braided rivers and their deltaic systems were also developed in the Central Junggar Basin. Sediments carried by braided rivers were deposited on upward slopes of the paleorelief, and braid-delta fronts were deposited on downward slopes. During the transgressive systems tract (TST), the tectonic movement of the basin was quiescent and the climate was warm and humid. Lake levels rose and accommodation increased quickly, shoal lines moved landward, and shore- to shallow-lake deposits, sublacustrine fans and deep-lake facies were deposited in shallow- to deep-lake environments. During the highstand systems tract (HST), the accommodation no longer increased but sediment supply continued, far exceeding accommodation. HST deposits slowly formed in shallow-lake to meandering river delta-front environments. Relatively low rates of structural subsidence and low accommodation resulted in coarse-grained successions that were fining upward. Deposits were controlled by structural movement and paleorelief within the LST to TST deposits in the Central subbasin. Fine- to medium-grained coarsening-upward successions developed during the HST. The sand bodies of braid-delta fronts on the downward slopes of the paleorelief in the LST and the sublacustrine fans in the TST became reservoirs for hydrocarbon accumulation. Petroleum plays have only been found in the Sangonghe Formation (J1s) located on structural ridges that consist of sand bodies comprising these sequences. Favorable conditions for petroleum plays in HST1-LST2 occur where the sand bodies have been fractured by faults and sealed by denudation and pinch-out lines, then overlain by deep lake mudstone in TST2. The favorable condition of the sand bodies within TST2 occurs where isolated sand bodies have been fractured by faults.

Dichotomy Boundary at Aeolis Mensae, Mars: Fretted Terrain Developed in a Sedimentary Deposit

NASA Astrophysics Data System (ADS)

Irwin, R. P., III; Watters, T. R.; Howard, A. D.; Maxwell, T. A.; Craddock, R. A.

2003-03-01

Fretted terrain in Aeolis Mensae, Mars, developed in a sedimentary deposit. A thick, massive unit with a capping layer or duricrust overlies a more durable layered sequence. Wind, collapse, and minor fluvial activity contributed to degradation.

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field.

PubMed

Crépeau, Valentin; Cambon Bonavita, Marie-Anne; Lesongeur, Françoise; Randrianalivelo, Henintsoa; Sarradin, Pierre-Marie; Sarrazin, Jozée; Godfroy, Anne

2011-06-01

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge) were investigated using molecular approaches. DNA and RNA were extracted from mat samples overlaying hydrothermal deposits and Bathymodiolus azoricus mussel assemblages. We constructed and analyzed libraries of 16S rRNA gene sequences and sequences of functional genes involved in autotrophic carbon fixation [forms I and II RuBisCO (cbbL/M), ATP-citrate lyase B (aclB)]; methane oxidation [particulate methane monooxygenase (pmoA)] and sulfur oxidation [adenosine-5'-phosphosulfate reductase (aprA) and soxB]. To gain new insights into the relationships between mats and mussels, we also used new domain-specific 16S rRNA gene primers targeting Bathymodiolus sp. symbionts. All identified archaeal sequences were affiliated with a single group: the marine group 1 Thaumarchaeota. In contrast, analyses of bacterial sequences revealed much higher diversity, although two phyla Proteobacteria and Bacteroidetes were largely dominant. The 16S rRNA gene sequence library revealed that species affiliated to Beggiatoa Gammaproteobacteria were the dominant active population. Analyses of DNA and RNA functional gene libraries revealed a diverse and active chemolithoautotrophic population. Most of these sequences were affiliated with Gammaproteobacteria, including hydrothermal fauna symbionts, Thiotrichales and Methylococcales. PCR and reverse transcription-PCR using 16S rRNA gene primers targeted to Bathymodiolus sp. symbionts revealed sequences affiliated with both methanotrophic and thiotrophic endosymbionts. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Site formation processes at Pinnacle Point Cave 13B (Mossel Bay, Western Cape Province, South Africa): resolving stratigraphic and depositional complexities with micromorphology.

PubMed

Karkanas, Panagiotis; Goldberg, Paul

2010-01-01

Site PP13B is a cave located on the steep cliffs of Pinnacle Point near Mossel Bay in Western Cape Province, South Africa. The depositional sequence of the cave, predating Marine Isotopic Stage 11 (MIS 11) and continuing to present, is in the form of isolated sediment exposures with different depositional facies and vertical and lateral variations. Micromorphological analysis demonstrated that a suite of natural sedimentation processes operated during the development of the sequence ranging from water action to aeolian activity, and from speleothem formations to plant colonization and root encrustation. At the same time, anthropogenic sediments that are mainly in the form of burnt remains from combustion features (e.g., wood ash, charcoal, and burnt bone) were accumulating. Several erosional episodes have resulted in a complicated stratigraphy, as discerned from different depositional and post-depositional features. The cave is associated with a fluctuating coastal environment, frequent changes in sea level and climate controlled patterns of sedimentation, and the presence or absence of humans. Copyright © 2010 Elsevier Ltd. All rights reserved.

Sequence stratigraphy and sedimentary study on Mishrif formation of Fauqi Oilfield of Missan in south east Iraq

NASA Astrophysics Data System (ADS)

Sang, Hua; Lin, Changsong; Jiang, Yiming

2017-05-01

The reservoir of Mishrif formation has a large scale distribution of marine facies carbonate sediments in great thickness in central and south east Iraq. Rudist reef and shoal facies limestones of the Mishrif Formation (Late Cenomanian - Middle Turonian) form a great potential reservoir rocks at oilfields and structures of Iraq. Facies modelling was applied to predict the relationship between facies distribution and reservoir characteristics to construct a predictive geologic model which will assist future exploration and development in south east Iraq. Microfacies analysis and electrofacies identification and correlations indicate that the limestone of the Mishrif Formation were mainly deposited in open platform setting. Sequence stratigraphic analyses of the Mishrif Formation indicate 3 third order depositional sequences.

The morphology, processes, and evolution of Monterey Fan: a revisit

USGS Publications Warehouse

Gardner, James V.; Bohannon, Robert G.; Field, Michael E.; Masson, Douglas G.

2010-01-01

Long-range (GLORIA) and mid-range (TOBI) sidescan imagery and seismic-reflection profiles have revealed the surface morphology and architecture of the complete Monterey Fan. The fan has not developed a classic wedge shape because it has been blocked for much of its history by Morro Fracture Zone. The barrier has caused the fan to develop an upper-fan and lower-fan sequence that are distinctly different from one another. The upper-fan sequence is characterized by Monterey and Ascension Channels and associated Monterey Channel-levee system. The lower-fan sequence is characterized by depositional lobes of the Ascension, Monterey, and Sur-Parkington-Lucia systems, with the Monterey depositional lobe being the youngest. Presently, the Monterey depositional lobe is being downcut because the system has reached a new, lower base level in the Murray Fracture Zone. A five-step evolution of Monterey Fan is presented, starting with initial fan deposition in the Late Miocene, about 5.5 Ma. This first stage was one of filling bathymetric lows in the oceanic basement in what was to become the upper-fan segment. The second stage involved filling the bathymetric low on the north side of Morro Fracture Zone, and probably not much sediment was transported beyond the fracture zone. The third stage witnessed sediment being transported around both ends of Morro Fracture Zone and initial sedimentation on the lower-fan segment. During the fourth stage Ascension Channel was diverted into Monterey Channel, thereby cutting off sedimentation to the Ascension depositional lobe.

[Analysis of FABP4 expression pattern in rump fat deposition and metabolism of Altay sheep].

PubMed

Ruixia, Xu; Lei, Gao; Weili, Zhao; Wei, Zhang; Guangchao, Song; Shangquan, Gan; Guoqing, Shi

2015-02-01

FABP4 (Fatty acid binding protein 4) is a hot candidate gene in fat deposition and lipid metabolism and participates in the transport and metabolism of intracellular free fatty acids. We aim to study the role of FABP4 in fat deposition and metabolism of the rump fat in Altay sheep. In this study, bioinformatics method was used to analyze the protein sequence homology among 10 species, and RT-PCR was employed to detect FABP4 tissue profiling of Altay sheep. An animal model simulating the rump fat deposition and metabolism of Altay sheep was established by continuous starvation, and qPCR and iTRAQ (isobaric tags for relative and absolute quantitation) were used to detecte FABP4 mRNA and protein expression changes in the control and continuous starvation groups, respectively. Sequence analysis showed that FABP4 protein sequence is highly conserved among species, suggesting an important biological function during evolution for FABP4. The RT-PCR result confirmed that FABP4 mRNA was highly expressed in intestinal and rump fat, suggesting that FABP4 plays an important physiological role in fat tissues. We did not find significant differences in FABP4 mRNA and protein between control and continuous starvation groups (P>0.05), which indicates that FABP4 may not be the key gene in fat deposition and metabolism in Altay sheep.The results above lay a foundation for further studies of FABP4 in rump or tail fat.

High-resolution sequence stratigraphy and continental environmental evolution: An example from east-central Argentina

NASA Astrophysics Data System (ADS)

Beilinson, Elisa; Veiga, Gonzalo D.; Spalletti, Luis A.

2013-10-01

The aims of this contribution is to establish a high-resolution sequence stratigraphic scheme for the continental deposits that constitute the Punta San Andrés Alloformation (Plio-Pleistocene) in east-central Argentina, to analyze the basin fill evolution and to identify and assess the role that extrinsic factors such as climate and sea-level oscillations played during evolution of the unit. For the high-resolution sequence stratigraphical study of the Punta San Andrés Alloformation, high- and low-accommodation system tracts were defined mainly on the basis of the architectural elements present in the succession, also taking into account the relative degree of channel and floodplain deposits. Discontinuities and the nature of depositional systems generated during variations in accommodation helped identify two fourth-order high-accommodation system tracts and two fourth-order low-accommodation system tracts. At a third-order scale, the Punta San Andrés Alloformation may be interpreted as the progradation of continental depositional systems, characterized by a braided system in the proximal areas, and a low-sinuosity, single-channel system in the distal areas, defined by a high rate of sediment supply and discharge peaks which periodically flooded the plains and generated high aggradation rates during the late Pliocene and lower Pleistocene.

A new third-order sequence stratigraphic framework applied to the Triassic of the Paraná Basin, Rio Grande do Sul, Brazil, based on structural, stratigraphic and paleontological data

NASA Astrophysics Data System (ADS)

Horn, B. L. D.; Melo, T. M.; Schultz, C. L.; Philipp, R. P.; Kloss, H. P.; Goldberg, K.

2014-11-01

The Santacruzodon assemblage zone was originally defined as a vertebrate fossil assemblage composed basically of non-mammalian cynodonts found in Santa Cruz do Sul and Venâncio Aires municipalities in Southern Brazil. This assemblage zone was positioned at the top of the Sequence I, in the Triassic Santa Maria Supersequence, Paraná Basin. However, the Santacruzodon assemblage zone does not occur across the entire area of the Santa Maria Supersequence. Based on new paleontological, structural and sedimentological data, we propose the existence of a new third-order sequence (Santa Cruz Sequence) between Sequences I and II in the Santa Maria Supersequence. Satellite image analysis was used to identify regional, NW- and NE-oriented lineaments that limit the occurrence zone. Outcrop data allowed the identification of a regional, angular unconformity that bounds the new sequence. The faunal content allowed the correlation of the new Santa Cruz Sequence with Madagascar's Isalo II fauna, corresponding to the Ladinian (Middle Triassic). New names were suggested for the sequences in the Santa Maria Supersequence, since the Santa Cruz Sequence was deposited between the former Sequences I and II. This unit was deposited or preserved exclusively on the hanging wall of normal faults, being absent from the adjacent structural blocks.

Identification of putative candidate genes involved in cuticle formation in Prunus avium (sweet cherry) fruit

PubMed Central

Alkio, Merianne; Jonas, Uwe; Sprink, Thorben; van Nocker, Steven; Knoche, Moritz

2012-01-01

Background and Aims The cuticular membrane (CM) of Prunus avium (sweet cherry) and other fleshy fruit is under stress. Previous research indicates that the resultant strain promotes microscopic cuticular cracking. Microcracks impair the function of the CM as a barrier against pathogens and uncontrolled water loss/uptake. Stress and strain result from a cessation of CM deposition during early development, while the fruit surface continues to expand. The cessation of CM deposition, in turn, may be related to an early downregulation of CM-related genes. The aims of this study were to identify genes potentially involved in CM formation in sweet cherry fruit and to quantify their expression levels. Methods Fruit growth and CM deposition were quantified weekly from anthesis to maturity and rates of CM deposition were calculated. Sequences of genes expressed in the sweet cherry fruit skin (exocarp) were generated using high-throughput sequencing of cDNA and de novo assembly and analysed using bioinformatics tools. Relative mRNA levels of selected genes were quantified in the exocarp and fruit flesh (mesocarp) weekly using reverse transcriptase-quantitative real-time PCR and compared with the calculated CM deposition rate over time. Key Results The rate of CM deposition peaked at 93 (±5) μg per fruit d−1 about 19 d after anthesis. Based on sequence analyses, 18 genes were selected as potentially involved in CM formation. Selected sweet cherry genes shared up to 100 and 98 % similarity with the respective Prunus persica (peach) and Arabidopsis thaliana genes. Expression of 13 putative CM-related genes was restricted to the exocarp and correlated positively with the CM deposition rate. Conclusions The results support the view that the cessation of CM deposition during early sweet cherry fruit development is accounted for by a downregulation of genes involved in CM deposition. Genes that merit further investigation include PaWINA, PaWINB, PaLipase, PaLTPG1, PaATT1, PaLCR, PaGPAT4/8, PaLACS2, PaLACS1 and PaCER1. PMID:22610921

Graben calderas of the Sierra Madre Occidental: The case of Guanajuato, central Mexico

NASA Astrophysics Data System (ADS)

Aguirre-Diaz, G. J.; Tristán-González, M.; Labarthe-Hernández, G.; Marti, J.

2013-12-01

The Sierra Madre Occidental (SMO) volcanic province is characterized by voluminous silicic ignimbrites that reach an accumulated thickness of 500 to 1500 m. A single ignimbrite can reach up to 350 m thick in its outflow facies. This ignimbrite sequence formed mostly within 38-23 Ma, building up a total estimated volume of ca. 580,000 km3 making the SMO the largest ignimbrite province of the world. We have showed that several and probably most of the SMO ignimbrites were erupted from fissures associated to Basin and Range fault systems or grabens (Geology, 2003), thus naming these volcano-tectonic structures as graben calderas (Caldera Volcanism book, Elsevier, 2008). Generally, the sequence observed in graben calderas include, from oldest to youngest, alluvial fan deposits combined with lacustrine deposits, pyroclastic surge deposits and minor volume ignimbrites, a large-volume ignimbrite that could be massive or made of successive layers, and sometimes silicic lava domes and/or mafic fissural lavas both with vents aligned with the graben trend. Fallout deposits, plinian or non-plinian, are not observed in the sequence. Thus, onset of caldera collapse represented by the major ignimbrite must occur just after deposition of continental sediments within the graben domain. A similar volcano-tectonic development is observed in pull-apart grabens. Therefore, extensional or transtensional tectonics, before and during caldera collapse, and the emplacement of a subgraben shallow silicic magma chamber are the necessary conditions for the development of graben calderas. We describe here the case of the Guanajuato graben caldera, located in the central part of Mexico and in the southeastern portion of the SMO volcanic province. The caldera is part of the economically important mining district of Guanajuato, with 28 silver mines, some active since the 16th century. The caldera structure, a rectangle of 10 x 16 km, was controlled by NW and NE regional fault systems. Most ore deposits occur along this orthogonal faulting network, but mainly along the NW fault of Veta Madre that crosses through the center of the caldera. The mid-Tertiary stratigraphy in Guanajuato follows the general sequence observed in graben calderas; i.e., from oldest to youngest includes 1) at least 1,500 m of alluvial fan deposits within a tectonic basin (Guanajuato Red Conglomerate), 2) pyroclastic flow deposits, consisting of surge deposits (Loseros Formation) that are concordant with a massive, large volume, rhyolitic ignimbrite (Bufa Rhyolite), which is covered by a layered series of pyroclastic flow deposits (Calderones Formation), and 3) effusive volcanism in the form of rhyolitic lava domes (Chichíndaro Rhyolite) and basaltic-andesite dikes and lavas (Cedros Andesite). The Guanajuato graben caldera formed at about 33 Ma, based on our new U-Pb zr age of the main ignimbrite, Bufa Rhyolite.

Lagoonal deposits in the Upper Cretaceous Rock Springs Formation (Mesaverde Group), southwest Wyoming

USGS Publications Warehouse

Kirschbaum, M.A.

1989-01-01

Most paleogeographic reconstructions of the Rock Springs Formation show shorelines having lobate to arcuate deltas. These shorelines are oriented NE-SW, with the sea to the southeast. Brackish-water bodies are usually shown in interdistributary areas or associated with abandoned delta lobes, and are open to the sea. In this study, a sedimentary sequence 30-50 m thick is interpreted as interdeltaic deposits. Brackish-water deposits within the sequence are interpreted as interdeltaic lagoons rather than interdistributary bays. Three facies associations (units) are recognized in nine measured sections of the study interval. Unit A consists of interbedded sandstone, mudrock and coal which occur in both fining- and coarsening-upward sequences less than 10 m thick. Fining-upward sequences decrease in thickness and frequency upwards in unit A and are interpreted as distributary channels. Coarsening-upward sequences associated with the channels are interpreted as crevasse splays that filled lakes or interdistributary bays. In the upper part of the unit where only minor channels are present, the coarsening-upward sequences are interpreted as bay deltas. Unit B consists of fossiliferous silty shale and bioturbated sandy siltstone. A low-diversity fauna of bivalves, gastropods, ostracods and foraminifers indicates that brackish-water conditions existed. Unit B intertongues with unit A to the northwest and with unit C to the southeast, and is interpreted as lagoonal deposits. Unit C consists of crossbedded and burrowed sandstone in beds 0.5-9 m thick. Sandstones are laterally continuous in the southeast but become tabular bodies enclosed within unit B to the northwest. Laterally continuous sandstones are interpreted as shoreface deposits on the basis of multidirectional crossbeds, marine trace fossils and continuity. Tabular sandstones are interpreted as flood-tidal deltas on the basis of NW-oriented crossbeds, pinchouts to the northwest and enclosure within unit B. Scoured surfaces and rip-up clasts within unit C indicate the presence of tidal channels or inlets. Interpreting unit B as an interdeltaic lagoon rather than an interdistributary bay is dependent on understanding its enclosing strata. The distributary channels of unit A supplied the majority of the sediment in the lower part of the sequence. However, after the lagoon formed, tidal channels and inlets of unit C supplied more sediment to the area than channels of unit A. The shift in sedimentation from a landward to a seaward source reflects the change from a delta plain to an interdeltaic lagoon following abandonment of distributary channels. ?? 1989.

Sequence stratigraphy of an Oligocene carbonate shelf, Central Kalimantan, Indonesia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saller, A.; Armin, R.; Ichram, L.O.

1991-03-01

Interpretations of Oligocene shelfal limestones from Central Kalimantan, Indonesia, suggest caution in predicting sea-level lowstands from seismic reflector patterns or published sea-level curves. Three major depositional sequences, each 200-400 m thick, were delineated in outcrops and seismic lines: late Eocene to early Oligocene (34-38 Ma), middle Oligocene (29.7-32 Ma), and early late Oligocene (28-29.7 Ma). The lowest sequence is mainly shale with tin sandstones and limestones (large-foram wackestone). The middle and upper sequences are carbonate with transgressive systems tracts (TSTs) overlain by highstand systems tracts (HSTs). TSTs contain large-foram wackestone-packstones and coral wackestone-packstones. HSTs are characterized by (1) shale andmore » carbonate debris flows deposited on the lower slope, (2) argillaceous large-foram wackestones on the upper slope, (3) discontinuous coral wackestones and boundstones on the shelf margin, (4) bioclastic packstones and grainstones on backreef flats and shelf-margin shoals, and (5) branching-coral and foraminiferal wackestones in the lagoon. Bases of sequences are characterized by transgression and onlap. Deepending and/or drowning of the carbonate shelf occurred at the top of the middle and upper sequences. Basinal strata that apparently onlap the middle and upper carbonate shelf margins might be misinterpreted as lowstand deposits, although regional studies indicate they are prodelta sediments baselapping against the shelf. Shallowing the subaerial exposure of the carbonates might be expected during the large mid-Oligocene (29.5-30 Ma) sea-level drop of Haq et al. (1987), instead of the observed deepening and local drowning.« less

The Cretaceous-Paleogene transition and Chicxulub impact ejecta in the northwestern Gulf of Mexico: Paleoenvironments, sequence stratigraphic setting and target lithologies

NASA Astrophysics Data System (ADS)

Schulte, Peter

2003-07-01

The Cretaceous-Paleogene (K-P) transition is characterized by a period of mass extinctions, the Chicxulub impact event, sea-level changes, and considerable climate changes (e.g., cooling). The Gulf of Mexico region is a key area for addressing these issues, specifically because of the proximity to the large Chicxulub impact structure in southern Mexico, and because of its shallow shelf areas throughout the Maastrichtian to Danian period. This study presents the results of a multidisciplinary investigation of Chicxulub impact ejecta and marine sediments from the K-P transition in the western Gulf of Mexico. Sedimentological, mineralogical, and geochemical aspects of K-P sections and cores from northeastern Mexico, Texas, and Alabama have been by studied with focus on Chicxulub ejecta, long- or short-term facies change, and sequence stratigraphic setting. CHICXULUB EJECTA: The Chicxulub ejecta (or impact spherule) deposits from northeastern Mexico and Texas revealed an unexpected complex and localized ejecta composition. Fe-Mg-rich chlorite- as well as Si-Al-K-rich glass-spherules are the predominant silicic ejecta components in northeastern Mexico, whereas in Texas, spherules of Mg-rich smectite compositions were encountered. Spherules contain Fe-Ti-K-rich schlieren, Fe-Mg-rich globules, and rare µm-sized metallic and sulfidic Ni-Co-(Ir-?) rich inclusions. This composition provides evidence for a distinct range of target rocks of mafic to intermediate composition, presumably situated in the northwestern sector of the Chicxulub impact structure, in addition to the possibility of contamination by meteoritic material. The absence of spinels and the ubiquitous presence of hematite and goethite points to high oxygen fugacity during the impact process. Besides these silicic phases, the most prominent ejecta component is carbonate.! Carbonate is found in ejecta deposits as unshocked clasts, accretionary lapilli-like grains, melt globules (often with quenching textures), and as microspar, suggesting that this area received ejecta mainly from shallow, carbonate-rich lithologies at the impact site on the Yucatán carbonate platform. Albeit the ejecta spherules are mostly altered to clay minerals and iron oxides, the microfacies and internal textures of the ejecta particles show a variety of distinct features, including welding and fusing of components and evidence for liquid immiscibility between silicic-silicic and carbonate-silicic melts. No evidence for binary mixing of ejecta phases was found. Therefore, it is assumed that ejecta in northeastern Mexico derived from less energetic parts of the ejecta curtain. The welding features of ejecta particles suggest an initial ground surge-like ejecta-dispersion mode. The specific morphological features and the compositional range of Chicxulub ejecta, as well as the results of petrological and rock magnetic characteristics reveal similarities to Chicxulub ejecta from K-P sections in the Gulf of Mexico area, the Caribbean, the Atlantic, the Pacific, and Northern America (Western Interior). In addition, Mg-rich smectite, K-feldspar, and iron oxide-rich microspherules are characteristic for the K-P boundary clay layer in sections from the Atlantic and Tethyan realm, suggestive of a relationship between the Chicxulub impact event and the basal K-P boundary clay layer. EJECTA DEPOSITS: The Chicxulub ejecta deposits are commonly associated with an event deposit that shows a complex succession of deposition from high-energetic (channelized) debris flows or turbidity currents derived from multiple source areas, followed by a period of decreasing current energy and intermittent periods of reworking. The uppermost parts of these deposits are often bioturbated, pointing to longer periods of deposition, as also sustained by the complex internal subdivision of the K-P event deposits. In northeastern Mexico, Chicxulub ejecta is also locally embedded within latest Maastrichtian marls, though common soft-sediment deformation opposes a clear age assignation of these deposits. However, individual spherule layers in the slumped and in the channelized spherule deposits are of similar petrological, mineralogical, and geochemical composition with no size-sorting and abrasion of ejecta, hence pointing to an origin from a single impact event (Chicxulub) and providing no evidence for extended periods between reworking of individual spherule layers. In the Brazos core from Texas, a m-thick shale interval, almost devoid of micro- and macrofossils and therefore of unclear stratigraphic age, is sandwiched between Chicxulub impact ejecta and the first appearance of Paleocene microfossils, indicating a period (of enhanced reworking?) between these two events. However, no mm-thick ferruginous layer with Ni-rich spinels, smectite spherules, and shocked quartz that defines the K-P boundary in the Global Stratotype Section and Point (GSSP) at El Kef, Tunisia, and elsewhere has been observed in any of the sections and cores studied. Therefore, an unequivocal positioning of the K-P boundary is difficult for the northwestern Gulf of Mexico region. PALEOCLIMATE RECORD: The long-term record of clay mineral species during the K-P transition of northeastern Mexico, Texas, and Alabama shows remarkably localized compositional patterns, indicating local sediment influx from topographically, petrologically, and probably climatically distinct source regions. Chlorite-illite-dominated clay assemblages in northwestern Mexico indicate mafic source rocks, predominance of physical weathering, and cooler climates, probably associated with the uplift of the Sierra Madre Oriental, whereas a smectite-dominated clay assemblage in Texas indicates semiarid-humid climates. In central Alabama, a distinct trend from tropically humid and warm climates to more seasonal and drier climate that already started in the late Maastrichtian was inferred from a prominent change of a kaolinite- to a smectite-dominated clay mineral assemblage. Hence, no unique climate conditions and distinct climate trends can be inferred for the northwestern Gulf of Mexico area from the data provided by this study. SEQUENCE STRATIGRAPHY: The sequence stratigraphic setting of the Maastrichtian to Danian strata in northeastern Mexico, Texas, and Alabama is also quite complex. The deep-water marls in northeastern Mexico were not amenable to a clear sequence stratigraphic subdivision, though the similar mineralogical (and geochemical) composition of the Maastrichtian to Danian marls provided no evidence for a distinct major facies change during this interval. In Texas, no facies change was observed for the (highstand) shale interval that includes the event bed, though a gradual sea-level lowering took place upon the appearance of the earliest Paleocene microfossils. A sequence boundary is present in the earliest Danian and overlain by transgressive systems tract. In central Alabama, a pronounced sea-level shallowing was recognized during a highstand systems tract in the late Maastrichtian, topped by a sequence boundary and subsequent (strongly) rising sea level throughout the latest Maastrichtian and the early Danian. Rapid and intense water-depth fluctuations are inferred from middle Danian carbonate-rich strata concomitant to a change from a mixed siliciclastic-carbonate depositional system to a more stable carbonate platform in central Alabama during this period. In summary, no universal pattern of facies and related sea-level changes was obtained from the northwestern Gulf of Mexico area, and particularly, no evidence for adverse an- or dysoxic sedimentary conditions were observed for the Maastrichtian to Danian interval governed by this study.

Laboratory test data on the stability of the STIS MAMAs

NASA Technical Reports Server (NTRS)

Joseph, Charles L.

1997-01-01

STIS has two MAMA detectors systems with distinctly different tube configurations. The first (designated BAND 1) has an opaque CsI photocathode deposited on the microchannel plate (MCP) providing wavelength coverage from 1150A to 1700A. The other MAMA (designated BAND 2) has a semitransparent CS2Te photocathode deposited on the faceplate in close proximity to the input of the MCP. It covers the 1650A to 3100A bandpass and serves as a backup for the short wavelength detector. Laboratory test data indicate that both of these detectors have good sensitivity, have good uniformity and provide stable response, making each capable of collecting data with a signal-to-noise ratio in excess of 100 per Space Telescope Imaging Spectrograph (STIS) optical resolution element. Over a multiyear development effort, a substantial body of laboratory test data (more than 6 GBytes spanning more than 6 years of collection) has accumulated on more than a dozen fabricated tubes. These tests even included a few destructive evaluations to examine the limitations and operating life. In addition, analyses where conducted regarding impact caused by the specified electronic tolerances and expected changes in the Hubble Space Telescope (HST) thermal environment. Perhaps the simplest test of stability is to collect a sequence of images, each with a uniform illumination, and use these individual "flat fields" to remove the pixel-to-pixel sensitivity in the other flat fields. These sequences typically spanned 3-5 weeks of time. The detectors are very stable, allowing the pixel-to-pixel sensitivity to be removed with good precision. The STIS specification for stability is 1% (sufficient for data with a S/N = 100) over a 1 week period and 2% over 30 days. All Engineering Model Units as well as Flight Detectors tested exceeded this specification.

Seismic stratigraphic characteristics of upper Louisiana continental slope: an area east of Green Canyon

USGS Publications Warehouse

Bouma, Arnold H.; Feeley, Mary H.; Kindinger, Jack G.; Stelting, Charles E.; Hilde, Thomas W.C.

1981-01-01

A high-resolution seismic reflection survey was conducted in a small area of the upper Louisiana Continental Slope known as Green Canyon Area. This area includes tracts 427, 428, 471, 472, 515, and 516, that will be offered for sale in March 1982 as part of Lease Sale 67.The sea floor of this region is, slightly hummocky and is underlain by salt diapirs that are mantled by early Tertiary shale. Most of the shale is overlain by younger Tertiary and Quaternary deposits, although locally some of the shale protrudes the sea floor. Because of proximity to older Mississippi River sources, the sediments are thick. The sediment cover shows an abundance of geologic phenomena such as horsts, grabens, growth faults, normal faults, and consolidation faults, zones with distinct and indistinct parallel reflections, semi-transparent zones, distorted zones, and angular unconformities.The major feature of this region is a N-S linear zone of uplifted and intruded sedimentary deposits formed due to diapiric intrusion.Small scale graben development over the crest of the structure can be attributed to extension and collapse. Large scale undulations of reflections well off the flanks of the uplifted structure suggest sediment creep and slumping. Dipping of parallel reflections show block faulting and tilting.Air gun (5 and 40 cubic inch) records reveal at least five major sequences that show masked onlap and slumping in their lower parts grading into more distinct parallel reflections in their upper parts. Such sequences can be related to local uplift and sea level changes. Minisparker records of this area show similar sequences but on a smaller scale. The distinct parallel reflections often onlap the diapir flanks. The highly reflective parts of these sequences may represent turbidite-type deposition, possibly at times of lower sea level. The acoustically more transparent parts of each sequence may represent deposits containing primarily hemipelagic and pelagic sediment.A complex ridge system is present along the west side of the area and distinct parallel reflections onlap onto this structure primarily from the east. Much of this deposition may be ascribed to sedimentation within a submarine canyon whose position is controlled by this ridge.

Stratigraphy and Age of Paleoproterozoic Birimian Volcaniclastic Sequence in the Cape Three Points area, Axim-Konongo (Ashanti) Belt, Southwest Ghana

NASA Astrophysics Data System (ADS)

Yoshimaru, S.; Kiyokawa, S.; Ito, T.; Ikehara, M.; Horie, K.; Takehara, M.; Sano, T.; Nyame, F. K.; Tetteh, G. M.

2016-12-01

This study investigated the depositional environments and bioactivities of well preserved volcaniclastic sequences in the Cape Three Points area in the Paleoproterozoic Axim-Konongo (Ashanti) belt in the Birimian of Ghana. Our current research outlines the stratigraphy, structure, approximate age and depositional setting of the volcaniclastic sequence in the Cape Three Points area in Ghana, West Africa.Axim-Konongo (Ashanti) belt is composed of mainly andesitic basalts, volcaniclastic rocks and belt type granitoids, which are unconformably overlain by Tarkwaian conglomerates and metasedimentary rocks. The rocks show NE-SW strike with maximum depositional age of overlying metasedimentary rocks of 2154±2 Ma (U-Pb zircon; Oberthür et al., 1998). The oldest age of an intrusive into Birimian volcanic rock near Sekondi is 2174±2 Ma (U-Pb zircon; Oberthür et al., 1998). Thick volcaniclastic succession over 4000 m thickness was reconstructed for 1000 m thickness after detailed field investigations. The succession shows approximately N-S strike mainly 60-80° dip to the east and generally upward sequence. The rocks were affected by greenschist facies metamorphism. TiO2/Al2O3 ratios of chromites and whole- rock trace elements compositions with low Nb concentration and high LREE concentration support deposition on mid-deep sea floor in a volcanic arc. New age data were obtained from foliated porphyritic dyke which occurs in the Cape Three Points area. Zircon grains, measured by SHRIMP at National Institute of Polar Research (NIPR), yielded a weighted mean 204Pb-corrected 207Pb/206Pb age of 2265.6±4.6 Ma (95% confidence). Thus, the volcaniclastic sequence was deposited before 2265.6±4.6 Ma and was deformed after 2265 Ma. 2260 Ma is the oldest age at which early volcanic activity in the Birimian terrane occurred (Loh and Hirdes, 1999). References Oberthür T et al. (1998) Precambrian Research 89: 129-143 Loh G and Hirdes W (1999) Exlplanatory Notes for the Geological Map of southwest Ghana, 1:100000. Ghana Geological Survey Bulletin No, 49, 106-112

The Inskip Formation, the Harmony Formation, and the Havallah Sequence of Northwestern Nevada - An Interrelated Paleozoic Assemblage in the Home of the Sonoma Orogeny

USGS Publications Warehouse

Ketner, Keith B.

2008-01-01

An area between the towns of Winnemucca and Battle Mountain in northwestern Nevada, termed the arkosic triangle, includes the type areas of the middle to upper Paleozoic Inskip Formation and Havallah sequence, the Upper Devonian to Mississippian Harmony Formation, the Sonoma orogeny, and the Golconda thrust. According to an extensive body of scientific literature, the Havallah sequence, a diverse assemblage of oceanic rocks, was obducted onto the continent during the latest Permian or earliest Triassic Sonoma orogeny by way of the Golconda thrust. This has been the most commonly accepted theory for half a century, often cited but rarely challenged. The tectonic roles of the Inskip and Harmony Formations have remained uncertain, and they have never been fully integrated into the accepted theory. New, and newly interpreted, data are incompatible with the accepted theory and force comprehensive stratigraphic and tectonic concepts that include the Inskip and Harmony Formations as follows: middle to upper Paleozoic strata, including the Inskip, Harmony, and Havallah, form an interrelated assemblage that was deposited in a single basin on an autochthonous sequence of Cambrian, Ordovician, and lowest Silurian strata of the outer miogeocline. Sediments composing the Upper Devonian to Permian sequence entered the basin from both sides, arkosic sands, gravel, limestone olistoliths, and other detrital components entered from the west, and quartz, quartzite, chert, and other clasts from the east. Tectonic activity was expressed as: (1) Devonian uplift and erosion of part of the outer miogeocline; (2) Late Devonian depression of the same area, forming a trough, probably fault-bounded, in which the Inskip, Harmony, and Havallah were deposited; (3) production of intraformational and extrabasinal conglomerates derived from the basinal rocks; and (4) folding or tilting of the east side of the depositional basin in the Pennsylvanian. These middle to upper Paleozoic deposits were compressed in the Jurassic, causing east-verging thrusts in the eastern part of the depositional basin (Golconda thrust) and west-verging thrusts and folds in the western part. Hypotheses involving a far-traveled allochthon that was obducted from an ocean or back-arc basin are incompatible with modern observations and concepts.

Haematobia irritans dataset of raw sequence reads from Illumina and Pac Bio sequencing of genomic DNA

USDA-ARS?s Scientific Manuscript database

The genome of the horn fly, Haematobia irritans, was sequenced using Illumina- and Pac Bio-based protocols. Following quality filtering, the raw reads have been deposited at NCBI under the BioProject and BioSample accession numbers PRJNA30967 and SAMN07830356, respectively. The Illumina reads are un...

Shallow-seated explosions in the construction of the Motukorea tuff ring (Auckland, New Zealand): Evidence from lithic and sedimentary characteristics

NASA Astrophysics Data System (ADS)

Agustín-Flores, Javier; Németh, Károly; Cronin, Shane J.; Lindsay, Jan M.; Kereszturi, Gábor

2015-10-01

At least 52 eruption centres are scattered within the 360 km2 Auckland Volcanic Field (AVF). Motukorea, now an island in the Waitemata Harbour, is one of 39 AVF volcanoes that experienced a phreatomagmatic explosive phase, before a magmatic phase. The volcano erupted through a 200-300 m-thick, consolidated, mudstone/sandstone sequence of the Miocene Waitemata Group, which overlies the Waipapa Terrane greywacke basement. Detailed field descriptions of the sedimentary characteristics of the early phreatomagmatic deposits were carried out, along with examination of lithics. The ejecta ring deposit comprises 55 to 60 vol.% lithics, of which Waitemata Group fragments constitute approximately 90 vol.%, whereas < 10 vol.% are Waipapa fragments, suggesting a dominance of shallow fragmentation. The sedimentary characteristics of the stratigraphic sequence at Motukorea suggest a dominance of wet surges at the beginning of the eruption with progression into drier sequences upwards. This is reflected in increasing inter-bedded juvenile-pyroclast-dominated fall deposits up-sequence. These characteristics are attributed to the changing hydrogeological conditions within the diatreme and the host rocks. These findings shed light on the eruption dynamics of phreatomagmatic eruptions through consolidated rocks in the AVF and enable the depiction of a scenario of future eruptions within the field in similar substrates.

Origin of phosphatic stromatolites in the Upper Cretaceous condensed sequence of the Polish Jura Chain

NASA Astrophysics Data System (ADS)

Krajewski, K. P.; Leśniak, P. M.; Łącka, B.; Zawidzki, P.

2000-10-01

The Turonian stromatolite-bearing condensed sequence in the Polish Jura Chain (the European epicontinental basin) provides good insight into the environment of formation of Cretaceous phosphatic stromatolites, owing to their purely phosphatic development and negligible post-depositional alteration. The sequence developed as a result of slow pelagic sedimentation and microbial mat phosphatization on a submarine swell surrounded by local basins with non-condensed carbonate deposition. Diagenesis of organic matter and dissolution of biogenic apatite were the major sources of reactive phosphorus for the microbial mat phosphatization. Stromatolite growth occurred due to pulses of amorphous or poorly ordered calcium phosphate precipitation followed by crystallization of carbonate fluorapatite (CFA). The phosphogenic environment left an imprint on the isotopic composition of limestone carbon and lattice-bound carbon and sulphur in CFA, and on the light rare-earth element (LREE) distribution in CFA. The δ13C of the stromatolite-bearing sequence shows a negative excursion (-1 to -3‰), standing in marked contrast to positive carbon values of the surrounding basinal carbonate. Most of the δ34S values of CFA (+20 to +21‰) fit the value range of the coeval seawater sulphate, and the LREE distribution shows a well-defined seawater pattern. This geochemical signature is indicative of intense diagenesis of organic matter at the seafloor, pelagic carbonate dissolution, and prolonged exposure of the deposited phosphate towards the water column. The enhanced deposition and diagenesis of organic phosphorus in the stromatolitic environment reflects elevated levels of the epicontinental basin nutrification related to sea-level rises and the associated oceanographic and geochemical changes.

Micromorphological aspects of various human activities recorded in the Scafati pedocomplex (Napoli, Italy).

NASA Astrophysics Data System (ADS)

Rellini, Ivano; Vogel, Sebastian; Märker, Michael

2014-05-01

The stratigraphic sequence of Scafati, about 3 km east of ancient Pompeii, is presented consisting of a multilayered sequence of repeated volcanic deposition and pedogenesis that was caused by several phases of volcanic activity and volcanic quiescence of Somma-Vesuvius, at least, the last 20,000 years. Micromorphological analysis were carried out at the soil material and selected volcanic deposits to establish a chronological succession of different phases of volcanic deposition, pedogenetic transformation but also to highlight the anthropogenic influence. The micromorphological analysis testified furrow irrigation and soil cultivation in the medieval stratigraphy and allowed the identification of very significant antropogenic features in the Bronze Age/Iron Age paleosol, i.e. complex depositional crusts and dusty clay coatings and hypocoatings, which are often used as an indicator for tillage activity. In contrast to the clear macroscopic and chemical evidence of ancient soil cultivation, the Roman paleosol did not exhibit distinct micromorphological signs of soil cultivation.

Geochemical Peculiarities of Galena and Sphalerite from Polymetallic Deposits of the Dal'negorskii Ore Region (Primorsky Krai, Russia)

NASA Astrophysics Data System (ADS)

Rogulina, L. I.; Moiseenko, V. G.; Ponomarchuk, V. A.

2018-04-01

New data on the composition of the major minerals from the skarn and vein polymetallic deposits of the Dal'negorskii ore region are reported. Analysis of galena and sphalerite was carried out by the X-ray fluorescent energy-dispersive method of synchrotron radiation for the first time. It is shown that the minor elements in major minerals of different deposits are typomorphic. Among these elements are Fe, Cu, Ni, Cd, Ag, Sn, and Sb, as well as In in sphalerite and Te in galena. The high concentrations of Ag, Cu, Te, Cd, and In in the extracted minerals indicate the complex character of mineralization. The compositional patterns of ore minerals characterize the sequence of mineral formation from the skarn to vein ores, and the sequence of deposits from the mesothermal to epithermal conditions. This provides geochemical evidence for the stage model of the formation of mineralization in the Dal'negorskii ore region.

Volcanic Hazard Education through Virtual Field studies of Vesuvius and Laki Volcanoes

NASA Astrophysics Data System (ADS)

Carey, S.; Sigurdsson, H.

2011-12-01

Volcanic eruptions pose significant hazards to human populations and have the potential to cause significant economic impacts as shown by the recent ash-producing eruptions in Iceland. Demonstrating both the local and global impact of eruptions is important for developing an appreciation of the scale of hazards associated with volcanic activity. In order to address this need, Web-based virtual field exercises at Vesuvius volcano in Italy and Laki volcano in Iceland have been developed as curriculum enhancements for undergraduate geology classes. The exercises are built upon previous research by the authors dealing with the 79 AD explosive eruption of Vesuvius and the 1783 lava flow eruption of Laki. Quicktime virtual reality images (QTVR), video clips, user-controlled Flash animations and interactive measurement tools are used to allow students to explore archeological and geological sites, collect field data in an electronic field notebook, and construct hypotheses about the impacts of the eruptions on the local and global environment. The QTVR images provide 360o views of key sites where students can observe volcanic deposits and formations in the context of a defined field area. Video sequences from recent explosive and effusive eruptions of Carribean and Hawaiian volcanoes are used to illustrate specific styles of eruptive activity, such as ash fallout, pyroclastic flows and surges, lava flows and their effects on the surrounding environment. The exercises use an inquiry-based approach to build critical relationships between volcanic processes and the deposits that they produce in the geologic record. A primary objective of the exercises is to simulate the role of a field volcanologist who collects information from the field and reconstructs the sequence of eruptive processes based on specific features of the deposits. Testing of the Vesuvius and Laki exercises in undergraduate classes from a broad spectrum of educational institutions shows a preference for the web-based interactive tools compared with traditional paper-based laboratory exercises. The exercises are freely accessible for undergraduate classes such as introductory geology, geologic hazards, or volcanology. Accompany materials, such as lecture-based Powerpoint presentations about Vesuvius and Laki, are also being developed for instructors to better integrate the web-based exercises into their existing curriculum.

Sequence Stratigraphic Analysis and Facies Architecture of the Cretaceous Mancos Shale on and Near the Jicarilla Apache Indian Reservation, New Mexico-their relation to Sites of Oil Accumulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ridgley, Jennie

2001-08-21

The purpose of phase 1 and phase 2 of the Department of Energy funded project Analysis of oil- bearing Cretaceous Sandstone Hydrocarbon Reservoirs, exclusive of the Dakota Sandstone, on the Jicarilla Apache Indian Reservation, New Mexico was to define the facies of the oil producing units within the Mancos Shale and interpret the depositional environments of these facies within a sequence stratigraphic context. The focus of this report will center on (1) redefinition of the area and vertical extent of the ''Gallup sandstone'' or El Vado Sandstone Member of the Mancos Shale, (2) determination of the facies distribution within themore » ''Gallup sandstone'' and other oil-producing sandstones within the lower Mancos, placing these facies within the overall depositional history of the San Juan Basin, (3) application of the principals of sequence stratigraphy to the depositional units that comprise the Mancos Shale, and (4) evaluation of the structural features on the Reservation as they may control sites of oil accumulation.« less

Lithostratigraphy and depositional environments of the Upper Jurassic Arab-C carbonate and associated evaporites in the Abqaiq Field, eastern Saudi Arabia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saner, S.; Abdulghani, W.M.

1995-03-01

Lithostratigraphy and depositional environment of the Arab-C carbonate in eastern Saudi Arabia were studied using cores and well logs from the Abqaiq oil field. A 275-m Upper Jurassic evaporite sequence occurs between the Sulaiy-Yamama (Thamama Group) and the Tuwaiq-Hanifa-Arab-D (Tuwaiq Group) carbonate sequences. Dolomite and limestone interbeds of 1-30 m in thickness within the evaporite sequence are continuous over long distances and have uniform thicknesses and log characteristics indicating an aggradational type of deposition. The lithologically heterogeneous Arab-C carbonate is the thickest interbed, reaching 26-30 m in thickness. Lithology types recognized in the Arab-C carbonate are (1) ooid bioclast grainstone,more » (2) oolite grainstone, (3) pellet grainstone, (4) pellet packstone, (5) skeletal wackestone, (6) mudstone, (7) anhydritic limestone, and (8) dolomite. The Arab-C carbonate has been divided into seven layers based on lithology and porosity variations. Four layers (1,3,5,7) are porous calcarenitic carbonates and the other three layers are nonporous.« less

Curated eutherian third party data gene data sets.

PubMed

Premzl, Marko

2016-03-01

The free available eutherian genomic sequence data sets advanced scientific field of genomics. Of note, future revisions of gene data sets were expected, due to incompleteness of public eutherian genomic sequence assemblies and potential genomic sequence errors. The eutherian comparative genomic analysis protocol was proposed as guidance in protection against potential genomic sequence errors in public eutherian genomic sequences. The protocol was applicable in updates of 7 major eutherian gene data sets, including 812 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets.

Uplift sequence of the Andes at 30°S: Insights from sedimentology and U/Pb dating of synorogenic deposits

NASA Astrophysics Data System (ADS)

Suriano, J.; Mardonez, D.; Mahoney, J. B.; Mescua, J. F.; Giambiagi, L. B.; Kimbrough, D.; Lossada, A.

2017-04-01

The South Central Andes at 30°S represent a key area to understand the Andes geodynamics as it is in the middle of the flat slab segment and all the morphotectonic units of the Central Andes are well developed. This work is focused in the proximal synorogenic deposits of the Western Precordillera, in the La Tranca valley, in order to unravel the uplift sequence of this belt. Nine facies associations were recognized; most of them represent piedmont facies with local provenance from Precordillera and were deposited in the wedge-top depozone, as is expected for proximal sinorogenic deposits. However there are intercalations of transference fluvial systems, which show mixed provenance indicating that Permo-Triassic igneous rocks were already exposed to the west (Frontal Cordillera). There are also lacustrine deposits which are interpreted as the result of damming by fault activity at east of the studied basin. Finally, two maximum depositional ages at ca. 11 Ma and 8 Ma of these deposits indicate that the onset of uplift of the Precordillera at 30°S is little older than 11 Ma. These data change two previous ideas about the evolution of the Precordillera: its uplift at 30° S is younger than proposed by previous works and it is nearly synchronous along strike.

Permian depositional history, Leach Mountains, northeastern Nevada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martindale, S.G.

1993-04-01

The 4,000 m thick Permian sequence in the Leach Mountains consists of carbonate rock, chert, terrigenous clastic rock and phosphatic rock. These rocks, in ascending order, comprise the Third Fork Fm., Badger Gulch Fm., Trapper Creek Fm., Grandeur Fm., Meade Peak Phosphatic Shale Tongue of the Phosphoria Fm., Murdock Mountain Fm. and Gerster Limestone. This sequence disconformably overlain by Triassic strata. Initial Permian deposition, represented by the late Wolfcampian to early Leonardian Third Fork Fm., was on a slope, at a water depth of about 50 m. Subsequently, a shallowing trend occurred during the early Leonardian to late Leonardian withmore » deposition of the Badger Gulch, Trapper Creek and Grandeur Fms. The Trapper Creek and Grandeur Fms. were deposited on the shelf, in very shallow subtidal to supratidal environments. The shelf persisted through the remainder of the Permian. In the late leonardian, the Meade Peak Tongue was deposited in very shallow subtidal and intertidal environments. A supratidal environment was re-established in latest Leonardian( ) to early Guadalupian with deposition of the lower Murdock Mountain Fm. The upper Murdock Mountain Fm. was deposited in very shallow subtidal to supratidal environments. Later during the early Guadalupian, intertidal to shallow subtidal deposition of the Gerster Limestone occurred. Angular phosphatic pebbles that were derived from phosphatic strata at the top of the Gerster Limestone are contained in the Triassic basal conglomerate. These pebbles indicate that the last Permian event was probably emergence and erosion of the top of the Gerster Limestone.« less

The effects of mannitol on the transport of ciprofloxacin across respiratory epithelia.

PubMed

Ong, Hui Xin; Traini, Daniela; Salama, Rania; Anderson, Sandra D; Daviskas, Evangelia; Young, Paul M

2013-08-05

Inhalation of antibiotics and mucolytics is the most important combination of inhaled drugs for chronic obstructive lung diseases and has become a standard part of treatment. However, it is yet to be determined whether the administration of a mucolytic has an effect on the transport rate of antibiotics across the airway epithelial cells. Consequently, the aim of this study was to investigate the effects of inhalation dry powder, specifically mannitol, on ciprofloxacin transport using a Calu-3 air-interface cell model. Transport studies of ciprofloxacin HCl were performed using different configurations including single spray-dried ciprofloxacin alone, co-spray-dried ciprofloxacin with mannitol, and deposition of mannitol prior to ciprofloxacin deposition. To understand the mechanism of transport and interactions between the drugs, pH measurements of apical surface liquid (ASL) and further transport studies were performed with ciprofloxacin base, with and without the presence of ion channel/transport inhibitors such as disodium cromoglycate and furosemide. Mannitol was found to delay absorption of ciprofloxacin HCl through the increase in ASL volume and subsequent reduction in pH. Conversely, ciprofloxacin base had a higher transport rate after mannitol deposition. This study clearly demonstrates that the deposition of mannitol prior to ciprofloxacin on the air-interface Calu-3 cell model has an effect on its transport rate. This was also dependent on the salt form of the drug and the timing and sequence of formulations administered.

Annual dynamics of halite precipitation in the Dead Sea: In situ observations and their geological implications

NASA Astrophysics Data System (ADS)

Sirota, Ido; enzel, Yehouda; Lensky, Nadav G.

2017-04-01

Layered halite sequences deposited in deep basins throughout the geological record. However, analogues of such sequences are commonly studied in sallow environments. Here we study active precipitation of halite layers from the only modern analog for deep, halite-precipitating basin, the hypersaline Dead Sea. In situ observations in the Dead Sea link seasonal thermohaline stratification, halite saturation, and the characteristics of the actively forming halite layers. The spatiotemporal evolution of halite precipitation in the Dead Sea was characterized by means of monthly observations of the i) lake thermohaline stratification (temperature, salinity, and density), ii) degree of halite saturation, and iii) textural evolution of the active halite deposits. We present the observed relationships between textural characteristics of layered halite deposits (i.e. grain size, consolidation, and roughness) and the degree of saturation, which in turn reflected the limnology and hydro-climatology. The lakefloor is divided into two principle environments: A deep, hypolimnetic and a shallow, epilimnetic lakefloor. In the deeper hypolimnetic lakefloor halite continuously precipitates with seasonal variations: (a) during summer, consolidated coarse halite crystals form rough surfaces under slight super-saturation. (b) During winter, unconsolidated, fine halite crystals form smooth seafloor deposits under high supersaturation. The observations also emphasize the thought regarding seasonal alternation of halite crystallization mechanism. The shallow epilimnetic lake floor is highly influenced by the seasonal temperature variations, and by intensive summer dissolution of part of the previous year's halite deposit which results in thin sequences with annual unconformities. This emphasizes the control of temperature seasonality on the precipitated halite layers characteristics. In addition, precipitation of halite in the hypolimnetic floor, on the expense of the dissolution of the epilimnetic floor, results in lateral focusing and thickening of halite deposit in the deeper part of the basin and thinning of the deposits in shallow marginal basins.

Paleocene-eocene lignite beds of southwest Alabama: Parasequence beds in highstand systems tracts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mancini, E.A.; Tew, B.H.; Carroll, R.E.

1993-09-01

In southwest Alabama, lignite beds are present in at least four stratigraphic intervals that span approximately 8 m.y. of geologic time. Lignite is found in the Paleocene Oak Hill Member and Coal Bluff Member of the Naheola Formation of the Midway Group and the Paleocene Tuscahoma Sand and the Eocene Hatchetigbee Formation of the Wilcox Group. Lignite beds range in thickness from 0.5 to 11 ft and consist of 32-53% moisture, 13-39% volatile matter, 4-36% fixed carbon, and 5-51% ash. These Paleocene and Eocene lignite beds occur as parasequence deposits in highstand systems tracts of four distinct third-order depositional sequences.more » The lignite beds are interpreted as strata within highstand systems tract parasequences that occur in mud-dominated regressive intervals. Lignite beds were deposited in coastal marsh and low-lying swamp environments as part of deltaic systems that prograded into southwestern Alabama from the west. As sediment was progressively delivered into the basin from these deltas, the effects of relative sea level rise during an individual cycle were overwhelmed, producing a net loss of accommodation and concomitant overall basinward progradation of the shoreline (regression). Small-scale fluctuations in water depth resulting from the interaction of eustasy, sediment yield, and subsidence led to cyclical flooding of the low-lying coastal marshes and swamps followed by periods of progradational and regression. Highstand systems tract deposition within a particular depositional sequence culminated with a relative sea level fall that resulted in a lowering of base level and an abrupt basinward shift in coastal onlap. Following sea level fall and the subsequent accumulation of the lowstand deposits, significant relative sea level rise resulted in the marine inundation of the area previously occupied by coastal marshes and swamps and deposition of the transgressive systems tract of the overlying sequence.« less

The Mount Edgecumbe tephra deposits, a marker horizon in southeastern Alaska near the Pleistocene-Holocene boundary

USGS Publications Warehouse

Riehle, J.R.; Mann, D.H.; Peteet, D.M.; Engstrom, D.R.; Brew, D.A.; Meyer, C.E.

1992-01-01

Late Pleistocene tephra deposits found from Sitka to Juneau and Lituya Bay are assigned to a source at the Mount Edgecumbe volcanic field, based on similarity of glass compositions to nearvent deposits and on thinning away from Kruzof Island. The sequence of near-vent layers is basaltic andesite and andesite at the base, rhyolite, and mixed dacite and rhyolite on top. The only breaks in the tephra sequence are two 1-mm-thick silt partings in a lake-sediment core, indicating a depositional interval from basaltic andesite to dacite of no more than about a millennium. Tephra deposits at sites >30 km from the vent are solely dacite and rhyolite and are 10,600 to 11,400 14C yr old based on interpretation of 18 radiocarbon ages, including 5 by accelerator mass spectrometry (AMS). Basaltic andesite and andesite deposits nearer the vent are as much as 12,000 yr old. Discrepancy among radiocarbon ages of upland tephra deposits provisionally correlated as the same grainfall is resolvable within ??2 ?? of analytical uncertainty. Comparison of bulk and AMS ages in one sediment core indicates a systematic bias of +600 to +1100 yr for the bulk ages; correlation of tephra deposits among upland and lacustrine sites implies an additional discrepancy of 200-400 yr between upland (relatively too young) and lacustrine ages. In any case, the Mount Edgecumbe tephra deposits are a widespread, latest Pleistocene stratigraphic marker that serves to emphasize the uncertainty in dating biogenic material from southeastern Alaska. ?? 1992.

Stratigraphic architecture and depositional history of lower Miocene, Planulina Zone, Southern Louisiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gates, B.C.; Galloway, W.E.

1988-01-01

The Planulina zone is a wedge of clastic sediment positioned between the Anahuac shale below and the Oakville sandstone interval above. Planulna sediments were deposited on an erosional surface, during a general rise in the sea level, and formed a retrogradational wedge. Within the study area, the Planulina zone consists of two large depositional complexes: the Mud Lake complex in west Cameron Parish, Louisiana, and the East Cameron complex in east Cameron Parish. The lowermost depositional sequence in the East Cameron complex is preserved in a network of submarine canyons that were eroded into the upper slope. Framework sands weremore » deposited in channel systems confined to the axis of the canyons, and the sands are encased in marine shale containing benthonic foraminifera indicative of an upper to middle slope paleoenvironment. Two younger depositional sequences overlie the submarine canyon facies and were deposited by deltaic systems that prograded basinward. A zone of expansion extends east to west through the Planulina interval and is named the ''Planulina flexure.'' The flexure is a large fault located at the relict shelf edge and soles out downdip inn the Anahuac shale. Several thousand feet of sediment downthrown on the flexure is equivalent to several hundred feet upthrown, and the flexure represented the boundary dividing updip deltaic processes from downdip slope processes during the beginning of Planulina deposition. The Planulina depositional history and stratigraphic architecture are directly related to the displacement along the flexure and the structural deformation of the underlying Anahuac shale.« less

Isotope geochemistry of mercury in source rocks, mineral deposits and spring deposits of the California Coast Ranges, USA

NASA Astrophysics Data System (ADS)

Smith, Christopher N.; Kesler, Stephen E.; Blum, Joel D.; Rytuba, James J.

2008-05-01

We present here the first study of the isotopic composition of mercury in rocks, ore deposits, and active spring deposits from the California Coast Ranges, a part of Earth's crust with unusually extensive evidence of mercury mobility and enrichment. The Franciscan Complex and Great Valley Sequence, which form the bedrock in the California Coast Ranges, are intruded and overlain by Tertiary volcanic rocks including the Clear Lake Volcanic Sequence. These rocks contain two types of mercury deposits, hot-spring deposits that form at shallow depths (< 300 m) and silica-carbonate deposits that extend to depths of 1000 m. Active springs and geothermal areas continue to precipitate Hg and Au and are modern analogues to the fossil hydrothermal systems preserved in the ore deposits. The Franciscan Complex and Great Valley Sequence contain clastic sedimentary rocks with higher concentrations of mercury than volcanic rocks of the Clear Lake Volcanic Field. Mean mercury isotopic compositions ( δ202Hg) for all three rock units are similar, although the range of values in Franciscan Complex rocks is greater than in either Great Valley or Clear Lake rocks. Hot spring and silica-carbonate mercury deposits have similar average mercury isotopic compositions that are indistinguishable from averages for the three rock units, although δ202Hg values for the mercury deposits have a greater variance than the country rocks. Precipitates from spring and geothermal waters in the area have similarly large variance and a mean δ202Hg value that is significantly lower than the ore deposits and rocks. These observations indicate that there is little or no isotopic fractionation (< ± 0.5‰) during release of mercury from its source rocks into hydrothermal solutions. Isotopic fractionation does appear to take place during transport and concentration of mercury in deposits, however, especially in their uppermost parts. Boiling of hydrothermal fluids, separation of a mercury-bearing CO 2 vapor or reduction and volatilization of Hg (0) in the near-surface environment are likely the most important processes causing the observed Hg isotope fractionation. This should result in the release of mercury with low δ202Hg values into the atmosphere from the top of these hydrothermal systems. Estimates of mass balance suggest that residual Hg reservoirs are not measurably enriched in heavy Hg isotopes as a result of this process because only a small amount of Hg (< 4%) leaves actively ore-forming systems.

Isotope geochemistry of mercury in source rocks, mineral deposits and spring deposits of the California Coast Ranges, USA

USGS Publications Warehouse

Smith, C.N.; Kesler, S.E.; Blum, J.D.; Rytuba, J.J.

2008-01-01

We present here the first study of the isotopic composition of mercury in rocks, ore deposits, and active spring deposits from the California Coast Ranges, a part of Earth's crust with unusually extensive evidence of mercury mobility and enrichment. The Franciscan Complex and Great Valley Sequence, which form the bedrock in the California Coast Ranges, are intruded and overlain by Tertiary volcanic rocks including the Clear Lake Volcanic Sequence. These rocks contain two types of mercury deposits, hot-spring deposits that form at shallow depths (< 300??m) and silica-carbonate deposits that extend to depths of 1000??m. Active springs and geothermal areas continue to precipitate Hg and Au and are modern analogues to the fossil hydrothermal systems preserved in the ore deposits. The Franciscan Complex and Great Valley Sequence contain clastic sedimentary rocks with higher concentrations of mercury than volcanic rocks of the Clear Lake Volcanic Field. Mean mercury isotopic compositions (??202Hg) for all three rock units are similar, although the range of values in Franciscan Complex rocks is greater than in either Great Valley or Clear Lake rocks. Hot spring and silica-carbonate mercury deposits have similar average mercury isotopic compositions that are indistinguishable from averages for the three rock units, although ??202Hg values for the mercury deposits have a greater variance than the country rocks. Precipitates from spring and geothermal waters in the area have similarly large variance and a mean ??202Hg value that is significantly lower than the ore deposits and rocks. These observations indicate that there is little or no isotopic fractionation (< ?? 0.5???) during release of mercury from its source rocks into hydrothermal solutions. Isotopic fractionation does appear to take place during transport and concentration of mercury in deposits, however, especially in their uppermost parts. Boiling of hydrothermal fluids, separation of a mercury-bearing CO2 vapor or reduction and volatilization of Hg(0) in the near-surface environment are likely the most important processes causing the observed Hg isotope fractionation. This should result in the release of mercury with low ??202Hg values into the atmosphere from the top of these hydrothermal systems. Estimates of mass balance suggest that residual Hg reservoirs are not measurably enriched in heavy Hg isotopes as a result of this process because only a small amount of Hg (< 4%) leaves actively ore-forming systems. ?? 2008 Elsevier B.V. All rights reserved.

Late Cretaceous base level lowering in Campanian and Maastrichtian depositional sequences, Kure Beach, North Carolina

USGS Publications Warehouse

Harris, W.B.; ,

2006-01-01

Campanian through Maastrichtian mixed carbonate and siliciclastic sediments in a 422 m continuous core drilled at Kure Beach, NC provide a record of sea-level change. Based on lithology and stratigraphy, depositional sequences are defined, and calcareous nannofossil zones and 87Sr/86Sr ratios and corresponding ages using the LOWESS Table determined. Campanian and Maastrichtian sediments comprise six depositional sequences. The oldest is Tar Heel 1 and contains calcareous nannofossils that indicate assignment to the upper part of Zones CC18a, CC18c and the lower part of CC19. 87Sr/86 Sr ratios indicate ages from 83.2 to 80.0 Ma or lower Campanian. Tar Heel II contains calcareous nannofossils that indicate assignment to the upper part of Zone CC 19 and CC20. 87Sr/86Sr ratios indicate ages from 78.0 to 76.3 Ma or middle Campanian. Donoho Creek I and II are thin and contain calcareous nannofossils referable to upper Zone CC21 and Zone CC22, and to CC23, respectively. The top of Donoho Creek II marks the Campanian-Maastrichtian boundary. Donoho Creek I 87Sr/86Sr ratios cluster into two groups, and provide ages from 78.0 to 76.2 Ma and 73.7 to 72.3 Ma, respectively. 87Sr/86Sr ratios in Donoho Creek II indicate ages from 71.4 to 69.6 Ma. Two Maastrichtian sequences are present; the lowermost Peedee I contains calcareous nannofossils that place it in Zones CC25a and CC25b. 87Sr/86Sr r ratios indicate an age from 69.3 to 66.9 Ma or late Maastrichtian. Peedee II is assigned to calcareous nannofossil Zone CC26a. 87Sr/86Sr ratios indicate ages from 66.4 to 65.2 Ma or late Maastrichtian. The four Campanian sequences correlate to three depositional sequences in New Jersey; the sequence boundary between upper Campanian Donoho Creek I and Donoho Creek II is not recognized in New Jersey. This boundary is interpreted to result from Gulf Stream impingement and subsequent erosion on the outer shelf. The two Maastrichtian sequences recognized in the Kure Beach core correlate to the two identified Maastrichtian sequences in New Jersey. These data support base-level lowering of sea-level during the Campanian-Maastrichtian, and suggest that the western margin of the North Atlantic may contain one of the best Late Cretaceous records of sea-level change.

A Study of the Magnetic Fingerprint of Tsunami Induced Deposits in the Ixtapa-Zihuatanejo Area (Western Mexico)

NASA Astrophysics Data System (ADS)

Goguitchaichrili, A.; Ramirez-Herrera, M.; Calvo-Rathert, M.; Aguilar, B.; Carrancho, Alonso; Morales, J.; Caballero, C. I.; Bautista, F.

2013-05-01

The Pacific coast of Mexico has repeatedly been exposed to destructive tsunamis. Recent studies have shown that rock-magnetic methods can be a promising approach for identification of tsunami or storm induced deposits. We present new rock-magnetic and anisotropy of magnetic susceptibility results to try to distinguish tsunami deposits in the Ixtapa-Zihuatanejo area (Western Mexico). The sampled, 80 cm deep sequence is characterised by the presence of two anomalous sand beds within fine-grained coastal deposits. The first lower lying sand bed is probably associated with the 14th March 1979 Petatlán earthquake (MW = 7.6) while the second one was originated by the September 21st 1985 Mexico earthquake (MW = 8.1). Rock magnetic experiments have shown significant variations within the analysed sequence. Thermomagnetic curves reveal two types of behaviour: In the upper part of the sequence, after the occurrence of the first tsunami and in the lower part of the sequence, during that event and below. Analysis of hysteresis parameter ratios in a Day-plot also allows distinguishing two kinds of behaviour. The samples associated to the second tsunami plot in the PSD area, while specimens associated to the first tsunami and the time between both tsunamis display a very different trend which can be ascribed to the production of a considerable amount of superparamagnetic grains which might be due to pedogenic processes after the first tsunami. The studied profile is characterised by a sedimentary fabric with almost vertical minimum principal susceptibilities. The maximum susceptibility axis shows a declination angle D = 27, suggesting a NNE flow direction which is equal for both tsunamis and normal currents. The standard AMS parameters display a significant enhancement within the transitional zone between both tsunamis. The study of rock-magnetic parameters may represent a useful tool for the identification and understanding of tsunami deposits.

Geology and mineral deposits of the Hekimhan-Hasancelebi iron district, Turkey

USGS Publications Warehouse

Jacobson, Herbert S.; Kendiro'glu, Zeki; ,; Celil, Bogaz; ,; Onder, Osman; Gurel, Nafis

1972-01-01

An area of 210 sq km was investigated in the Hekimhan-Hasancelebi district. of central Turkey as part of the Maden Tetkik ve Arama Institusu(MTA)-U. S. Geological Survey(USGS) mineral exploration and training project to explore for iron deposits and to provide on-.the-job training for MTA geologists. The rocks of the area are Cretaceous and Tertiary sedimentary and volcanic rocks intruded by syenite and a serpentinized mafic and ultramafic complex and overlain unconformably by late .Tertiary basalt. The base of the section is a thick mafic volcanic-sedimentary sequence with diverse rocks that include conglomerate, sandstone, shale, tuff, limestone, and basalt. The upper part of the sequence is metasomatized near syenite contacts. The sequence is conformably overlain by trachyte and unconformably overlain by massive limestone. Overlying the limestone is a Tertiary sedimentary sequence which is dominantly conglomerate and sandstone with local limestone and volcanic rocks. This series is in turn overlain by olivine basalt. Mineral deposits are associated with the two types of intrusive rocks. Hematite-magnetite in the Karakuz mine area and in the Bahcedami-Hasancelebi area is related to the syenite, and siderite in the Deveci mine area is possibly related to the mafic-ultramafic rocks. Significant iron resources are found, only in the Karakuz and Deveci areas. In the Karakuz area disseminations, veins, and replacements consisting of hematite and magnetite are present. Most of the material is low grade. In the Deveci mine area a large deposit of siderite apparently is a replacement of carbonate beds adjacent to serpentinized igneous rock. The upper part of the siderite deposit is weathered and enriched to a mixture of iron and manganese oxides of direct shipping ore grade. Additional investigation of both the Karakuz and .Deveci mine areas is recommended including: 1. A detailed gravity and magnetic survey of part of the Karakuz area. 2. Diamond drilling at both the Karakuz and Deveci areas.

Late-kinematic timing of orogenic gold deposits and significance for computer-based exploration techniques with emphasis on the Yilgarn Block, Western Australia

USGS Publications Warehouse

Groves, D.I.; Goldfarb, R.J.; Knox-Robinson, C. M.; Ojala, J.; Gardoll, S.; Yun, G.Y.; Holyland, P.

2000-01-01

Orogenic gold deposits are a widespread coherent group of epigenetic ore deposits that are sited in accretionary or collisional orogens. They formed over a large crustal-depth range from deep-seated low-salinity H2O-CO2 + CH4 + N2 ore fluids and with Au transported as thio-complexes. Regional structures provide the main control on deposit distribution. In many terranes, first-order faults or shear zones appear to have controlled regional fluid flow, with greatest ore-fluid fluxes in, and adjacent to, lower-order faults, shear zones and/or large folds. Highly competent and/or chemically reactive rocks are the most common hosts to the larger deposits. Focusing of supralithostatic ore fluids into dilatant zones appears to occur late during the evolutionary history of the host terranes, normally within D3 or D4 in a D1-D4 deformation sequence. Reactivation of suitably oriented pre-existing structures during a change in far-field stress orientation is a factor common to many deposits, and repeated reactivation may account for multiple mineralization episodes in some larger deposits. Absolute robust ages of mineralization support their late-kinematic timing, and, in general, suggest that deposits formed diachronously towards the end of the 100 to 200 m.y. long evolutionary history of hosting orogens. For example, in the Yilgarn Block, a region specifically emphasised in this study, orogenic gold deposits formed in the time interval between 40 and 90 m.y., with most about 60 to 70 m.y., after the youngest widespread basic-ultrabasic volcanism and towards the end of felsic magmatism. The late timing of orogenic gold deposits is pivotal to geologically-based exploration methodologies. This is because the present structural geometries of: (i) the deposits, (ii) the hosting goldfields, and (iii) the enclosing terranes are all essentially similar to those during gold mineralization, at least in their relative position to each other. Thus, interpretation of geological maps and cross-sections and three-dimensional models can be used to accurately simulate the physical conditions that existed at the time of ore deposition. It is particularly significant that the deposits are commonly related to repetitive and predictable geometries, such as structural heterogeneities within or adjacent to first-order structures, around rigid granitoid bodies, or in specific "locked-up" fold-thrust structures. Importantly, the two giant greenstone-hosted goldfields, Kalgoorlie and Timmins, show a remarkably similar geometry at the regional scale. Computer-based stress mapping and GIS-based prospectivity mapping are two computer-based quantitative methodologies that can utilize and take advantage of the late timing aspect of this deposit type to provide important geological aids in exploration, both in broad regions and more localized goldfields. Both require an accurate and consistent solid geology map, stress mapping requires knowledge of the far-field stresses during mineralization, and the empirical prospectivity mapping requires data from a significant number of known deposits in the terrane. The Kalgoorlie Terrane, in the Yilgarn Block, meets these criteria, and illustrates the potential of these methodologies in the exploration for orogenic gold deposits. Low minimum stress anomalies, interpreted to represent dilational zones during gold-related deformation, coincide well with the positions of known goldfields rather than individual gold deposits in the terrane, and there are additional as-yet unexplained anomalies. The prospectivity analysis confirms that predictable and repetitive factors controlling the siting of deposits are: (i) proximity to, and orientation and curvature of, granitoid-greenstone contacts, (ii) proximity to segments of crustal faults which strike in a preferred direction, (iii) proximity to specific lithological contacts which have similar preferred strike, (iv) proximity to anticlinal structures, and (v) the presence of preferred

Depositional sequences and facies in the Torok Formation, National Petroleum Reserve, Alaska (NPRA)

USGS Publications Warehouse

Houseknecht, David W.; Schenk, Christopher J.

2002-01-01

Brookian turbidites (Cretaceous through Tertiary) have become oil exploration objectives on the NorthSlope of Alaska during the past decade, and it is likely this focus will extend into the National Petroleum Reserve-Alaska (NPRA). A regional grid of 2-D seismic data, sparse well control, and field work in the Brooks Range foothills provide constraints for an ongoing effort to establish a sequence stratigraphic framework for Brookian turbidites in the Torok Formation across NPRA. The Torok Formation and overlying Nanushuk Formation (both mostly Albian) display the overall seismic geometry of bottomset-clinoform-topset strata indicating northeastward migration of a shelf margin. Within bottomset and clinoform strata of the Torok, depositional sequences have been identified that represent four distinct phases of shelf-margin sedimentation. (1) Regression, representing low relative sea level, is characterized by the development of an erosional surface on the shelf and upper slope, and the deposition of turbidite channel deposits on the middle to lower slope and submarine fan deposits at the base of slope. These deposits constitute a lowstand systems tract (LST). (2) Transgression, representing rising relative sea level, is characterized by the deposition of a mudstone drape on the basin floor, slope, and outer shelf. This drape comprises relatively condensed facies that constitute a transgressive systems tract (TST). (3) Aggradation, representing high relative sea level, is characterized by the deposition of relatively thick strata on the outer shelf and moderately thick mudstones on the slope. (4) Progradation, also representing high relative sea level, is characterized by the deposition of relatively thin strata on the outer shelf and very thick mudstones on the slope. Together, deposits of the aggradation and progradation phases constitute a highstand systems tract (HST). Large scale geometries of Torok strata vary across the Colville basin. In southern NPRA, high rates of subsidence accommodated the deposition of a "foredeep clinoform wedge" that contains a high proportion of sand-rich LST deposits. In northern NPRA, lower rates of subsidence favored the accumulation of mud-rich HST deposits. The most favorable stratigraphic trapping geometries in the Torok Formation occur where amalgamated sandstones deposited in turbidite channels incised on the mid- to lower-slope and on the proximal parts of submarine fans during regression (LSTs) are capped by relatively condensed mudstone facies deposited during transgression (TSTs). Common successions observed in Torok cores include a spectrum of slope and turbidite facies. Upper slope facies comprise laminated mudstones and siltstones that locally display evidence of slumping, sliding, and chaotic failure. Lower slope facies comprise heterolithic turbidites at some locations and interlaminated mudstones and thin, very fine-grained sandstones at others. Torok turbidites include amalgamated sandstones deposited in channel systems as well as thin-bedded, widespread sandstones deposited by unconfined flows on lobes or in channel overbank settings. These turbidite facies likely occur in both channel-lobe systems and slope apron systems within the Torok.

The Bouma Sequence and the turbidite mind set

NASA Astrophysics Data System (ADS)

Shanmugam, G.

1997-11-01

Conventionally, the Bouma Sequence [Bouma, A.H., 1962. Sedimentology of some Flysch Deposits: A Graphic Approach to Facies Interpretation. Elsevier, Amsterdam, 168 pp.], composed of T a, T b, T c, T d, and T e divisions, is interpreted to be the product of a turbidity current. However, recent core and outcrop studies show that the complete and partial Bouma sequences can also be interpreted to be deposits formed by processes other than turbidity currents, such as sandy debris flows and bottom-current reworking. Many published examples of turbidites, most of them hydrocarbon-bearing sands, in the North Sea, the Norwegian Sea, offshore Nigeria, offshore Gabon, Gulf of Mexico, and the Ouachita Mountains, are being reinterpreted by the present author as dominantly deposits of sandy debris flows and bottom-current reworking with only a minor percentage of true turbidites (i.e., deposits of turbidity currents with fluidal or Newtonian rheology in which sediment is suspended by fluid turbulence). This reinterpretation is based on detailed description of 21,000 ft (6402 m) of conventional cores and 1200 ft (365 m) of outcrop sections. The predominance of interpreted turbidites in these areas by other workers can be attributed to the following: (1) loose applications of turbidity-current concepts without regard for fluid rheology, flow state, and sediment-support mechanism that result in a category of 'turbidity currents' that includes debris flows and bottom currents; (2) field description of deep-water sands using the Bouma Sequence (an interpretive model) that invariably leads to a model-driven turbidite interpretation; (3) the prevailing turbidite mind set that subconsciously forces one to routinely interpret most deep-water sands as some kind of turbidites; (4) the use of our inability to interpret transport mechanism from the depositional record as an excuse for assuming deep-water sands as deposits of turbidity currents; (5) the flawed concept of high-density turbidity currents that allows room for interpreting debris-flow deposits as turbidites; (6) the flawed comparison of subaerial river currents (fluid-gravity flows dominated by bed-load transport) with subaqueous turbidity currents (sediment-gravity flows dominated by suspended load transport) that results in misinterpreting ungraded or parallel-stratified deep-sea deposits as turbidites; and (7) the attraction to use obsolete submarine-fan models with channels and lobes that require a turbidite interpretation. Although the turbidite paradigm is alive and well for now, the turbidites themselves are becoming an endangered facies!

Paleovalley systems: Insights from Quaternary analogs and experiments

NASA Astrophysics Data System (ADS)

Blum, M.; Martin, J.; Milliken, K.; Garvin, M.

2013-01-01

Ancient fluvial valley systems are long recognized as important features in the stratigraphic record, but emerged as a specific focus of attention with publication of first-generation sequence-stratigraphic concepts. This paper reviews current understanding of paleovalley systems from the perspective of Quaternary analogs and experimental studies. Paleovalley systems can include distinct mixed bedrock-alluvial, coastal-plain, and cross-shelf segments. Mixed bedrock-alluvial segments are long-lived, cut across bedrock of significantly older age, and have an overall degradational architecture. By contrast, coastal-plain and cross-shelf segments are non-equilibrium responses to high-frequency cycles of relative sea-level change: most coastal-plain and cross-shelf segments form as a geometric response to relative sea-level fall, as river systems cut through coastal-plain and inner shelf clinothems, and extend basinward to track the shoreline. After incision and cross-shelf extension, lateral channel migration and contemporaneous channel-belt deposition creates a valley-scale feature. Coastal-plain and cross-shelf paleovalley widths are set by the number of channel-belt sandbodies deposited during this time. Paleovalley systems play a key role in source-to-sink sediment routing. Early views included the model of incision and complete sediment bypass in response to relative sea-level fall. However, this model does not stand up to empirical, theoretical, or experimental scrutiny. Instead, there is a complex dynamic between incision, deposition, and sediment export from an evolving valley: periods of incision correspond with sediment export minima, whereas periods of lateral migration and channel-belt construction result in increased flux to the river mouth. Sediment export from evolving valleys, and merging of drainages during cross-shelf transit, play key roles in sediment transfer to the shelf-margin and genetically-linked slope to basin-floor systems. Connection between the river mouth and the shelf margin likely occurs for different periods of time depending on gradient of the river and shelf, as well as amplitude of high-frequency sea-level changes. Late Quaternary analogs and experimental studies provide an alternative sequence-stratigraphic interpretation for paleovalley systems. In coastal-plain paleovalleys, basal valley-fill surfaces meet criteria for an unconformity and a classically-defined sequence boundary: however, this surface is mostly everywhere of the same age as overlying fluvial deposits, and does not correspond to a long period of incision and sediment bypass. In cross-shelf paleovalleys, the basal contact between fluvial and deltaic or shoreface deposits is commonly interpreted as a sequence boundary, but is not an unconformity characterized by incision and sediment bypass. Instead, this surface is a facies contact that separates genetically-related fluvial and deltaic strata: the surface that correlates to the basal valley-fill surface within the coastal-plain paleovalley dips below cross-shelf prograding deltaic and/or shoreface strata, which are fed by deposition within the evolving valley itself, and should be the downlap surface. Many issues deserve attention in the future. We have stressed understanding the inherent scales and physical processes that operate during the formation and evolution of paleovalley systems. We also suggest the relative roles of allogenic forcing vs. autogenic dynamics, and the potential significance of high-frequency isostatic adjustments should be topics for future discussion.

Metazen – metadata capture for metagenomes

PubMed Central

2014-01-01

Background As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusions Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility. PMID:25780508

Metazen - metadata capture for metagenomes.

PubMed

Bischof, Jared; Harrison, Travis; Paczian, Tobias; Glass, Elizabeth; Wilke, Andreas; Meyer, Folker

2014-01-01

As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.

Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

PubMed

Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

2015-05-25

The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

Shoreline deposits and diagenesis resulting from two Late Pleistocene highstands near +5 and +6 metres, Durban, South Africa

USGS Publications Warehouse

Cooper, J.A.G.; Flores, R.M.

1991-01-01

In exposures of Pleistocene rocks on the east coast of South Africa, eight sedimentary facies were distinguished on the basis of petrology, grain size, internal structures and field relationships. These are interpreted as deposits of surf zone, breaker zone, swash zone, backbeach, boulder beach and dune environments. Three phases of deposition and diagenesis are recognized. As a result of the stabilising effect of pre-existing coastal facies, the deposits from successive sea level stands are stacked vertically in a narrow coast-normal strip. Early cementation prevented erosion of the deposits during subsequent transgressions. Deposition of subsequent facies took place on an existing coastal dune (Facies 1). A terrace was cut into this dune at a sea level 4.5 to 5 m above present. At this sea level, clastic shoreline sediments were deposited which make up the main sedimentary sequence exposed (Facies 2-7). The steep swash zone, coarse grain size, and comparison with modern conditions in the study area indicate clastic deposition on a high-energy, wave-dominated, microtidal coastline. Vertical stacking of progressively shallower water facies indicates progradation associated with slightly regressive conditions, prior to stranding of the succession above sea level. During a subsequent transgression to 5.5 or 6 m above present sea level, a second terrace was cut across the existing facies, which by then were partly lithified. A boulder beach (Facies 8) deposited on this terrace is indicative of high wave energy and a rocky coastline, formed by existing cemented coastal facies. Comparison with dated deposits from other parts of the South African coast suggest a Late Pleistocene age for Facies 2-8. Deposition was terminated by subsequent regression and continuing low sea levels during the remainder of the Pleistocene. Cementation of the facies took place almost entirely by carbonate precipitation. The presence of isopachous fibrous cements suggests early cementation of Facies 1, 2, 3 and 4 under marine conditions, initially as aragonite which has since inverted to calcite. Facies 5, 6 and 7 are cemented only by equant calcite spar, evidence of cementation in the meteoric phreatic and vadose zones. Lowering of the water table during regression caused the remaining pore space in Facies 1, 2, 3 and 4 to be filled with equant calcite spar. Decementation in a 130 cm wide zone is attributed to water table shifts associated with the later transgression which deposited Facies 8. The vertical stacking of the two depositional sequences may be attributed to rapid cementation of Facies 2, 3, 4, 5, 6 and 7 under humid, subtropical conditions. This lithified sequence then acted as a focus for deposition of coarse-grained shoreline facies (Facies 8) during the subsequent transgression. ?? 1991.

Sequence Stratigraphy of the Dakota Sandstone, Eastern San Juan Basin, New Mexico, and its Relationship to Reservoir Compartmentalization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varney, Peter J.

2002-04-23

This research established the Dakota-outcrop sequence stratigraphy in part of the eastern San Juan Basin, New Mexico, and relates reservoir quality lithologies in depositional sequences to structure and reservoir compartmentalization in the South Lindrith Field area. The result was a predictive tool that will help guide further exploration and development.

Sedimentary development and correlation of Late Quaternary terraces in the Kyrenia Range, northern Cyprus, using a combination of sedimentology and optical luminescence data

NASA Astrophysics Data System (ADS)

Palamakumbura, Romesh N.; Robertson, Alastair H. F.; Kinnaird, Tim C.; Sanderson, David C. W.

2016-01-01

This study focuses on the younger of a series of Quaternary terraces along the flanks of the Kyrenia Range in northern Cyprus, specifically the Kyrenia (Girne) and the Koupia terraces. The Kyrenia (Girne) terrace is tentatively correlated with oxygen isotope stage 5 (125 Ka), and the Koupia terrace with oxygen isotope stage 3 (<50 Ka). Along the northern flank of the range, the Kyrenia (Girne) terrace deposits (5-20 m above modern sea level) typically begin with a basal lag conglomerate and then pass upwards into shallow-marine calcarenites and then into variable aeolianites, paleosols and fluvial deposits (up to 20 m thick). In contrast, the Koupia terrace (<2 m above modern sea level) consists of aeolianites and shallow-marine calcarenites (up to 8 m thick). The equivalent deposits along the southern flank of the range are entirely non-marine fluvial mud, sands and conglomerates. The marine to continental terrace systems can be tentatively correlated based on mapping, height above modern sea level and sedimentary facies. However, variable preservation and patchy exposure require such correlations to be independently tested. To achieve this, a portable optically stimulated luminescence (OSL) reader was used to determine the luminescence characteristics of the two terrace systems. Luminescence profiles show major differences in luminescence characteristics between the two terrace depositional systems, which can be related to sedimentary processes, provenance and age. These features allow sections in different areas to be effectively correlated. Individual sections show luminescence properties that are generally consistent with an expected up-sequence decrease in age. However, the younger Koupia terrace deposits show higher luminescence intensities compared with the older Kyrenia (Girne) terrace deposits. This can be explained by multiple phases of reworking of the Kyrenia (Girne) terrace deposits, which changed the luminescence characteristics of the sediment. The use of the portable OSL reader is therefore an effective means of correlating Late Quaternary terrace deposits in northern Cyprus and probably also elsewhere.

Total and regional deposition of inhaled aerosols in supine healthy subjects and subjects with mild-to-moderate COPD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darquenne, Chantal; Lamm, Wayne J.; Fine, Janelle M.

Despite substantial development of sophisticated subject-specific computational models of aerosol transport and deposition in human lungs, experimental validation of predic- tions from these new models is sparse. We collected aerosol retention and exhalation profiles in seven healthy volunteers and six subjects with mild-to-moderate COPD (FEV1 ¼ 50–80%predicted) in the supine posture. Total deposition was measured during continuous breathing of 1 and 2.9 mm-diameter particles (tidal volume of 1 L, flow rate of 0.3 L/s and 0.75 L/s). Bolus inhalations of 1 mm particles were performed to penetration volumes of 200, 500 and 800 mL (flow rate of 0.5 L/s). Aerosolmore » bolus dispersion (H), deposition, and mode shift (MS) were calculated from these data. There was no significant difference in total deposition between healthy subjects and those with COPD. Total deposition increased with increasing particle size and also with increasing flow rate. Similarly, there was no significant difference in aerosol bolus deposition between subject groups. Yet, the rate of increase in dispersion and of decrease in MS with increasing penetration volume was higher in subjects with COPD than in healthy volunteers (H: 0.79870.205 vs. 0.52770.122 mL/mL, p¼ 0.01; MS: - 0.27170.129 vs. - 0.145 70.076 mL/mL, p¼ 0.05) indicating larger ventilation inhomogeneities (based on H) and increased flow sequencing (based on MS) in the COPD than in the healthy group. In conclusion, in the supine posture, deposition appears to lack sensitivity for assessing the effect of lung morphology and/or ventilation distribution alteration induced by mild-to- moderate lung disease on the fate of inhaled aerosols. However, other parameters such as aerosol bolus dispersion and mode shift may be more sensitive parameters for evaluating models of lungs with moderate disease.« less

Trace fossils, storm beds, and depositional sequences in a clastic shelf setting, Upper Cretaceous of Utah

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frey, R.W.

In Coal Creek Canyon, Utah the Spring Canyon Member of the Blackhawk Formation is divisible into four regressive hemicycles of deposition each representing the downdip part of a nearshore-to-offshore sequence punctuated locally by hummocky cross-stratification. Bedding units span middle shoreface to lower offshore shelf lithofacies, the latter corresponding to a transgressive intertongue of the Mancos Shale. Trace fossil assemblage include 21 ichnospecies distributed among 17 ichnogenera: Ancorichnus, Aulichnites, Chondrites, Cylindrichnus, Ophiomorpha, Palaeophycus, Phoebichnus, Planolites, Rosselia, Schaubcylindrichnus, Scolicia, Skolithos, Taenidium, Teichichnus, Terebellina, Thalassinoides, and Uchirites. Distal deposits are typified by bioturbate textures; Cylindrichnus concentricus, Palaeophycus heberti, and Rosselia socialis otherwise aremore » prevalent throughout the lithofacies suite. Ophiomorpha irregulaire and Schaubcylindrichnus are most common in middle shoreface beds and Chondrites sp. in upper offshore beds; O. nodosa and O. annulata also are common in this part of the sequence. Planolites-type feeding burrows must have been predominant in many depositional settings but now remain inconspicuous and poorly preserved. Despite gradients in environmental distributions of trace fossils, all resident ichnofaunas are referable to the archetypical Cruziana ichnocoenose. Ichnofaunas in hummocky beds mainly represent either an archetypical Skolithos ichnocoenose or mixed Skolithos-Cruziana ichnocoenose. These post-storm ichnocoenoses correspond primarily to a sere of opportunistic pioneers and secondarily to ensuing seres of resilient resident populations. Differences in ichnofacies also are related to differences in post-storm rates of deposition: the slower the rate of sediment accumulation, the greater the degree of overprinting by burrows from subsequent seres or equilibrium communities.« less

Numeric stratigraphic modeling: Testing sequence Numeric stratigraphic modeling: Testing sequence stratigraphic concepts using high resolution geologic examples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armentrout, J.M.; Smith-Rouch, L.S.; Bowman, S.A.

1996-08-01

Numeric simulations based on integrated data sets enhance our understanding of depositional geometry and facilitate quantification of depositional processes. Numeric values tested against well-constrained geologic data sets can then be used in iterations testing each variable, and in predicting lithofacies distributions under various depositional scenarios using the principles of sequence stratigraphic analysis. The stratigraphic modeling software provides a broad spectrum of techniques for modeling and testing elements of the petroleum system. Using well-constrained geologic examples, variations in depositional geometry and lithofacies distributions between different tectonic settings (passive vs. active margin) and climate regimes (hothouse vs. icehouse) can provide insight tomore » potential source rock and reservoir rock distribution, maturation timing, migration pathways, and trap formation. Two data sets are used to illustrate such variations: both include a seismic reflection profile calibrated by multiple wells. The first is a Pennsylvanian mixed carbonate-siliciclastic system in the Paradox basin, and the second a Pliocene-Pleistocene siliciclastic system in the Gulf of Mexico. Numeric simulations result in geometry and facies distributions consistent with those interpreted using the integrated stratigraphic analysis of the calibrated seismic profiles. An exception occurs in the Gulf of Mexico study where the simulated sediment thickness from 3.8 to 1.6 Ma within an upper slope minibasin was less than that mapped using a regional seismic grid. Regional depositional patterns demonstrate that this extra thickness was probably sourced from out of the plane of the modeled transect, illustrating the necessity for three-dimensional constraints on two-dimensional modeling.« less

Stratigraphy of a proposed wind farm site southeast of Block Island: Utilization of borehole samples, downhole logging, and seismic profiles

NASA Astrophysics Data System (ADS)

Sheldon, Dane P. H.

Seismic stratigraphy, sedimentology, lithostratigraphy, downhole geophysical logging, mineralogy, and palynology were used to study and interpret the upper 70 meters of the inner continental shelf sediments within a proposed wind farm site located approximately two to three nautical miles to the southeast of Block Island, Rhode Island. Core samples and downhole logging collected from borings drilled for geotechnical purposes at proposed wind turbine sites along with seismic surveys in the surrounding area provide the data for this study. Cretaceous coastal plain sediments that consist of non-marine to marine sand, silt, and clay are found overlying bedrock at a contact depth beyond the sampling depth of this study. The upper Cretaceous sediments sampled in borings are correlated with the Magothy/Matawan formations described regionally from New Jersey to Nantucket. An unconformity formed through sub-aerial, fluvial, marine, and glacial erosion marks the upper strata of the Cretaceous sediments separating them from the overlying deposits. The majority of Quaternary deposits overlying the unconformity represent the advance, pulsing, and retreat of the Laurentide ice sheet that reached its southern terminus in the area of Block Island approximately 25,000 to 21,000 years before present. The sequence consists of a basal glacial till overlain by sediments deposited by meltwater environments ranging from deltaic to proglacial lakefloor. A late Pleistocene to early Holocene unconformity marks the top of the glacial sequence and was formed after glacial retreat through fluvial and subaerial erosion/deposition. Overlying the glacial sequence are sediments deposited during the late Pleistocene and Holocene consisting of interbedded gravel, sand, silt, and clay. Sampling of these sediments was limited and surficial reflectors in seismic profiles were masked due to a hard bottom return. However, two depositional periods are interpreted as representing fluvial and estuarine/marine environments respectively. One sample recovered at five meters contained shell fragments within a gray fine to coarse sand possibly representing a shallow estuarine to marine environment. A coarse near surface deposit described but not recovered in all borings may represent a transgressive unconformity and resulting lag deposit however due to lack of sampling and seismic resolution in the upper 5 meters, the nature of this deposit is merely speculation. In areas where depth to the glacial surface increased, sediments ranging from sand to fine-grained silt and clay were encountered in borings. In summary, the upper 70 meters of the inner continental shelf section within the study site consists of unconsolidated sediments spanning three major depositional periods. Sediments derived from glacial activity represent the bulk of samples collected. The glacial sequences represent various depositional environments, although most samples are interpreted to be the product of glacial meltwater deposition with distribution determined by source as well as highs and lows present in the antecedent topography. Finely laminated (varved) sediment to the south of Block Island indicates the presence of proglacial lakes in the area during the time of glacial retreat. Overlying sediments represent environments ranging from fluvial to marine.

Chronostratigraphic and depositional sequences of the Fort Union formation (Paleocene), Williston Basin, North Dakota, South Dakota, and Montana

USGS Publications Warehouse

Warwick, Peter D.; Flores, Romeo M.; Nichols, Douglas J.; Murphy, Edward C.; Pashin, Jack C.; Gastaldo, Robert A.

2004-01-01

The Fort Union Formation in the Williston Basin of North Dakota, South Dakota, and Montana comprises chronostratigraphic and depositional sequences of Paleocene age. Individual chronostratigraphic sequences are defined by palynostratigraphic (pollen and spore) biozones and radiometric (40Ar/39Ar) ages obtained from tonsteins or volcanic ash layers. Analyses of depositional sequences are based on lithofacies constrained by the radiometric ages and biozones.The lower Paleocene (biozones P1-P3) contains three marine parasequences (landward stepping) in southwestern North Dakota that sequentially onlapped westward between 65 and 61 Ma (lower Ludlow and Cannonball Members). Maximum flooding (transgressive systems tract) occurred during an approximate 1-m.y. interval from 65 to 64 Ma, which regionally is correlated biostratigraphically to a tidally influenced, distributary-shoreface, and fluvial-channel complex in the Cave Hills, northwestern South Dakota, and to channel-dominated fluvial (low-stand incised paleovalley systems) and tidally influenced, flood-plain-deltaic transition facies in the Ekalaka area of southeastern Montana.The progradational parasequences in the Cannonball Member consist of shore-face sandstone beds (with ravinement lag deposits) deposited by strand-plain barrier systems. Landward of the barrier systems, tidal-estuarine and mire deposits included thick but laterally discontinuous peat accumulations (e.g., Beta and Yule coal beds in the Ludlow Member, southwestern North Dakota). However, landward of the coastal deposits, the laterally equivalent T-Cross-Big Dirty coal zone (dated 64.78 Ma) in southeastern Montana formed as thick, laterally extensive peat accumulations in mires in a fluvial setting. In the flood-plain-deltaic, tidal transition zone near Ekalaka, Montana, the Ludlow Member consists of flood-plain facies, discontinuous coal beds, and rooted and burrowed horizons that contain the marine or brackish trace fossil Skolithos. The flood-plain-deltaic tidal transition zone facies are incised by a massive, agglomerated channel sandstone complex (paleovalley fill) that is exposed along the modern Snow Creek drainage south of Mill Iron, Montana. The flood-plain-tidal transition zone was reworked during the maximum sea level highstand during the early Paleocene. This event was followed by a fall of sea level and deposition of the paleovalley fill.Sea level fall during the mid-Paleocene (biozones P3 and P4) produced a regressive shallow-marine and lower deltaic tidal system (seaward stepping) that deposited strata that thin toward the east. These strata are overlain by a widespread paleosol (Rhame bed) and, in turn, a lignite-bearing fluvial facies (Tongue River Member) containing the laterally persistent Harmon-Hanson coal zone (61.23 Ma). Upper Paleocene biozone P5 is represented by fluvial, coal-bearing strata that contain several economically minable coal beds (HT Butte, Hagel, and Beulah-Zap zones, Sentinel Butte Member).The Fort Union Formation of the Williston Basin contains significant coal resources. These coal deposits are now being explored for their potential coal-bed gas resources. A better understanding of the depositional setting for these deposits can lead to improved exploration and exploitation practices and a better understanding of regional paleogeography and paleoclimate during the Paleocene.

Allelic Variants of Complement Genes Associated with Dense Deposit Disease

PubMed Central

Abrera-Abeleda, Maria Asuncion; Nishimura, Carla; Frees, Kathy; Jones, Michael; Maga, Tara; Katz, Louis M.; Zhang, Yuzhou

2011-01-01

The alternative pathway of the complement cascade plays a role in the pathogenesis of dense deposit disease (DDD). Deficiency of complement factor H and mutations in CFH associate with the development of DDD, but it is unknown whether allelic variants in other complement genes also associate with this disease. We studied patients with DDD and identified previously unreported sequence alterations in several genes in addition to allelic variants and haplotypes common to patients with DDD. We found that the likelihood of developing DDD increases with the presence of two or more risk alleles in CFH and C3. To determine the functional consequence of this finding, we measured the activity of the alternative pathway in serum samples from phenotypically normal controls genotyped for variants in CFH and C3. Alternative pathway activity was higher in the presence of variants associated with DDD. Taken together, these data confirm that DDD is a complex genetic disease and may provide targets for the development of disease-specific therapies. PMID:21784901

Solidification Sequence of Spray-Formed Steels

NASA Astrophysics Data System (ADS)

Zepon, Guilherme; Ellendt, Nils; Uhlenwinkel, Volker; Bolfarini, Claudemiro

2016-02-01

Solidification in spray-forming is still an open discussion in the atomization and deposition area. This paper proposes a solidification model based on the equilibrium solidification path of alloys. The main assumptions of the model are that the deposition zone temperature must be above the alloy's solidus temperature and that the equilibrium liquid fraction at this temperature is reached, which involves partial remelting and/or redissolution of completely solidified droplets. When the deposition zone is cooled, solidification of the remaining liquid takes place under near equilibrium conditions. Scanning electron microscopy (SEM) and optical microscopy (OM) were used to analyze the microstructures of two different spray-formed steel grades: (1) boron modified supermartensitic stainless steel (SMSS) and (2) D2 tool steel. The microstructures were analyzed to determine the sequence of phase formation during solidification. In both cases, the solidification model proposed was validated.

Depositional evolution of permo-triassic karoo basins in Tanzania with reference to their economic potential

NASA Astrophysics Data System (ADS)

Kreuser, T.; Wopfner, H.; Kaaya, C. Z.; Markwort, S.; Semkiwa, P. M.; Aslandis, P.

The Karoo basins of Tanzania contain in excess of 3000 m of sediments which were preserved in several NNE-NE striking half grabens or other structural basin conditions. They are all intracratonic basins, most of which filled with terrestrial sediments. In some basins situated nearer the coastal region short marine incursions occurred in the Late Permian. The Ruhuhu Rasin in SW Tanzania provides a typical depositional sequence of a Karoo basin in eastern Africa. Sedimentation commenced with glacigene deposits. These are of Late Carboniferous to Early Permian age and may be equated with other glacial successions in Africa and elsewhere in Gondwana. The glacigene beds are overlain by fluvial-deltaic coal-bearing deposits succeeded by arkoses and continental red beds. A transitionary formation of carbonaceous shales with impure coals gradually develops into thick lacustrine series which are topped by Late Permian bone bearing beds. The Triassic is characterized by a very thick fluvio-deltaic succession of siliciclastics resting with regional unconformity on the Permian. This Early Triassic sequence exhibits well-developed repetitive depositional cycles. Current azimuth measurements indicate fluctuating flow regimes in the Early Permian but relative stable source areas to the west of the basin later on. The depositional evolution of the Ruhuhu Basin is controlled by both tectonic and climatic factors. During basin evolution important energy resources were deposited such as considerable reserves of coal and source rocks of moderate potential for hydrocarbon generation. Uranium enrichment is observed in the Triassic arenaceous series where diagenetic alterations and subsequent cementation processes led to the formation of laumontite. Post Karoo dykes and plugs had only local effect on thermal evolution of potential source rocks. Enrichments of elements, i.e., Nb, Zr, Rb, Cr, and V present additional exploration targets. A comparison with the Karoo basins of the coastal region indicates possible lithological correlation by the application of sequence stratigraphy. No early Permian deposits are exposed in the coastal Karoo basins but their existence within the deeper parts of these basins cannot be ruled out. There, composition of organic matter analysed so far suggests subsidence and heat exposure exceeding post maturity stage.

Tectonic and climatic controls on continental depositional facies in the Karoo Basin of northern Natal, South Africa

NASA Astrophysics Data System (ADS)

Turner, Brian R.

1986-02-01

The eastern Karoo Basin, South Africa, contains a thick sequence of terrigenous clastic sediments comprising a meanderbelt facies, braided channel facies divided into coarse and fine subfacies, fluviolacustrine facies and aeolian facies. Depositional trends and changes in fluvial style reflect a progressive increase in aridity of the climate under stable tectonic conditions, interrupted by two phases of source area tectonism and the development of fine and coarse clastic wedges of the braided channel subfacies; the latter signifying a short interlude of cool, wet conditions. The fine braided channel subfacies occurs in the upper part of the meanderbelt facies, which was deposited by ephemeral, meandering mixed-load streams of variable discharge and sinuosity, under dry, semi-arid climatic conditions. These deposited complex, internally discordant channel sands and well-developed levee deposits. Following deposition of the coarse braided channel subfacies semi-arid conditions returned and fluvial deposition was dominated by ephemeral, straight to slightly sinuous mixed load streams characterised by simple channel sand bodies. As the aridity of the climate increased, the streams became more localised and carried an increasing proportion of fines. Interbedded with and overlying the fluvial deposits is a mudstone-dominated lacustrine sequence grading up into aeolian sands suggesting a playa lake-type situation. The general absence of evaporites from these sediments is attributed to the fresh nature of the lake waters, as evidenced by the freshwater aquatic organisms and clay-mineral suite, the lack of adequate inflow for solute accumulation and the removal of dust impregnated by salts from the surface of the dry lake bed during the dry season by superheated, upward-spiralling columns of air. Broadly similar environments to the fluvio-lacustrine and aeolian facies sequence are to be found in the Lake Eyre Basin of central Australia and the Okavango "delta" of northern Botswana. The Okavango "delta" model has an important bearing on patterns of fluvial sedimentation in arid regions since it shows many characteristics of temperate, well-vegetated anastomosed fluvial systems despite its location in the Kalahari Desert.

Deposition model of a Miocene barred wave- and storm-dominated shoreface and shelf, southeastern Malay basin, offshore west Malaysia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramli, N.

1986-01-01

The J sandstone is an important hydrocarbon-bearing reservoir in the southeastern part of the Malay basin. The lower and upper members of the J sandstone are composed of shoreface and offshore sediments. The shoreface sequence contains depositional structures characteristic of a barred wave- and storm-dominated shoreface. Each shoreface sequence is laterally associated with a series of stacked offshore bars. Offshore bars can be subdivided into proximal and distal types. Two types of proximal offshore bars have been identified: (1) proximal bars formed largely above fair-weather wave base (inner proximal bars), and (2) proximal bars formed below fair-weather wave base (outermore » proximal bars). The inner proximal bars are closely associated with the shoreface sequence and are similar to the middle and lower shoreface. The presence of poorly sorted, polymodal, very fine to very coarse-grained sandstone beneath well-sorted crestal sandstones of inner proximal bars suggests that these offshore bars may have been deposited rapidly by storms. The crests of the inner proximal offshore bars were subsequently reworked by fair-weather processes, and the crests of the outer proximal and distal offshore bars were reworked by waning storm currents and oscillatory waves. Thick marine shales overlying offshore bars contain isolated sheet sandstones. Each sheet sandstone exhibits features that may be characteristic of distal storm shelf deposits. 15 figures, 2 tables.« less

Miocene and Pliocene lacustrine and fluvial sequences, Upper Ramparts and Canyon village, Porcupine river, east-central Alaska

USGS Publications Warehouse

Fouch, T.D.; Carter, L.D.; Kunk, Michael J.; Smith, C.A.S.; White, J.M.

1994-01-01

Cenozoic strata exposed along the Porcupine River between the Upper Ramparts and Canyon Village, Alaska, can be divided into five unconformity-bounded units (sequences) which are: lower and middle Miocene unit A, the white sandy fluvial sequence with peat beds; middle Miocene unit B, the basalt sequence-part B1 is basalt, and part B2 is organic-rich sedimentary beds; upper Miocene unit C, mudrock-dominated lake sequence; late Miocene or Pliocene to Pleistocene unit D, terrace gravels, detrital organic matter and associated sediments, and Holocene unit E, mixed sand and gravel-rich sediment and other sedimentary material including peat and eolian silt. The sequence (unit A) of lower and middle Miocene fluvial deposits formed in streams and on flood plains, just before the inception of local volanism. Fossil pollen from unit A suggests conifer-dominated regional forests and cool temperate climates. Peat beds and lake deposits from unit B contain pollen that indicates a warmer temperate climate coinciding with the middle Miocene thermal maximum. The lake deposits (unit C) downstream from the basalts accumulated in a small basin which resulted from a hydrologic system that was dammed in the late Miocene but breached soon thereafter. The lower part of the terrace gravels (unit D) expresses breaching of the dammed hydrologic system (of unit C). The Porcupine River became a major tributary of the Yukon River in late Pleistocene time when Laurentide ice blocked drainage from the Yukon interior basins causing meltwater to spill over the low divide separating it from the Porcupine River drainage initiating erosion and capture of the Yukon interior basins. ?? 1994.

Petroleum system elements within the Late Cretaceous and Early Paleogene sediments of Nigeria's inland basins: An integrated sequence stratigraphic approach

NASA Astrophysics Data System (ADS)

Dim, Chidozie Izuchukwu Princeton; Onuoha, K. Mosto; Okeugo, Chukwudike Gabriel; Ozumba, Bertram Maduka

2017-06-01

Sequence stratigraphic studies have been carried out using subsurface well and 2D seismic data in the Late Cretaceous and Early Paleogene sediments of Anambra and proximal onshore section of Niger Delta Basin in the Southeastern Nigeria. The aim was to establish the stratigraphic framework for better understanding of the reservoir, source and seal rock presence and distribution in the basin. Thirteen stratigraphic bounding surfaces (consisting of six maximum flooding surfaces - MFSs and seven sequence boundaries - SBs) were recognized and calibrated using a newly modified chronostratigraphic chart. Stratigraphic surfaces were matched with corresponding foraminiferal and palynological biozones, aiding correlation across wells in this study. Well log sequence stratigraphic correlation reveals that stratal packages within the basin are segmented into six depositional sequences occurring from Late Cretaceous to Early Paleogene age. Generated gross depositional environment maps at various MFSs show that sediment packages deposited within shelfal to deep marine settings, reflect continuous rise and fall of sea levels within a regressive cycle. Each of these sequences consist of three system tracts (lowstand system tract - LST, transgressive system tract - TST and highstand system tract - HST) that are associated with mainly progradational and retrogradational sediment stacking patterns. Well correlation reveals that the sand and shale units of the LSTs, HSTs and TSTs, that constitute the reservoir and source/seal packages respectively are laterally continuous and thicken basinwards, due to structural influences. Result from interpretation of seismic section reveals the presence of hanging wall, footwall, horst block and collapsed crest structures. These structural features generally aid migration and offer entrapment mechanism for hydrocarbon accumulation. The combination of these reservoirs, sources, seals and trap elements form a good petroleum system that is viable for hydrocarbon exploration and development.

Revised stratigraphy and reinterpretation of the Miocene Pohang basinfill, SE Korea: sequence development in response to tectonism and eustasy in a back-arc basin margin

NASA Astrophysics Data System (ADS)

Sohn, Y. K.; Rhee, C. W.; Shon, H.

2001-09-01

The Miocene Pohang Basin is a pull-apart basin formed along the eastern continental margin of Korea (ECMK) during the back-arc opening of the East Sea (Sea of Japan). The basin is filled by more than 1 km thick, nonmarine to deep-marine strata. These strata show extreme vertical and lateral lithofacies changes and have caused decades-long controversies on their nature and stratigraphy. Previous sedimentological studies suggest that the basinfill was deposited by a series of contemporaneously developed depositional systems, including fan delta, prodelta, slope apron, and basin plain. Detailed mapping and magnetotelluric surveying show, however, that the basinfill is composed of several packages of strata (sequences) that are bounded by distinct and laterally persistent stratigraphic discontinuities (sequence boundaries). This suggests that the depositional systems in the Pohang Basin developed sequentially rather than contemporaneously. Six packages of strata are identified in the basin: a nonmarine to shallow marine (transgressive) sequence (Sequence 1), a Gilbert-type-delta conglomerate (Sequence 2), and alternations of submarine conglomerates and hemipelagic mudstones (Sequences 3-6). The conglomerates and hemipelagic mudstones of the latter four sequences are interpreted to represent lowstand depositional systems (slope apron, submarine fan, and high-gradient delta) and condensed intervals, respectively. Compilation of geochronologic, paleomagnetic, and biostratigraphic data suggests that Sequence 1 formed during the gradual subsidence of the ECMK prior to 17 Ma, whereas Sequence 2 formed in response to abrupt downfaulting of the Pohang Basin at about 17 Ma. Both sequences are interpreted to have developed in response to the early Miocene back-arc-opening tectonism of the East Sea. On the other hand, Sequences 3-6 formed between 17 and about 10.5 Ma. The Pohang Basin was subject to only minor tectonism during this period and could record global sea-level fluctuations. We suggest that the four alternations of conglomerates (lowstand systems) and hemipelagic mudstones (condensed intervals) resulted most probably from the 3rd-order glacioeustatic cycles during the middle Miocene. This finding implies that the signatures of global sea-level fluctuations can be deciphered from a tectonically active sedimentary basin if the timing of regional tectonic development is well constrained, and the global sea-level chart of Haq et al. ( Haq, B.W., Hardenbol, J., Vail, P.R., 1987, Chronology of fluctuating sea levels since the Triassic. Science 235, 1156-1167; Haq, B.U., Hardenbol, J., Vail, P.R., 1988. Mesozoic and Cenozoic chronostratigraphy and eustatic cycles. In: Wilgus, C.K., Hastings, B.S., Posamentier, H., Van Wagoner, J., Ross, C.A., Kendall, C.G.S.C. (Eds.), Sea-Level Changes: an Integrated Approach: Soc. Econ. Paleont. Mineral. Spec. Publ. 42, pp. 71-108) may serve as a guide to basinfill interpretation even in tectonically active sedimentary basins.

Therapeutic Oligonucleotides Targeting Liver Disease: TTR Amyloidosis.

PubMed

Niemietz, Christoph; Chandhok, Gursimran; Schmidt, Hartmut

2015-09-30

The liver has become an increasingly interesting target for oligonucleotide therapy. Mutations of the gene encoding transthyretin (TTR), expressed in vast amounts by the liver, result in a complex degenerative disease, termed familial amyloid polyneuropathy (FAP). Misfolded variants of TTR are linked to the establishment of extracellular protein deposition in various tissues, including the heart and the peripheral nervous system. Recent progress in the chemistry and formulation of antisense (ASO) and small interfering RNA (siRNA) designed for a knockdown of TTR mRNA in the liver has allowed to address the issue of gene-specific molecular therapy in a clinical setting of FAP. The two therapeutic oligonucleotides bind to RNA in a sequence specific manner but exploit different mechanisms. Here we describe major developments that have led to the advent of therapeutic oligonucleotides for treatment of TTR-related disease.

Stratigraphic architecture and gamma ray logs of deeper ramp carbonates (Upper Jurassic, SW Germany)

NASA Astrophysics Data System (ADS)

Pawellek, T.; Aigner, T.

2003-07-01

The objective of this paper is to contribute to the development of sequence stratigraphic models for extensive epicontinental carbonate systems deposited over cratonic areas. Epicontinental carbonates of the SW German Upper Jurassic were analysed in terms of microfacies, sedimentology and sequence stratigraphy based on 2.5 km of core, 70 borehole gamma ray logs and 24 quarries. Facies analysis revealed six major facies belts across the deeper parts of the carbonate ramp, situated generally below fair-weather wave base, and mostly below average storm wave base but in the reach of occasional storm events. Observed stratigraphic patterns differ in some aspects from widely published sequence stratigraphic models: Elementary sedimentary cycles are mostly more or less symmetrical and are, thus, referred to as "genetic sequences" or "genetic units" [AAAPG Bull. 55 (1971) 1137; Frazier, D.E., 1974. Depositional episodes: their relationship to the Quaternary stratigraphic framework in the northwestern portion of the Gulf Basin. University of Texas, Austin, Bureau of Economic Geology Geologicalo Circular 71-1; AAPG Bull. 73 (1989) 125; Galloway, W.E., Hobday, D.K., 1996. Terrigenous Clastic Depositional Systems. 489 pp., Springer; Cross, T.A., Baker, M.R., Chapin, M.S., Clark, M.S., Gardner, M.H., Hanson, M.S., Lessenger, M.A., Little, L.D., McDonough, K.J., Sonnenfeld, M.D., Valasek, D.W., Williams, M.R., Witter, D.N., 1993. Applications of high-resolution sequence stratigraphy to reservoir analysis. Edition Technip 1993, 11-33; Bull. Cent. Rech. Explor. Prod. Elf-Aquitaine 16 (1992) 357; Homewood, P., Mauriaud, P., Lafont, F., 2000. Best practices in sequence stratigraphy. Elf EP Mem. 25, 81 pp.; Homewood, P., Eberli, G.P., 2000. Genetic stratigraphy on the exploration and production scales. Elf EP Mem. 24, 290 pp.], in contrast to the asymmetrical, shallowing-upward "parasequences" of the EXXON approach. Neither sequence boundaries nor maximum flooding surfaces could be clearly delineated. Cycle boundaries are generally not represented by sharp stratal surfaces but are always transitional and, thus, referred to as "turnarounds" [Nor. Pet. Soc. Spec. Publ. 8 (1998) 171]. Several types of genetic sequences were delineated. Both major types of facies and sequences show characteristic gamma ray log signatures. Based on the cycle stacking and the gamma ray patterns, a hierarchy of sequences was recognized, probably driven in part by 100,000- and 400,000-year Milankovitch signals. The cyclicity allowed regional correlations across various depositional environments such as sponge-microbial bioherms and coeval basins. The basin-wide correlation revealed evidence for a subtle clinoform-type stratigraphic architecture along very gentle slopes, rather than a so far assumed simple "layer cake" pattern.

In vivo Proton Electron Double Resonance Imaging of Mice with Fast Spin Echo Pulse Sequence

PubMed Central

Sun, Ziqi; Li, Haihong; Petryakov, Sergey; Samouilov, Alex; Zweier, Jay L.

2011-01-01

Purpose To develop and evaluate a 2D fast spin echo (FSE) pulse sequence for enhancing temporal resolution and reducing tissue heating for in vivo proton electron double resonance imaging (PEDRI) of mice. Materials and Methods A four-compartment phantom containing 2 mM TEMPONE was imaged at 20.1 mT using 2D FSE-PEDRI and regular gradient echo (GRE)-PEDRI pulse sequences. Control mice were infused with TEMPONE over ∼1 min followed by time-course imaging using the 2D FSE-PEDRI sequence at intervals of 10 – 30 s between image acquisitions. The average signal intensity from the time-course images was analyzed using a first-order kinetics model. Results Phantom experiments demonstrated that EPR power deposition can be greatly reduced using the FSE-PEDRI pulse sequence compared to the conventional gradient echo pulse sequence. High temporal resolution was achieved at ∼4 s per image acquisition using the FSE-PEDRI sequence with a good image SNR in the range of 233-266 in the phantom study. The TEMPONE half-life measured in vivo was ∼72 s. Conclusion Thus, the FSE-PEDRI pulse sequence enables fast in vivo functional imaging of free radical probes in small animals greatly reducing EPR irradiation time with decreased power deposition and provides increased temporal resolution. PMID:22147559

Formation and tectonic evolution of the Pattani Basin, Gulf of Thailand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bustin, R.M.; Chonchawalit, A.

The stratigraphic and structural evolution of the Pattani Basin, the most prolific petroleum basin in Thailand, reflects the extensional tectonic regime of continental Southeast Asia. E-W extension resulting from the northward collision of India with Eurasia since the Early Tertiary resulted in the formation of a series of N-S-trending sedimentary basins, which include the Pattani Basin. The sedimentary succession in the Pattani Basin is divisible into synrift and postrift sequences. Deposition of the synrift sequence accompanied rifting and extension, with episodic block faulting and rapid subsidence. The synrift sequence comprises three stratigraphic units: (1) Upper Eocene to Lower Olikgocene alluvial-fan,more » braided-river, and floodplain deposits; (2) Upper oligocene to Lowe Miocene floodplain and channel deposits; and (3) a Lower Miocene regressive package consisting of marine to nonmarine sediments. Post-rift succession comprises: (1) a Lower to Middle Miocene regressive package of shallow marine sediments through floodplain and channel deposits; (2) an upper Lower Miocene transgressive sequence; and (3) and Upper Miocene to Pleistocene transgressive succession. The post-rift phase is characterized by slower subsidence and decreased sediment influx. The present-day shallow-marine condition in the Gulf of Thailand is the continuation of this latest transgressive phase. The subsidence and thermal history of the Pattani Basin is consistent with a nonuniform lithospheric-stretching model. The amount of extension as well as surface heat flow generally increases from the margin to the basin center. The crustal stretching factor ({beta}) varies form 1.3 at the basin margin to 2.8 in the center. The subcrustal stretching factor ({delta}) ranges from 1.3 at the basin margin to more than 3.0 in the basin center. 31 refs., 13 figs., 4 tabs.« less

Paleoecology of the Devonian-Mississippian black-shale sequence in eastern Kentucky with an atlas of some common fossils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barron, L.S.; Ettensohn, F.R.

The Devonian-Mississippian black-shale sequence of eastern North America is a distinctive stratigraphic interval generally characterized by low clastic influx, high organic production in the water column, anaerobic bottom conditions, and the relative absence of fossil evidence for biologic activity. The laminated black shales which constitute most of the black-shale sequence are broken by two major sequences of interbedded greenish-gray, clayey shales which contain bioturbation and pyritized micromorph invertebrates. The black shales contain abundant evidence of life from upper parts of the water column such as fish fossils, conodonts, algae and other phytoplankton; however, there is a lack of evidence ofmore » benthic life. The rare brachiopods, crinoids, and molluscs that occur in the black shales were probably epiplanktic. A significant physical distinction between the environment in which the black sediments were deposited and that in which the greenish-gray sediments were deposited was the level of dissolved oxygen. The laminated black shales point to anaerobic conditions and the bioturbated greenish-gray shales suggest dysaerobic to marginally aerobic-dysaerobic conditions. A paleoenvironmental model in which quasi-estuarine circulation compliments and enhances the effect of a stratified water column can account for both depletion of dissolved oxygen in the bottom environments and the absence of oxygen replenishment during black-shale deposition. Periods of abundant clastic influx from fluvial environments to the east probably account for the abundance of clays in the greenish-gray shale as well as the small amounts of oxygen necessary to support the depauparate, opportunistic, benthic faunas found there. These pulses of greenish-gray clastics were short-lived and eventually were replaced by anaerobic conditions and low rates of clastic sedimentation which characterized most of black-shale deposition.« less

Biothems: Sequence stratigraphic units and their implications for regional tectono-stratigraphic interpretations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lane, H.R.; Frye, M.W.; Couples, G.D.

1992-01-01

Biothems are regional wedge- or lens-shaped bodies of strata that are bounded shelfward or cratonward by paleontologically recognizable unconformities; generally thicken on marine shelves, where they are typically conformable with underlying and overlying biothems; are commonly thinner or represent starved sequences further basinward; and in their most basinward extent, are either bounded by biostratigraphically recognizable unconformities or are conformable with underlying and overlying biothems. As recognized to date, biothems have a logical distribution of faunal and floral components, as well as facies groupings that represent internally consistent and logical sequences of depositional environments. A west-to-east transect within the North Americanmore » Mississippian System which extends from the Basin and Range Province, across the Transcontinental Arch (TA), into the Anadarko Basin, was constructed to demonstrate the regional distribution and tectono-stratigraphic significance of biothems relative to the axis of the TA. The relationships portrayed on the transect, tied to an understanding of North American Mississippian paleogeography, imply that biothems deposited during relative highstand events on one flank of the TA are time-equivalent to biothems deposited during relative lowstand events on the opposite flank of the TA. This distribution is interpreted to have been controlled by intraplate tectonic events that formed piano key basins along the flanks of the TA. The spatial patterns of these basins are not consistent with published models of basin evolution. A further conclusion is that the lack of coincident, transgressive or regressive Mississippian biothems on either flank of the TA suggests that it is inadvisable to impose the Mississippi Valley-derived eustasy curve on western flank depositional sequences.« less

Facies analysis, diagenesis and sequence stratigraphy of the carbonate-evaporite succession of the Upper Jurassic Surmeh Formation: Impacts on reservoir quality (Salman Oil Field, Persian Gulf, Iran)

NASA Astrophysics Data System (ADS)

Beigi, Maryam; Jafarian, Arman; Javanbakht, Mohammad; Wanas, H. A.; Mattern, Frank; Tabatabaei, Amin

2017-05-01

This study aims to determine the depositional facies, diagenetic processes and sequence stratigraphic elements of the subsurface carbonate-evaporite succession of the Upper Jurassic (Kimmeridgian-Tithonian) Surmeh Formation of the Salman Oil Field (the Persian Gulf, Iran), in an attempt to explore their impacts on reservoir quality. The Surmeh Formation consists mainly of carbonate rocks, intercalated with evaporite layers. Petrographically, the Surmeh Formation consists of nine microfacies (MF1-MF9). These microfacies are grouped into three facies associations related to three depositional environments (peritidal flat, lagoon and high-energy shoal) sited on the inner part of a homoclinal carbonate ramp. The recorded diagenetic processes include dolomitization, anhydritization, compaction, micritization, neomorphism, dissolution and cementation. Vertical stacking patterns of the studied facies reveal the presence of three third-order depositional sequences, each of which consists of transgressive systems tract (TST) and highstand systems tract (HST). The TSTs comprise intertidal and lagoon facies whereas the HSTs include supratidal and shoal facies. In terms of their impacts on reservoir quality, the shoal facies represent the best reservoir quality, whereas the peritidal and lagoonal facies exhibit moderate to lowest reservoir quality. Also, poikilotopic anhydrite cement played the most significant role in declining the reservoir quality, whereas the widespread dissolution of labile grains and formation of moldic and vuggy pores contributed in enhancing the reservoir quality. In addition, the HSTs have a better reservoir quality than the TSTs. This study represents an approach to use the depositional facies, diagenetic alterations and sequence stratigraphic framework of carbonate -evaporite succession for a more successful reservoir characterization.

Stratigraphy and Petrology of the Grande Soufriere Hills Volcano, Dominica, Lesser Antilles

NASA Astrophysics Data System (ADS)

Daly, G.; Smith, A. L.; Garcia, R.; Killingsworth, N.

2007-12-01

The Grande Soufriere Hills volcanic center is located on the south east coast of the island of Dominica in the Lesser Antilles. Although the volcano is deeply dissected, a distinct circular crater that opens to the east can be observed. Within the crater is a lava dome and unconsolidated pyroclastic deposits mantle the southeast flanks of the volcano. These pyroclastic deposits are almost entirely matrix-supported block and ash flows and surges suggesting that Pelean-style eruptions have dominated its most recent activity. Within this sequence is a relatively thin (30-50 cm) clast-supported deposit that has been interpreted as a possible blast deposit. Two age dates from these younger deposits suggest that much of this activity occurred between l0,000 and 12,000 years ago. On the southeastern coast at Pointe Mulâtre and extending approximately 4 km north and at a maximum 2 km west, is a megabreccia of large (up to 3 m) flow-banded andesite clasts set in a semi-lithified medium grained ash matrix. At Pointe Mulâtre this megabreccia is overlain by unconsolidated block and ash flow deposits. To the north of the megabreccia, exposures in the sea cliffs reveal a consolidated sequence of well-bedded alternating coarse and fine deposits suggesting deltaic foreset beds; which in turn appears to be overlain by a yellow- colored relatively coarse flow deposit with an irregular upper surface. The uppermost deposits in the sea cliffs are a sequence of unconsolidated block and ash flow deposits and interbedded fluviatile conglomerates equivalent to the younger flow deposits logged inland. Volcanic rocks from the Grande Soufriere Hills are all porphyritic andesites often containing hypabyssal inclusions. Dominant phenocrysts are plagioclase often with inclusion-rich cores and well developed zoning. Mafic phenocrysts include hornblende, augite and hypersthene. Geochemically these andesites range from 58- 63% SiO2 and show trends of decreasing values for Al2O3, FeO, MgO, CaO, TiO2, Sr, V, and Sc and increasing values for Na2O, K2O, Ba, Rb, and Zr with increasing silica. Samples from the megabreccia can be chemically distinguished from the younger rocks of this center. Petrologic models suggest that the younger rocks from the Grand Soufriere Hills can be produced by fractional crystallization of basaltic magma such as those erupted from other centers (such as Morne Anglais to the west). Minor variations within this suite of andesites can be related to upper crustal fractionation of phenocryst phases.

Tracing sources of crustal contamination using multiple S and Fe isotopes in the Hart komatiite-associated Ni-Cu-PGE sulfide deposit, Abitibi greenstone belt, Ontario, Canada

NASA Astrophysics Data System (ADS)

Hiebert, R. S.; Bekker, A.; Houlé, M. G.; Wing, B. A.; Rouxel, O. J.

2016-10-01

Assimilation by mafic to ultramafic magmas of sulfur-bearing country rocks is considered an important contributing factor to reach sulfide saturation and form magmatic Ni-Cu-platinum group element (PGE) sulfide deposits. Sulfur-bearing sedimentary rocks in the Archean are generally characterized by mass-independent fractionation of sulfur isotopes that is a result of atmospheric photochemical reactions, which produces isotopically distinct pools of sulfur. Likewise, low-temperature processing of iron, through biological and abiotic redox cycling, produces a range of Fe isotope values in Archean sedimentary rocks that is distinct from the range of the mantle and magmatic Fe isotope values. Both of these signals can be used to identify potential country rock assimilants and their contribution to magmatic sulfide deposits. We use multiple S and Fe isotopes to characterize the composition of the potential iron and sulfur sources for the sulfide liquids that formed the Hart deposit in the Shaw Dome area within the Abitibi greenstone belt in Ontario (Canada). The Hart deposit is composed of two zones with komatiite-associated Ni-Cu-PGE mineralization; the main zone consists of a massive sulfide deposit at the base of the basal flow in the komatiite sequence, whereas the eastern extension consists of a semi-massive sulfide zone located 12 to 25 m above the base of the second flow in the komatiite sequence. Low δ56Fe values and non-zero δ34S and Δ33S values of the komatiitic rocks and associated mineralization at the Hart deposit is best explained by mixing and isotope exchange with crustal materials, such as exhalite and graphitic argillite, rather than intrinsic fractionation within the komatiite. This approach allows tracing the extent of crustal contamination away from the deposit and the degree of mixing between the sulfide and komatiite melts. The exhalite and graphitic argillite were the dominant contaminants for the main zone of mineralization and the eastern extension zone of the Hart deposit, respectively. Critically, the extent of contamination, as revealed by multiple S and Fe isotope systematics, is greatest within the deposit and decreases away from it within the komatiite flow. This pattern points to a local source of crustal contamination for the mantle-derived komatiitic melt and a low degree of homogenization between the mineralization and the surrounding lava flow. Coupled S and Fe isotope patterns like those identified at the Hart deposit may provide a useful tool for assessing the potential of a komatiitic sequence to host Ni-Cu-(PGE).

Molecular Analysis of Carbon Monoxide-Oxidizing Bacteria Associated with Recent Hawaiian Volcanic Deposits†

PubMed Central

Dunfield, Kari E.; King, Gary M.

2004-01-01

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity. PMID:15240307

High Resolution Climatic Variations Recorded by Mollusk Fauna at Nussloch (Rhine Valley, Germany) During the Last Glaciation

NASA Astrophysics Data System (ADS)

Moine, O.; Rousseau, D.; Antoine, P.

2002-12-01

During the last 31 and 19 kyr interval important eolian sediment deposited in Western Europe at Nussloch (Rhine Valley, Germany) favored by the enhanced atmospheric circulation at mid-latitudes and large areas of deflation providing quantities of material such as the English Channel, the North Sea or the dry Rhine valley. The 10m-high studied sequence is composed of an alternation of nine gley-loess cycles. Except for few adjoining assemblages, the composition of the malacofauna is almost constant all along the sequence and typical of a humid loess facies and a steppe environment. Each cycle is composed of three parts. The first is the deposit of loess in windy, dry and cold climate, with associated malacofauna in equilibrium with these conditions. The second is the development of a gley in a colder and more humid context, with a very reduced particle deposition and, in the first half of the sequence, the presence of a permafrost. The associated malacofauna are characterized by a more or less important decrease in the diversity and equitability indicating the influence of a climatic drop. The third part is not characterized by any particular deposit, but by the thaw of the permafrost, when it is present, and by a demographic explosion of the mollusk fauna if the climate is not too dry. Such lithological alternations have been evidenced in all the Late Pleistocene deposits in Western Europe. They suggest that global climatic variations had a strong influence on the continental domain in Europe during this interval. Precedent results obtained from this site have shown that the variations in a grain size index can be correlated with those of the dust content recorded in the GRIP ice-core, both being influenced by the eolian dynamics. Thus, the timescale of the GRIP ice-core has been applied to the loess sequence of Nussloch, and allowed us the comparison of our mollusk index with the d18O of the GRIP core. From this correlation it appears that the abundance in terrestrial mollusks fits the d18O variations in the ice-core supporting that the high biological abundance regularly occurring in the sequence would due to climate ameliorations and not related to sedimentological artifacts. Nevertheless the strong dryness occurring in the upper part of the sequence, and indicated by both the mollusk species richness and the d13C of the organic matter of the soil, seems to have restrained the development of the malacofauna, preventing the malacofauna to record any climatic improvement during this period.

Engineering secondary cell wall deposition in plants

PubMed Central

Yang, Fan; Mitra, Prajakta; Zhang, Ling; Prak, Lina; Verhertbruggen, Yves; Kim, Jin-Sun; Sun, Lan; Zheng, Kejian; Tang, Kexuan; Auer, Manfred; Scheller, Henrik V; Loqué, Dominique

2013-01-01

Lignocellulosic biomass was used for thousands of years as animal feed and is now considered a great sugar source for biofuels production. It is composed mostly of secondary cell walls built with polysaccharide polymers that are embedded in lignin to reinforce the cell wall structure and maintain its integrity. Lignin is the primary material responsible for biomass recalcitrance to enzymatic hydrolysis. During plant development, deep reductions of lignin cause growth defects and often correlate with the loss of vessel integrity that adversely affects water and nutrient transport in plants. The work presented here describes a new approach to decrease lignin content while preventing vessel collapse and introduces a new strategy to boost transcription factor expression in native tissues. We used synthetic biology tools in Arabidopsis to rewire the secondary cell network by changing promoter-coding sequence associations. The result was a reduction in lignin and an increase in polysaccharide depositions in fibre cells. The promoter of a key lignin gene, C4H, was replaced by the vessel-specific promoter of transcription factor VND6. This rewired lignin biosynthesis specifically for vessel formation while disconnecting C4H expression from the fibre regulatory network. Secondly, the promoter of the IRX8 gene, secondary cell wall glycosyltransferase, was used to express a new copy of the fibre transcription factor NST1, and as the IRX8 promoter is induced by NST1, this also created an artificial positive feedback loop (APFL). The combination of strategies—lignin rewiring with APFL insertion—enhances polysaccharide deposition in stems without over-lignifying them, resulting in higher sugar yields after enzymatic hydrolysis. PMID:23140549

Sequence characterization and spatiotemporal expression patterns of PbS26-RNase gene in Chinese White Pear (Pyrus bretschneideri).

PubMed

Zhang, Lin; Jia, Baoguang; Zou, Feng; Tan, Xiaofeng; Liu, Min; Song, Zhibo; Zeng, Yanling; Jiang, Nan; Yuan, Deyi

2014-01-01

Many flowering plants exhibit an important intraspecific reproductive barrier phenomenon, that is, self-incompatibility (SI), in which S-RNase genes play a significant role. To clarify the specific function of S-RNase genes in Chinese pears, the full length cDNA of PbS 26 -RNase was isolated by rapid amplification of cDNA ends (RACE) technology from Chinese white pear (Pyrus bretschneideri) cultivar "Hongpisu." The cDNA sequence for PbS 26 -RNase was deposited in GenBank under accession number EU081888. At the amino acid level, the PbS 26 -RNase displayed the highest similarity (96.9%) with PcSa-RNase of P. communis, and only seven amino acid differences were present in the two S-RNases. Phylogenetic analysis of rosaceous S-RNases indicated that the PbS 26 -RNase clustered with maloideous S-RNases, forming a subfamily-specific not a species-specific group. The PbS 26 -RNase gene was specifically expressed in the style but not other tissues/organs. The expression level of the PbS 26 -RNase gene rapidly increased at bell balloon stage (BBS), and then it dropped after pollination. However, the abundance of the PbS 26 -RNase gene transcript in the style was greater after cross-pollination than after self-pollination. In addition, a method for rapidly detecting the PbS 26 -RNase gene was developed via allele-specific primers design. The present study could provide a scientific basis for fully clarifying the mechanism of pear SI at the molecular level.

Sequence Characterization and Spatiotemporal Expression Patterns of PbS 26 -RNase Gene in Chinese White Pear (Pyrus bretschneideri)

PubMed Central

Jia, Baoguang; Liu, Min; Song, Zhibo; Zeng, Yanling; Jiang, Nan; Yuan, Deyi

2014-01-01

Many flowering plants exhibit an important intraspecific reproductive barrier phenomenon, that is, self-incompatibility (SI), in which S-RNase genes play a significant role. To clarify the specific function of S-RNase genes in Chinese pears, the full length cDNA of PbS 26 -RNase was isolated by rapid amplification of cDNA ends (RACE) technology from Chinese white pear (Pyrus bretschneideri) cultivar “Hongpisu.” The cDNA sequence for PbS 26 -RNase was deposited in GenBank under accession number EU081888. At the amino acid level, the PbS 26 -RNase displayed the highest similarity (96.9%) with PcSa-RNase of P. communis, and only seven amino acid differences were present in the two S-RNases. Phylogenetic analysis of rosaceous S-RNases indicated that the PbS 26 -RNase clustered with maloideous S-RNases, forming a subfamily-specific not a species-specific group. The PbS 26 -RNase gene was specifically expressed in the style but not other tissues/organs. The expression level of the PbS 26 -RNase gene rapidly increased at bell balloon stage (BBS), and then it dropped after pollination. However, the abundance of the PbS 26 -RNase gene transcript in the style was greater after cross-pollination than after self-pollination. In addition, a method for rapidly detecting the PbS 26 -RNase gene was developed via allele-specific primers design. The present study could provide a scientific basis for fully clarifying the mechanism of pear SI at the molecular level. PMID:24737959

Functional Characterization of the Poplar R2R3-MYB Transcription Factor PtoMYB216 Involved in the Regulation of Lignin Biosynthesis during Wood Formation

PubMed Central

Lu, Wanxiang; Yang, Li; Jiang, Yuanzhong; Luo, Keming

2013-01-01

Because of the importance of wood in many industrial applications, tremendous studies have been performed on wood formation, especially in lignin biosynthesis. MYB transcription factors (TFs), which consist of a large family of plant TFs, have been reported to directly regulate lignin biosynthetic genes in a number of plants. In this study, we describe the cloning and functional characterization of PtoMYB216, a cDNA isolated from Chinese white poplar (Populus tomentosa Carr.). PtoMYB216 encodes a protein belonging to the R2R3-MYB family and displays significant similarity with other MYB factors shown to regulate lignin synthesis in Arabidopsis. Gene expression profiling studies showed that PtoMYB216 mRNA is specifically expressed during secondary wall formation in wood. The 1.8-kb promoter sequence of PtoMYB216 was fused to the GUS coding sequence and introduced into wild-type A. thaliana. GUS expression was shown to be restricted to tissues undergoing secondary cell wall formation. Overexpression of PtoMYB216 specifically activated the expression of the upstream genes in the lignin biosynthetic pathway and resulted in ectopic deposition of lignin in cells that are normally unligninified. These results suggest that PtoMYB216 is specific transcriptional activators of lignin biosynthesis and involved in the regulation of wood formation in poplar. PMID:24204619

Geomorphology, facies architecture, and high-resolution, non-marine sequence stratigraphy in avulsion deposits, Cumberland Marshes, Saskatchewan

USGS Publications Warehouse

Farrell, K.M.

2001-01-01

This paper demonstrates field relationships between landforms, facies, and high-resolution sequences in avulsion deposits. It defines the building blocks of a prograding avulsion sequence from a high-resolution sequence stratigraphy perspective, proposes concepts in non-marine sequence stratigraphy and flood basin evolution, and defines the continental equivalent to a parasequence. The geomorphic features investigated include a distributary channel and its levee, the Stage I crevasse splay of Smith et al. (Sedimentology, vol. 36 (1989) 1), and the local backswamp. Levees and splays have been poorly studied in the past, and three-dimensional (3D) studies are rare. In this study, stratigraphy is defined from the finest scale upward and facies are mapped in 3D. Genetically related successions are identified by defining a hierarchy of bounding surfaces. The genesis, architecture, geometry, and connectivity of facies are explored in 3D. The approach used here reveals that avulsion deposits are comparable in process, landform, facies, bounding surfaces, and scale to interdistributary bayfill, i.e. delta lobe deposits. Even a simple Stage I splay is a complex landform, composed of several geomorphic components, several facies and many depositional events. As in bayfill, an alluvial ridge forms as the feeder crevasse and its levees advance basinward through their own distributary mouth bar deposits to form a Stage I splay. This produces a shoestring-shaped concentration of disconnected sandbodies that is flanked by wings of heterolithic strata, that join beneath the terminal mouth bar. The proposed results challenge current paradigms. Defining a crevasse splay as a discrete sandbody potentially ignores 70% of the landform's volume. An individual sandbody is likely only a small part of a crevasse splay complex. The thickest sandbody is a terminal, channel associated feature, not a sheet that thins in the direction of propagation. The three stage model of splay evolution proposed by Smith et al. (Sedimentology, vol. 36 (1989) 1) is revised to include facies and geometries consistent with a bayfill model. By analogy with delta lobes, the avulsion sequence is a parasequence, provided that its definition is modified to be independent from sea level. In non-marine settings, facies contacts at the tops of regional peats, coals, and paleosols are analogous to marine flooding surfaces. A parasequence is redefined here as a relatively conformable succession of genetically related strata or landforms that is bounded by regional flooding surfaces or their correlative surfaces. This broader definition incorporates the concept of landscape evolution between regional flooding surfaces in a variety of depositional settings. With respect to landscape evolution, accommodation space has three spatial dimensions - vertical (x), lateral (y), and down-the-basin (z). A flood basin fills in as landforms vertically (x) and laterally accrete (y), and prograde down-the-basin (z). Vertical aggradation is limited by the elevation of maximum flood stage (local base level). Differential tectonism and geomorphology control the slope of the flood basin floor and the direction of landscape evolution. These processes produce parasequences that include inclined stratal surfaces and oriented, stacked macroforms (clinoforms) that show the magnitude and direction of landscape evolution. ?? 2001 Elsevier Science B.V. All rights reserved.

Geomorphology, facies architecture, and high-resolution, non-marine sequence stratigraphy in avulsion deposits, Cumberland Marshes, Saskatchewan

NASA Astrophysics Data System (ADS)

Farrell, K. M.

2001-02-01

This paper demonstrates field relationships between landforms, facies, and high-resolution sequences in avulsion deposits. It defines the building blocks of a prograding avulsion sequence from a high-resolution sequence stratigraphy perspective, proposes concepts in non-marine sequence stratigraphy and flood basin evolution, and defines the continental equivalent to a parasequence. The geomorphic features investigated include a distributary channel and its levee, the Stage I crevasse splay of Smith et al. (Sedimentology, vol. 36 (1989) 1), and the local backswamp. Levees and splays have been poorly studied in the past, and three-dimensional (3D) studies are rare. In this study, stratigraphy is defined from the finest scale upward and facies are mapped in 3D. Genetically related successions are identified by defining a hierarchy of bounding surfaces. The genesis, architecture, geometry, and connectivity of facies are explored in 3D. The approach used here reveals that avulsion deposits are comparable in process, landform, facies, bounding surfaces, and scale to interdistributary bayfill, i.e. delta lobe deposits. Even a simple Stage I splay is a complex landform, composed of several geomorphic components, several facies and many depositional events. As in bayfill, an alluvial ridge forms as the feeder crevasse and its levees advance basinward through their own distributary mouth bar deposits to form a Stage I splay. This produces a shoestring-shaped concentration of disconnected sandbodies that is flanked by wings of heterolithic strata, that join beneath the terminal mouth bar. The proposed results challenge current paradigms. Defining a crevasse splay as a discrete sandbody potentially ignores 70% of the landform's volume. An individual sandbody is likely only a small part of a crevasse splay complex. The thickest sandbody is a terminal, channel associated feature, not a sheet that thins in the direction of propagation. The three stage model of splay evolution proposed by Smith et al. (Sedimentology, vol. 36 (1989) 1) is revised to include facies and geometries consistent with a bayfill model. By analogy with delta lobes, the avulsion sequence is a parasequence, provided that its definition is modified to be independent from sea level. In non-marine settings, facies contacts at the tops of regional peats, coals, and paleosols are analogous to marine flooding surfaces. A parasequence is redefined here as a relatively conformable succession of genetically related strata or landforms that is bounded by regional flooding surfaces or their correlative surfaces. This broader definition incorporates the concept of landscape evolution between regional flooding surfaces in a variety of depositional settings. With respect to landscape evolution, accommodation space has three spatial dimensions — vertical ( x), lateral ( y), and down-the-basin ( z). A flood basin fills in as landforms vertically ( x) and laterally accrete ( y), and prograde down-the-basin ( z). Vertical aggradation is limited by the elevation of maximum flood stage (local base level). Differential tectonism and geomorphology control the slope of the flood basin floor and the direction of landscape evolution. These processes produce parasequences that include inclined stratal surfaces and oriented, stacked macroforms (clinoforms) that show the magnitude and direction of landscape evolution.

Orpheus recombination : a comprehensive bacteriophage system for murine targeting vector construction by transplacement.

PubMed

Woltjen, Knut; Ito, Kenichi; Tsuzuki, Teruhisa; Rancourt, Derrick E

2008-01-01

In recent years, methods to address the simplification of targeting vector (TV) construction have been developed and validated. Based on in vivo recombination in Escherichia coli, these protocols have reduced dependence on restriction endonucleases, allowing the fabrication of complex TV constructs with relative ease. Using a methodology based on phage-plasmid recombination, we have developed a comprehensive TV construction protocol dubbed Orpheus recombination (ORE). The ORE system addresses all necessary requirements for TV construction; from the isolation of genespecific regions of homology to the deposition of selection/disruption cassettes. ORE makes use of a small recombination plasmid, which bears positive and negative selection markers and a cloned homologous "probe" region. This probe plasmid may be introduced into and excised from phage-borne murine genomic clones by two rounds of single crossover recombination. In this way, desired clones can be specifically isolated from a heterogeneous library of phage. Furthermore, if the probe region contains a designed mutation, it may be deposited seamlessly into the genomic clone. The complete removal of operational sequences allows unlimited repetition of the procedure to customize and finalize TVs within a few weeks. Successful gene-specific clone isolation, point mutations, large deletions, cassette insertions, and finally coincident clone isolation and mutagenesis have all been demonstrated with this method.

Stratigraphic palaeobiology around the Pliocene-Pleistocene boundary at Altavilla Milicia (Sicily, Italy)

NASA Astrophysics Data System (ADS)

Dominici, Stefano; Benvenuti, Marco; Garilli, Vittorio; Uchman, Alfred; Pollina, Francesco

2017-04-01

The Pliocene-Pleistocene around Altavilla Milicia, near Palermo (Sicily), includes a thick siliciclastic succession rich with shell beds, dominated by molluscs, brachiopods and annelids in fine-grained, totally bioturbated sandstones. Taphonomy of fossil assemblages indicates the importance of taphonomic feedback and within-habitat time-averaging in proximity of maximum flooding intervals. The trace fossil suite is characterized by the abundance of Thalassinoides paradoxicus boxworks and by local occurence of Scalichnus, Piscichnus, ?Scolicia, ?Bichordites, Ophiomorpha, ?Gyrolithes, Palaeophycus, Diopatrichnus and ?Taenidium. These trace fossils are typical of the archetypal Cruziana ichnofacies, with local elements of the proximal Cruziana ichnofacies, which point to deposition mainly below the fairweather wave base. Three depositional sequences, characterized by geometries driven by the interplay of eustatism and regional tectonics, were recognized through sedimentary facies analysis. Biostratigraphic data frame the oldest sequence in the upper Pliocene, whereas the thickest part of the succession, occupied by the second sedimentary sequence, includes biozone NN16b/17 of calcareous nannoplankton stratigraphy, thereby comprising the base of the Pleistocene. Transgressive deposits of the third and uppermost sequence are marked by encrusted and bioeroded pebbles with sparse oyster shells. The whole time interval is characterized by glacio-eustatic fluctuations in the 50-100 m range and with 100 ky-periodicity. We performed a multivariate analysis of 22 samples yielding 92 species of mollusks collected in the first and second sequences. Clustering and ordination analysis allowed to recognize a gradient controlled by depth-related environmental variables. At one end of the continuum we have a very-shallow water assemblage dominated by the bivalve Loripes orbiculatus, indicating an organic-rich seagrass bottom. Opposite in the continuum is an offshore assemblage dominated by Corbula gibba and the extinct gastropod Petaloconchus intortus. Both the shallowest and the deepest assemblages are from the first (Piacenzian) sequence. The gradient at intermediate depths is better characterized by restricting the analysis to 17 collections from the second sequence (Piacenzian-Gelasian). The shallowest assemblage is here dominated by upper shoreface species, such as Tellina spp. and Spisula subtruncata, and the deepest by muddy bottom, offshore transition species, such as Venus nux, the extinct gastropod Nassarius semistriatus and deposit-feeding nuculanoid bivalves. Plotting samples along the composite section allows to recognize two deepening-upward trends and two intervals of maximum flooding, in accordance with the sequence-stratigraphic interpretation. Stratigraphic palaeobiology proves to be a powerful tool to understand factors that control the geologic record during an interval of intense climate change.

Heteroepitaxial growth of 3-5 semiconductor compounds by metal-organic chemical vapor deposition for device applications

NASA Technical Reports Server (NTRS)

Collis, Ward J.; Abul-Fadl, Ali

1988-01-01

The purpose of this research is to design, install and operate a metal-organic chemical vapor deposition system which is to be used for the epitaxial growth of 3-5 semiconductor binary compounds, and ternary and quaternary alloys. The long-term goal is to utilize this vapor phase deposition in conjunction with existing current controlled liquid phase epitaxy facilities to perform hybrid growth sequences for fabricating integrated optoelectronic devices.

Sedimentary facies analysis of the Mesozoic clastic rocks in Southern Peru (Tacna, 18°S): Towards a paleoenvironmental Redefinition and stratigraphic Reorganization

NASA Astrophysics Data System (ADS)

Alván, Aldo; Jacay, Javier; Caracciolo, Luca; Sánchez, Elvis; Trinidad, Inés

2018-07-01

The Mesozoic rocks of southern Peru comprise a Middle Jurassic to Early Cretaceous sedimentary sequence deposited during a time interval of approximately 34 Myr. In Tacna, these rocks are detrital and constitute the Yura Group (Callovian to Tithonian) and the Hualhuani Formation (Berriasian). Basing on robust interpretation of facies and petrographic analysis, we reconstruct the depositional settings of such units and provide a refined stratigraphic framework. Accordingly, nine types of sedimentary facies and six architectural elements are defined. They preserve the record of a progradational fluvial system, in which two styless regulated the dispersion of sediments: (i) a high-to moderate-sinuosity meandering setting (Yura Group), and a later (ii) incipient braided setting (Hualhuani Formation). The Yura Group (Callovian-Tithonian) represents the onset of floodplain deposits and lateral accretion of point-bar deposits sited on a semi-flat topography. Nonetheless, the progradational sequence was affected by at least two rapid marine ingressions occurred during Middle Callovian and Tithonian times. Such marine ingressions reveal the proximity of a shallow marine setting and incipient carbonate deposition. In response to increase in topographic gradient, the Hualhuani Formation (Berriasian) deposited as extensive multistory sandy channels. The mineralogy of the Mesozoic sediments suggests sediment supplies and intense recycling from a craton interior (i.e. Amazon Craton and/or plutonic sources) located eastward of the study area.

Molecular confirmation of Hepatozoon canis in Mauritius.

PubMed

Daskalaki, Aikaterini Alexandra; Ionică, Angela Monica; Jeetah, Keshav; Gherman, Călin Mircea; Mihalca, Andrei Daniel

2018-01-01

In this study, Hepatozoon species was molecularly identified and characterized for the first time on the Indian Ocean island of Mauritius. Partial sequences of the 18S rRNA gene of the Hepatozoon isolates were analysed from three naturally infected dogs. The sequences of H. canis were similar to the 18S rRNA partial sequences (JX112783, AB365071 99%) from dog blood samples from West Indies and Nigeria. Our sequences were deposited in the GenBank database. Copyright © 2017 Elsevier B.V. All rights reserved.

Preliminary examination of uranium deposits near Marysvale, Piute County, Utah

USGS Publications Warehouse

Granger, Harry C.; Bauer, Herman L.

1950-01-01

Autunite and other uranium minerals were discovered in 1948 by Pratt Seegmiller about 3 1/4 miles north of Marysvale, Piute County, Utah. Mining operations were begun in the summer of 1949 by the Vanadium Corporation of America on the Prospector and the Freedom claims, and by the Bullion Monarch Mining Company a the Bullion Monarch claims. These claims were examined briefly in December 1949 and January 1950 by the writers. The uranium deposits of the Marysvale district are in north-easterly striking fault zones in quartz monzonite that intrudes rocks of the "older" Tertiary volcanic sequence. Flows and tuffs of the "younger" Tertiary volcanic sequence uncomfortably overlie the earlier rocks. Autunite, tobernite, uranophane, schroeckingerite, and at least one unidentified secondary uranium mineral occur in the upper parts of the deposits. Pitchblende has been mined from the underground workings of the Prospector No. 1 mine. The uranium minerals are associated with dense quartz veins and intensely argillized wall rock. In the upper parts of the deposits pyrite is completely oxidized. The secondary uranium minerals probably were formed by the alteration of primary pitchblende by circulating meteoric waters.

Sequence stratigraphy on an early wet Mars

NASA Astrophysics Data System (ADS)

Barker, Donald C.; Bhattacharya, Janok P.

2018-02-01

The evolution of Mars as a water-bearing body is of considerable interest for the understanding of its early history and evolution. The principles of terrestrial sequence stratigraphy provide a useful conceptual framework to hypothesize about the stratigraphic history of the planets northern plains. We present a model based on the hypothesized presence of an early ocean and the accumulation of lowland sediments eroded from highland terrain during the time of the valley networks and later outflow channels. Ancient, global environmental changes, induced by a progressively cooling climate would have led to a protracted loss of surface and near surface water from low-latitudes and eventual cold-trapping at higher latitudes - resulting in a unique and prolonged, perpetual forced regression within basins and lowland depositional environments. The Messinian Salinity Crisis (MSC) serves as a potential terrestrial analogue of the depositional and environmental consequences relating to the progressive removal of large standing bodies of water. We suggest that the evolution of similar conditions on Mars would have led to the emplacement of diagnostic sequences of deposits and regional scale unconformities, consistent with intermittent resurfacing of the northern plains and the progressive loss of an early ocean by the end of the Hesperian era.

Volcanic Hazards Associated with the NE Sector of Tacaná Volcano, Guatemala.

NASA Astrophysics Data System (ADS)

Hughes, S. R.; Saucedo, R.; Macias, J.; Arce, J.; Garcia-Palomo, A.; Mora, J.; Scolamacchia, T.

2003-12-01

Tacaná volcano, with a height of 4,030 m above sea level, straddles the southern Mexico/Guatemala border. Last active in 1986, when there was a small phreatic event with a duration of a few days, this volcano presents an impending hazard to over 250,000 people. The NE sector of the volcano reveals the violent volcanic history of Tacaná that may be indicative of a serious potential risk to the area. Its earliest pyroclastic history appears to consist of fall, flow, and surge deposits, together with lavas, that have formed megablocks within a series of old debris avalanche deposits. This sector collapse event is overlain by a sequence of pumice fall and ash flow deposits, of which the youngest, less-altered pumice fall deposit shows a minimum thickness of > 4 m, with a dispersal axis trending toward the NE. A second debris avalanche deposit, separated from the above deposits by a paleosoil, is dominated by megablocks of lava and scoriaceous dome material. The current topography around the northeastern flank of the volcano is determined by a third, and most recent debris avalanche deposit, a thick (> 20 m) sequence of six block and ash flows dated at around 16,000 years BP, each separated by 1-10 cm thick ash cloud surge deposit, together with secondary lahar deposits. These are followed by a at least 4 lava flows that extend 2 km down the flank of the volcano. It appears that the most recent pyroclastic event at Tacaná is also recorded in this sector of the volcano: above the block and ash flows occurs a > 1 m thick ash flow unit that can be seen at least 5 km from the vent. Lastly, the Santa Maria Ash fall deposit, produced in 1902, has capped most of the deposits at Tacaná.

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

2015-01-01

The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evidence of orbital forcing in 510 to 530 million year old shallow marine cycles, Utah and western Canada

NASA Technical Reports Server (NTRS)

Bond, Gerard C.; Beavan, John; Kominz, Michelle A.; Devlin, William

1992-01-01

Spectral analyses of two sequences of shallow marine sedimentary cycles that were deposited between 510 and 530 million years ago were completed. One sequence is from Middle Cambrian rocks in southern Utah and the other is from Upper Cambrian rocks in the southern Canadian Rockies. In spite of the antiquity of these strata, and even though there are differences in the age, location, and cycle facies between the two sequences, both records have distinct spectral peaks with surprisingly similar periodicities. A null model constructed to test for significance of the spectral peaks and circulatory in the methodology indicates that all but one of the spectral peaks are significant at the 90 percent confidence level. When the ratios between the statistically significant peaks are measured, we find a consistent relation to orbital forcing; specifically, the spectral peak ratios in both the Utah and Canadian examples imply that a significant amount of the variance in the cyclic records is driven by the short eccentricity (approximately 109 ky) and by the precessional (approximately 21 ky) components of the Earth's orbital variations. Neither section contains a significant component of variance at the period of the obliquity cycle, however.

Model for turbidite-to-contourite continuum and multiple process transport in deep marine settings: examples in the rock record

NASA Astrophysics Data System (ADS)

Stanley, Daniel Jean

1993-01-01

Petrological analysis of geological sections in St. Croix in the Caribbean, the Niesenflysch in Switzerland and the Annot Sandstone in the French Maritime Alps sheds light on multiple process transport in deep marine settings. A model depicting a turbidite-to-contourite continuum of stratal types is applied to these three rock units. Recognition of a diverse suite of bedforms, coupled with analysis of paleocurrents, helps to better interpret depositional origin and basin paleogeography. The St. Croix strata record emplacement by gravity flows and, subsequently, by bottom currents flowing parallel to the base of slope; these sediments accumulated on a lower slope apron. A Niesenflysch section in the Swiss Alps west of Adelboden includes turbidites which were deposited at fairly regular intervals beyond the base of slope, in a setting more distal than that of the St. Croix sequences. Most of these turbidites appear to have been partially reworked by bottom currents related to basin circulation or to density flows from the basin margins. In the Annot Sandstone, reworked turbidites (termed transitional variants) and packets of entirely rippled strata are observed in submarine fan and slope sequences in the Peira-Cava area. In contrast to those in St. Croix and the Niesenflysch, the current-emplaced deposits of the Annot Sandstone are directly associated with fan-valley deposits. Such rippled strata in channels are deposits of gravity flow origin which were subsequently reworked downslope by currents generated by successive gravity flows; they also occur on levees by overbank flow. Consideration of multiple process transport is of special help to interpret sections which are poorly exposed, or which can be examined in cores, or which are located in sequences that have been highly deformed structurally.

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

PubMed

Salzberg, Steven L; Dunning Hotopp, Julie C; Delcher, Arthur L; Pop, Mihai; Smith, Douglas R; Eisen, Michael B; Nelson, William C

2005-01-01

The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

Valles Marineris Basin Beds: a Complex Story

NASA Technical Reports Server (NTRS)

Lucchitta, B. K.

1985-01-01

High resolution stereoimages of the central Valles Marineris enabled detailed geologic mapping on Ophir and Candor Chasmata. Abundant light colored deposits, both layered and massive, fill the chasmata in this region. Units within these deposits were identified by their erosional characteristics and superposition and cross cutting relations. The Valles Marineris beds reflect a history of repeated faulting, volcanic eruptions, and deposition and erosion, resulting in stratigraphic sequences with several unconformities. Because of the preponderance of apparent volcanic deposits inside the troughs, the chasmata may not be simple grabens, but rather giant volcano tectonic depressions. Major events in chasmata development are examined.

The basal fallout and surge deposits of the mafic ignimbrite-forming Villa Senni Eruption Unit, (Colli Albani volcano, Italy)

NASA Astrophysics Data System (ADS)

Vinkler, A.; Ort, M. H.; Giordano, G.

2009-12-01

The Villa Senni Eruption Unit (350ka) represents the youngest large caldera-forming eruption of the Colli Albani volcano near Rome (Italy). The Colli Albani magma is marked by very undersaturated chemistry (tephritic to K-foiditic) and low viscosity. The total volume of the Villa Senni Eruption Unit is estimated at > 50 km3 and 30 km3 DRE (Watkins et al., 2002). The unit includes a sequence of a basal fallout/surge deposit, two main ignimbrites emplaced during the same eruptive event, a series of breccia deposits positioned between the two ignimbrites, and a rarely preserved final fallout. The basal surge and fallout sequence may help answer questions regarding the beginning of a large mafic ignimbrite eruption. The entire surge and fallout deposit is 190 cm thick at the caldera wall, consisting of 19 individual, parallel to faintly cross-stratified layers. The deposit distally thins to 25 cm at 18 km east of the caldera and to 2.5 cm at 21 km NW of the caldera. The eruption started with fine ash surges showing cross-stratification at proximal locations and being vesicular distally. The deposit consists mainly of juvenile clasts, which are angular, poorly vesicular, and rich in leucite microlites (~80 µm). Clasts around 100-150 μm show signs of magma-water interaction: quench fracturing: conchoidal and step fractures, smooth surfaces, adhering clasts and melt film. These features are present in several thin alternating surge and fall sequences at the base of the deposit. The lithic clasts in these first deposits are concentrated in layers, indicating pulsatory behavior of the eruption. Upward, the deposit consists of thicker, coarse ash to lapilli fallout layers from more sustained columns. The juvenile clasts in these deposits are more irregular, with higher vesicularity (but less than 50%) and smaller leucite microlites (~60 μm). The uppermost part of the basal fallout/surge deposit shows features transitional to the first large ignimbrite: fallout deposits alternate with poorly sorted flow units, with an increase in free leucite crystals and lithic content, with more abundant deep lithic clasts and a further leucite microlite size decrease (~20 μm) , which could indicate an accelerating magma in the conduit. We think that external factors, such as magma-water interaction and consequent gas explosions, triggered the highly explosive Villa Senni Eruption. Low vesicularity of the early juvenile clasts suggests the magma was relatively low in volatiles at the outset and did not start as a gas-driven eruption. Later in the eruption, the high ascent rate and fast decompression of the magma sustained a large explosive eruption.

Calibration of high frequency pollen sequences and tree-ring records

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wigand, P.E.; Rose, M.R.

This paper examines two radiocarbon dated paleoenvironmental records from southern Nevada for the possibility of correlating high-frequency pollen samples with nearby long-term tree-ring sequences. Variable deposition rate are discussed. Radiocarbon dating control of the pollen cores, as well as closer interval sampling is presented.

Event sand layers suggesting the possibility of tsunami deposits identified in the upper Holocene sequence nearby the Kuwana fault, central Japan

NASA Astrophysics Data System (ADS)

Niwa, Y.; Sugai, T.; Matsuzaki, H.

2012-12-01

The Kuwana fault is located on coastal area situated on inner part of the Ise Bay, central Japan, which opens to the Nankai Trough. This reverse fault displaces a late Pleistocene terrace surface with 1 to 2 mm/yr of average vertical slip rate, and a topset of delta at several meters, respectively. And, this fault is estimated to have generated two historical earthquakes (the AD 745 Tempyo and the AD 1586 Tensho earthquakes). We identified two event sand layers from upper Holocene sequence on the upthrown side of the Kuwana fault. Upper Holocene deposits in this study area show prograding delta sequence; prodelta mud, delta front sandy silt to sand, and flood plain sand/mud, respectively, from lower to upper. Two sand layers intervene in delta front sandy silt layer, respectively. Lower sand layer (S1) shows upward-coarsening succession, whereas upper sand layer (S2) upward-fining succession. These sand layers contain sharp contact, rip-up crust, and shell fragment, indicating strong stream flow. Radiocarbon ages show that these strong stream flow events occurred between 3000 and 1600 years ago. Decreasing of salinity is estimated from decreasing trend of electrical conductivity (EC) across S1. Based on the possibility that decreasing of salinity can be occurred by shallowing of water depth caused by coseismic uplift, and that S1 can be correlated with previously known faulting event on the Kuwana fault, S1 is considered to be tsunami deposits caused by faulting on the Kuwana fault. On the other hand, S2, which cannot be correlated with previously known faulting events on the Kuwana fault, may be tsunami deposits by ocean-trench earthquake or storm deposits. In the presentation, we will discuss more detail correlation of these sand deposits not only in the upthrown side of the Kuwana fault, but also downthrown side of the fault.

Unifying tephrostratigraphic approaches to redefine major Holocene marker tephras, Mt. Taranaki, New Zealand

NASA Astrophysics Data System (ADS)

Damaschke, M.; Cronin, S. J.; Torres-Orozco, R.; Wallace, R. C.

2017-05-01

In this study, geochemical fingerprinting of glass shards and titanomagnetite phenocrysts was used to match twenty complex pyroclastic deposits from the flanks of Mt. Taranaki to major tephra fall ;marker beds; in medial and distal deposition sites. These correlations hinged upon identifying time-bound compositional changes (a chemostratigraphy) in distal Taranaki tephra-fall sequences preserved in lake and peat sediment records around the volcano. The current work shows that previous soil-stratigraphy based studies led to miscorrelations, because they relied upon radiocarbon dates, a ;counting back; approach, and an underestimate of the number of eruptions that actually occurred in any time frame. The new tephrostratigraphy proposed at Mt. Taranaki resulted from stratigraphic rearranging of several earlier-defined units. Some tephra units are older than previously determined (e.g., Waipuku, Tariki, and Mangatoki; 6 to 9 cal ka BP), while one of the most prominent Taranaki marker tephra deposit, the Korito, is shown to lie stratigraphically above a widespread rhyolitic marker bed from Taupo volcano, the Stent Tephra (also known as unit Q; 4.3 cal ka BP). Pyroclastic tephra deposits previously dated between 6 to 4 cal ka BP at a key tephra section, c. 40 km NE of Mt. Taranaki's summit, were misidentified and are now shown to comprise new marker tephra deposits, including the Kokowai ( 4.7 cal ka BP), which is a prominent marker horizon on the eastern flanks of the volcano. A new local proximal stratigraphy for < 5 cal ka BP tephra units can be well correlated to tephra layers within distal lake and peat sequences, but the differences between the two records indicates an overall larger number of eruptions have occurred at this volcano than previously thought. This study additionally demonstrates the utility of titanomagnetite chemistry for discrimination and correlation of groups or sequences of tephra deposits - even if unique compositions cannot be identified.

A new stratigraphic model for the deposition of the Dammam Formation

NASA Astrophysics Data System (ADS)

Lokier, Stephen; Fiorini, Flavia; Min, Jina

2017-04-01

In recent years, mixed siliciclastic-carbonate successions have increasingly become targets for hydrocarbon exploration and production activities. Despite the abundance of these successions throughout the Middle East, there have been very few attempts to employ quantitative techniques to interpret their depositional settings and to develop constrained sequence stratigraphic models for their deposition. This study focuses on the Eocene age Dammam Formation that crops out on the flanks of the Jebel Hafeet anticline south of Al Ain in the United Arab Emirates. The Dammam Formation comprises units alternating between poorly-lithified, easily-weathered, siliciclastic and marly horizons and well-lithified limestones. These units were deposited in a foreland basin that formed in association with the Late Cretaceous obduction of the Semail Ophiolite onto the northeastern margin of the Arabian Plate. The Paleogene infilling of this basin is recorded in the shallowing-upward sedimentary sequence of the lithologies of the Pabdeh Group. This succession records the transition from marine carbonate sedimentation, through increasingly evaporitic-dominated units during the late Eocene to early Miocene to a fluvial-alluvial system by mid to late Miocene times. The Dammam Formation was deposited in an open shallow-marine setting strongly influenced by the influx of siliciclastic material sourced from the close-by uplifted massif of the obducted ophiolite. The skeletal assemblage of the Dammam Formation is dominated by Nummulites and Assilina larger benthic foraminifera along with subordinate smaller foraminifera, echinoids, bivalves, corals, bryozoan, gastropods, echinoids and calcareous algae. Previous studies of the Dammam Formation have employed the biotic component in the reconstruction of water depth. However, these studies neglected to consider that turbidity, associated with the abundant siliciclastic component, resulted in a reduction in the depth of the euphotic zone and a consequent response of the benthic biota. We employ a range of quantitative analytical techniques in order to constrain the influence of the siliciclastic component on the lithofacies of the Dammam Formation and present a new sequence stratigraphic model for the deposition of the formation.

The dating and interpretation of a Mode 1 site in the Luangwa Valley, Zambia.

PubMed

Barham, Lawrence; Phillips, William M; Maher, Barbara A; Karloukovski, Vassil; Duller, Geoff A T; Jain, Mayank; Wintle, Ann G

2011-05-01

Flake based assemblages (Mode 1) comprise the earliest stone technologies known, with well-dated Oldowan sites occurring in eastern Africa between ~2.6-1.7 Ma, and in less securely dated contexts in central, southern and northern Africa. Our understanding of the spread and local development of this technology outside East Africa remains hampered by the lack of reliable numerical dating techniques applicable to non-volcanic deposits. This study applied the still relatively new technique of cosmogenic nuclide burial dating ((10)Be/(26)Al) to calculate burial ages for fluvial gravels containing Mode 1 artefacts in the Luangwa Valley, Zambia. The Manzi River, a tributary of the Luangwa River, has exposed a 4.7 m deep section of fluvial sands with discontinuous but stratified gravel layers bearing Mode 1, possibly Oldowan, artefacts in the basal layers. An unconformity divides the Manzi section, separating Mode 1 deposits from overlying gravels containing Mode 3 (Middle Stone Age) artefacts. No diagnostic Mode 2 (Acheulean) artefacts were found. Cosmogenic nuclide burial dating was attempted for the basal gravels as well as exposure ages for the upper Mode 3 gravels, but was unsuccessful. The complex depositional history of the site prevented the calculation of reliable age models. A relative chronology for the full Manzi sequence was constructed, however, from the magnetostratigraphy of the deposit (N>R>N sequence). Isothermal thermoluminescence (ITL) dating of the upper Mode 3 layers also provided consistent results (~78 ka). A coarse but chronologically coherent sequence now exists for the Manzi section with the unconformity separating probable mid- or early Pleistocene deposits below from late Pleistocene deposits above. The results suggest Mode 1 technology in the Luangwa Valley may post-date the Oldowan in eastern and southern Africa. The dating programme has contributed to a clearer understanding of the geomorphological processes that have shaped the valley and structured its archaeological record. Copyright © 2010 Elsevier Ltd. All rights reserved.

Seep carbonates and chemosynthetic coral communities in the Early Paleocene alpine accretionary wedge: evidences from the Bocco Shale (Internal Liguride ophiolitic sequence, Northern Apennine, Italy)

NASA Astrophysics Data System (ADS)

Pandolfi, Luca; Boschi, Chiara; Luvisi, Edoardo; Alessandro, Ellero; Marroni, Michele; Meneghini, Francesca

2014-05-01

In Northern Apennines, the Internal Liguride units are characterized by an ophiolite sequence that represents the stratigraphic base of a Late Jurassic-Early Paleocene sedimentary cover. The Bocco Shale represents the youngest deposit recognized in the sedimentary cover of the ophiolite sequence, sedimented just before the inception of subduction-related deformation history. The Bocco Shale has been interpreted as a fossil example of deposits related to the frontal tectonic erosion of the alpine accretionary wedge slope. The frontal tectonic erosion resulted in a large removal of material from the accretionary wedge front reworked as debris flows and slide deposits sedimented on the lower plate above the trench deposits. These trench-slope deposits may have been successively deformed and metamorphosed during the following accretion processes. The frontal tectonic erosion can be envisaged as a common process during the convergence-related evolution of the Ligure-Piemontese oceanic basin in the Late Cretaceous-Early Tertiary time span. In the uppermost Internal Liguride tectonic unit (Portello Unit of Pandolfi and Marroni. 1997), that crops-out in Trebbia Valley, several isolated blocks of authigenic carbonates, unidentificated corals and intrabasinal carbonatic arenites have been recognized inside the fine-grained sediments that dominate the Early Paleocene Lavagnola Fm. (cfr. Bocco Shale Auctt.). The preliminary data on stable isotopes from blocks of authigenic carbonates (up to 1 m thick and 3 m across) and associated corals archive a methane signatures in their depleted carbon isotope pattern (up to δ13C -30‰ PDB) and suggest the presence of chemosynthetic paleocommunities. The seep-carbonates recognized at the top of Internal Liguride succession (cfr. Bocco Shale Auctt.) occur predominantly as blocks in very thick mudstone-dominated deposits and probably developed in an environment dominated by the expulsion of large volume of cold methane-bearing fluids focused in the frontal part of the Early Paleocene alpine accretionary wedge.

Coastal evidence for Holocene subduction-zone earthquakes and tsunamis in central Chile

USGS Publications Warehouse

Dure, Tina; Cisternas, Marco; Horton, Benjamin; Ely, Lisa; Nelson, Alan R.; Wesson, Robert L.; Pilarczyk, Jessica

2015-01-01

The ∼500-year historical record of seismicity along the central Chile coast (30–34°S) is characterized by a series of ∼M 8.0–8.5 earthquakes followed by low tsunamis (<4 m) occurring on the megathrust about every 80 years. One exception is the AD 1730 great earthquake (M 9.0–9.5) and high tsunami (>10 m), but the frequency of such large events is unknown. We extend the seismic history of central Chile through a study of a lowland stratigraphic sequence along the metropolitan coast north of Valparaíso (33°S). At this site, higher relative sea level during the mid Holocene created a tidal marsh and the accommodation space necessary for sediment that preserves earthquake and tsunami evidence. Within this 2600-yr-long sequence, we traced six laterally continuous sand beds probably deposited by high tsunamis. Plant remains that underlie the sand beds were radiocarbon dated to 6200, 5600, 5000, 4400, 3800, and 3700 cal yr BP. Sediment properties and diatom assemblages of the sand beds—for example, anomalous marine planktonic diatoms and upward fining of silt-sized diatom valves—point to a marine sediment source and high-energy deposition. Grain-size analysis shows a strong similarity between inferred tsunami deposits and modern coastal sediment. Upward fining sequences characteristic of suspension deposition are present in five of the six sand beds. Despite the lack of significant lithologic changes between the sedimentary units under- and overlying tsunami deposits, we infer that the increase in freshwater siliceous microfossils in overlying units records coseismic uplift concurrent with the deposition of five of the sand beds. During our mid-Holocene window of evidence preservation, the mean recurrence interval of earthquakes and tsunamis is ∼500 years. Our findings imply that the frequency of historical earthquakes in central Chile is not representative of the greatest earthquakes and tsunamis that the central Chilean subduction zone has produced.

Sedimentology and Sedimentary Dynamics of the Desmoinesian Cherokee Group, Deep Anadarko Basin, Texas Panhandle

NASA Astrophysics Data System (ADS)

Hu, N.; Loucks, R.; Frebourg, G.

2015-12-01

Understanding the spatial variability of deep-water facies is critical to deep-water research because of its revealing information about the relationship between desity flow processes and their resultant sedimentary sequences. The Cherokee Group in the Anadarko Basin, northeastern Texas Panhandle, provides an opportunity to investigate an icehouse-greenhouse Pennsylvanian hybrid system that well demonstrates the intricacies of vertical and lateral facies relationships in an unconfined fan-delta fed deep-water slope to basinal setting. The stratigraphic section ranges in thickness from 150 to 460 m. The cyclic sedimentation and foreland basin tectonics resulted in a complex stratal architecture that was sourced by multiple areas of sediment input. This investigation consists of wireline-log and core data. Five-thousand wireline logs were correlated in an area of over 9500 sq km to map out six depositional sequences that are separated by major flooding events. These events are correlative over the whole area of study. Six cores, that sample nearly the complete section, were described for lithofacies. Lithofacies are recognized based on depositional features and mineralogy:(1) Subarkose, (2) Lithicarkoses, (3) Sandy siliciclastic conglomerate, (4) Muddy calcareous conglomerate, (5) Crinoidal packstone, (6) Oodic grainstone, (7)Pelodic grainstone, (8) Ripple laminated mudrock, (9) faint laminated mudrock. The integration of isopachs of depositional sequences with the lithofacies has allowed the delineation of the spatial and temporal evolution of the slope to basin-floor system. Thin-to-thick bedded turbidites, hyperconcentrated density flow deposits (slurry beds), and debris and mud flow deposits were observed and can be used to better predicte lithofacies distributions in areas that have less data control. These mixed siliciclastic and carbonate deposits can be carrier beds for the hydrocarbons generated from the enclosing organic-rich (TOC ranges from 0.55 to 6.77wt%), dysareobic to anaerobic mudstones.

Inversion Recovery Ultrashort Echo Time Magnetic Resonance Imaging: A Method for Simultaneous Direct Detection of Myelin and High Signal Demonstration of Iron Deposition in the Brain – A Feasibility Study

PubMed Central

Sheth, Vipul R.; Fan, Shujuan; He, Qun; Ma, Yajun; Annesse, Jacopo; Switzer, Robert; Corey-Bloom, Jody; Bydder, Graeme M; Du, Jiang

2017-01-01

Multiple sclerosis (MS)causes demyelinating lesions in the white matter and increased iron deposition in the subcortical gray matter. Myelin protons have an extremely short T2* (less than 1 ms) and are not directly detected with conventional clinical magnetic resonance (MR) imaging sequences. Iron deposition also reduces T2*, leading to reduced signal on clinical sequences. In this study we tested the hypothesis that the inversion recovery ultrashort echo time (IR-UTE) pulse sequence can directly and simultaneously image myelin and iron deposition using a clinical 3T scanner. The technique was first validated on a synthetic myelinphantom (myelin powder in D2O) and a Feridex iron phantom. This was followed by studies of cadaveric MS specimens, healthy volunteers and MS patients. UTE imaging of the synthetic myelin phantom showed an excellent bi-component signal decay with two populations of protons, one with a T2* of 1.2 ms (residual water protons) and the other with a T2* of 290 μs (myelin protons). IR-UTE imaging shows sensitivity to a wide range of iron concentrations from 0.5 to ∼30 mM. The IR-UTE signal from white matter of the brain of healthy volunteers shows a rapid signal decay with a short T2* of ∼300 μs, consistent with the T2* values of myelin protons in the synthetic myelin phantom. IR-UTE imaging in MS brain specimens and patients showed multiple white matter lesions as well as areas of high signal in subcortical gray matter. This in specimens corresponded in position to Perl's diaminobenzide staining results, consistent with increased iron deposition. IR-UTE imaging simultaneously detects lesions with myelin loss in the white matter and iron deposition in the gray matter. PMID:28038965

The dating and interpretation of a Mode 1 site in the Luangwa Valley, Zambia

USGS Publications Warehouse

Barham, L.; Phillips, W.M.; Maher, B.A.; Karloukovski, V.; Duller, G.A.T.; Jain, M.; Wintle, A.G.

2011-01-01

Flake based assemblages (Mode 1) comprise the earliest stone technologies known, with well-dated Oldowan sites occurring in eastern Africa between ??? 2.6-1.7 Ma, and in less securely dated contexts in central, southern and northern Africa. Our understanding of the spread and local development of this technology outside East Africa remains hampered by the lack of reliable numerical dating techniques applicable to non-volcanic deposits. This study applied the still relatively new technique of cosmogenic nuclide burial dating (10Be/26Al) to calculate burial ages for fluvial gravels containing Mode 1 artefacts in the Luangwa Valley, Zambia. The Manzi River, a tributary of the Luangwa River, has exposed a 4.7 m deep section of fluvial sands with discontinuous but stratified gravel layers bearing Mode 1, possibly Oldowan, artefacts in the basal layers. An unconformity divides the Manzi section, separating Mode 1 deposits from overlying gravels containing Mode 3 (Middle Stone Age) artefacts. No diagnostic Mode 2 (Acheulean) artefacts were found. Cosmogenic nuclide burial dating was attempted for the basal gravels as well as exposure ages for the upper Mode 3 gravels, but was unsuccessful. The complex depositional history of the site prevented the calculation of reliable age models. A relative chronology for the full Manzi sequence was constructed, however, from the magnetostratigraphy of the deposit (N>R>N sequence). Isothermal thermoluminescence (ITL) dating of the upper Mode 3 layers also provided consistent results (???78 ka). A coarse but chronologically coherent sequence now exists for the Manzi section with the unconformity separating probable mid- or early Pleistocene deposits below from late Pleistocene deposits above. The results suggest Mode 1 technology in the Luangwa Valley may post-date the Oldowan in eastern and southern Africa. The dating programme has contributed to a clearer understanding of the geomorphological processes that have shaped the valley and structured its archaeological record. ?? 2010 Elsevier Ltd.

Sedimentation and basin-fill history of the Neogene clastic succession exposed in the southeastern fold belt of the Bengal Basin, Bangladesh: a high-resolution sequence stratigraphic approach

NASA Astrophysics Data System (ADS)

Royhan Gani, M.; Mustafa Alam, M.

2003-02-01

The Tertiary basin-fill history of the Bengal Basin suffers from oversimplification. The interpretation of the sedimentary history of the basin should be consistent with the evolution of its three geo-tectonic provinces, namely, western, northeastern and eastern. Each province has its own basin generation and sediment-fill history related mainly to the Indo-Burmese and subordinately to the Indo-Tibetan plate convergence. This paper is mainly concerned with facies and facies sequence analysis of the Neogene clastic succession within the subduction-related active margin setting (oblique convergence) in the southeastern fold belt of the Bengal Basin. Detailed fieldwork was carried out in the Sitapahar anticline of the Rangamati area and the Mirinja anticline of the Lama area. The study shows that the exposed Neogene succession represents an overall basinward progradation from deep marine through shallow marine to continental-fluvial environments. Based on regionally correlatable erosion surfaces the entire succession (3000+ m thick) has been grouped into three composite sequences C, B and A, from oldest to youngest. Composite sequence C begins with deep-water base-of-slope clastics overlain by thick slope mud that passes upward into shallow marine and nearshore clastics. Composite sequence B characteristically depicts tide-dominated open-marine to coastal depositional systems with evidence of cyclic marine regression and transgression. Repetitive occurrence of incised channel, tidal inlet, tidal ridge/shoal, tidal flat and other tidal deposits is separated by shelfal mudstone. Most of the sandbodies contain a full spectrum of tide-generated structures (e.g. herringbone cross-bedding, bundle structure, mud couplet, bipolar cross-lamination with reactivation surfaces, 'tidal' bedding). Storm activities appear to have played a subordinate role in the mid and inner shelf region. Rizocorallium, Rosselia, Planolites and Zoophycos are the dominant ichnofacies within the shelfal mudstone. This paralic sedimentation of Neogene succession in the study area can serve as a good point of reference for tide-dominated regressive shelf depositional systems. The top of the composite sequence B is marked by a pronounced erosion surface indicating the final phase of marine regression followed by the gradual establishment of continental-fluvial depositional systems represented by composite sequence A. In this composite sequence, stacked channel bars of low-sinuosity braided rivers gradually pass upsequence into high-sinuosity meandering river deposits. A sequence stratigraphic approach has been adopted to interpret the basin-fill history with respect to relative sea-level changes; and to subdivide the rock record into several sequences and units (systems tracts and parasequences) based on identified bounding discontinuities, such as transgressive erosion surface (TES), regressive erosion surface (RES), marine flooding surface (MFS), and incised valley floor (IVF). This approach provides new insight for both exploration and exploitation strategy for hydrocarbon plays that may prove vital to the oil companies engaged in exploration activities in the Bengal Basin. It is strongly recommended here that the traditional lithostratigraphic classification of this part of the basin, which is based on the Assam stratigraphy, be abandoned or at least revised. A tentative allostratigraphic scheme is presented, and it is suggested that to formalize the scheme further study, both surface and subsurface, is needed.

sAPP modulates iron efflux from brain microvascular endothelial cells by stabilizing the ferrous iron exporter ferroportin

PubMed Central

McCarthy, Ryan C; Park, Yun-Hee; Kosman, Daniel J

2014-01-01

A sequence within the E2 domain of soluble amyloid precursor protein (sAPP) stimulates iron efflux. This activity has been attributed to a ferroxidase activity suggested for this motif. We demonstrate that the stimulation of efflux supported by this peptide and by sAPPα is due to their stabilization of the ferrous iron exporter, ferroportin (Fpn), in the plasma membrane of human brain microvascular endothelial cells (hBMVEC). The peptide does not bind ferric iron explaining why it does not and thermodynamically cannot promote ferrous iron autoxidation. This peptide specifically pulls Fpn down from the plasma membrane of hBMVEC; based on these results, FTP, for ferroportin-targeting peptide, correctly identifies the function of this peptide. The data suggest that in stabilizing Fpn via the targeting due to the FTP sequence, sAPP will increase the flux of iron into the cerebral interstitium. This inference correlates with the observation of significant iron deposition in the amyloid plaques characteristic of Alzheimer’s disease. PMID:24867889

Economic geology of the Zipaquira quadrangle and adjoining area, Department of Cundinamarca, Colombia

USGS Publications Warehouse

McLaughlin, Donald H.; Arce Herrera, Marino

1970-01-01

At least four evaporite sequences are interbedded with Cretaceous strata in the Bogotga area of the Cordillera Oriental of Colombia. The easternmost and oldest evaporite interval is of probable Berriasian-Valanglnian age; the next oldest is of probable late Barremian-early Aptian age, and is followed by a possible late Aptian sequence. The westernmost and best known sequence is Turonian-early Coniacian in age, in the Sabana de Bogota. This youngest sequence contains the thickest known salt deposits and is probably the most widespread geographically. Three gypsum deposits of probable Barremian-Valanginian age are in the eastern part of the area under investigation. These deposits may have been leached from former salt accumulations. No other evaporites are exposed, but numerous brine springs are known, That the sources of these brines are neither deep not distant is suggested by the generally high concentrations, of the brines, the local presence of rute (leached salt residue), and the commonly significant amounts of H2S gas emitted at these springs. The rock salt exposed in three accessible mines commonly has a characteristic lamination caused by alternating layers of relatively pure halite and very argillaceous halite. Ubiquitously scattered throughout all salt deposits are small clasts of black, commonly pyritic, marly claystone. This lithology is also present as large claystone bodies conformably interbedded in the salt strata. Anhydrite is rare and is apparently more abundant at the Zipaquira mine that at the Nemocon and Upin mine. Paleontologic evidence in the Sabana de Bogota demonstrates that the salt-claystone series, hematite impregnated strata, and carbonaceous to locally coaly claystone are coeval. The salt-claystone facies may have been deposited in shallow evaporite pans that were separated within the overall evaporite interval by barriers on which the locally hematitic strata were deposited. The carbonaceous facies may also have formed in barrier areas or on the edges of the evaporite basins. Whether or not this facies relationship prevails in the older evaporite intervals is not known; meager evidence suggests that it does. Nonmetallic mineral resources other than the evaporite minerals are phosphate rock, limestone, kaolinite, and emeralds. Metallic mineral deposits present in the Zone include hematite at Pericos, La Caldera, Tibirita, Nueva Vizcaya, and Cerro de Montecristo; chalcopyrite at Cerro do Cobre and at Farallones de Medina; galena in several places along the Rio Farallones and Rio Gacheta; and spahlerite in the Junin district.

Two examples of subaqueously welded ash-flow tuffs: the Visean of southern Vosges (France) and the Upper Cretaceous of northern Anatolia (Turkey)

NASA Astrophysics Data System (ADS)

Schneider, Jean-Luc; Fourquin, Claude; Paicheler, Jean-Claude

1992-02-01

Pyroclastic deposits interpreted as subaqueous ash-flow tuff have been recognized within Archean to Recent marine and lacustrine sequences. Several authors proposed a high-temperature emplacement for some of these tuffs. However, the subaqueous welding of pyroclastic deposits remains controversial. The Visean marine volcaniclastic formations of southern Vosges (France) contain several layers of rhyolitic and rhyodacitic ash-flow tuff. These deposits include, from proximal to distal settings, breccia, lapilli and fine-ash tuff. The breccia and lapilli tuff are partly welded, as indicated by the presence of fiamme, fluidal and axiolitic structures. The lapilli tuff form idealized sections with a lower, coarse and welded unit and an upper, bedded and unwelded fine-ash tuff. Sedimentary structures suggest that the fine-ash tuff units were deposited by turbidity currents. Welded breccias, interbedded in a thick submarine volcanic complex, indicate the close proximity of the volcanic source. The lapilli and fine-ash tuff are interbedded in a thick marine sequence composed of alternating sandstones and shales. Presence of a marine stenohaline fauna and sedimentary structures attest to a marine depositional environment below storm-wave base. In northern Anatolia, thick massive sequences of rhyodacitic crystal tuff are interbedded with the Upper Cretaceous marine turbidites of the Mudurnu basin. Some of these tuffs are welded. As in southern Vosges, partial welding is attested by the presence of fiamme and fluidal structures. The latter are frequent in the fresh vitric matrix. These tuff units contain a high proportion of vitroclasis, and were emplaced by ash flows. Welded tuff units are associated with non-welded crystal tuff, and contain abundant bioclasts which indicate mixing with water during flowage. At the base, basaltic breccia beds are associated with micritic beds containing a marine fauna. The welded and non-welded tuff sequences are interbedded in an alternation of limestones and marls. These limestones are rich in pelagic microfossils. The evidence above strongly suggest that in both examples, tuff beds are partly welded and were emplaced at high temperature by subaqueous ash flows in a permanent marine environment. The sources of the pyroclastic material are unknown in both cases. We propose that the ash flows were produced during submarine fissure eruptions. Such eruptions could produce non-turbulent flows which were insulated by a steam carapace before deposition and welding. The welded ash-flow tuff deposits of southern Vosges and northern Anatolia give strong evidence for existence of subaqueous welding.

Whole-genome sequence of Clostridium lituseburense L74, isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus.

PubMed

Lee, Yookyung; Lim, Sooyeon; Rhee, Moon-Soo; Chang, Dong-Ho; Kim, Byoung-Chan

2016-03-01

Clostridium lituseburense L74 was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus collected in Yeong-dong, Chuncheongbuk-do, South Korea and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession NZ_LITJ00000000.

Complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from lettuce (Lactuca sativa) originating from a conventional field in Norway.

PubMed

Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

2016-12-01

Here, we present the 3,795,952 bp complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from conventionally grown lettuce ( Lactuca sativa ) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017580.

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

PubMed Central

Sundaram, Vasavi; Choudhary, Mayank N. K.; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A.; Wang, Ting

2017-01-01

Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF to control gene expression in specific cellular contexts. Transposable elements (TEs) are uniquely equipped to deposit their regulatory sequences across a genome, which could also contain cis-regulatory modules that coordinate the control of multiple genes with the same regulatory logic. We provide the first evidence of mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs). The majority (77%) of the individual TEs tested exhibited enhancer activity in mouse ESCs. By mutating individual TF-binding sites within the TE, we identified a module of TF-binding motifs that cooperatively enhanced gene expression. Interestingly, we also observed the same motif module in the in silico constructed ancestral TE that also acted cooperatively to enhance gene expression. Our results suggest that ancestral TE insertions might have brought in cis-regulatory modules into the mouse genome. PMID:28348391

Conservatism of Late Pennsylvanian vegetational patterns during short-term cyclic and long-term directional environmental change, western equatorial Pangea.

PubMed

Tabor, Neil J; Romanchock, Charles M; Looy, Cynthia V; Hotton, Carol L; Dimichele, William A; Chaney, Dan S

2013-09-19

Patterns of plant distribution by palaeoenvironment were examined across the Pennsylvanian-Permian transition in North-Central Texas. Stratigraphically recurrent packages of distinct lithofacies, representing different habitats, contain qualitatively and quantitatively different macrofloras and microfloras. The species pools demonstrate niche conservatism, remaining closely tied to specific habitats, during both short-term cyclic environmental change and a long-term trend of increasing aridity. The deposits examined principally comprise the terrestrial Markley and its approximate marine equivalent, the Harpersville Formation and parts of lower Archer City Formation. Fossiliferous deposits are lens-like, likely representing fill sequences of channels formed during abandonment phases. Palaeosols, represented by blocky mudstones, comprise a large fraction of the deposits. They suggest progressive climate change from minimally seasonal humid to seasonal subhumid to seasonal dry subhumid. Five lithofacies yielded plants: kaolinite-dominated siltstone, organic shale, mudstone beds within organic shale, coarsening upward mudstone-sandstone interbeds and channel sandstone. Both macro- and microflora were examined. Lithofacies proved compositionally distinct, with different patterns of dominance diversity. Organic shales (swamp deposits), mudstone partings (swamp drainages) and coarsening upward mudstone-sandstone interbeds (floodplains) typically contain Pennsylvanian wetland vegetation. Kaolinite-dominated siltstones and (to the extent known) sandstones contain taxa indicative of seasonally dry substrates. Some kaolinite-dominated siltstones and organic shales/coals yielded palynomorphs. Microfloras are more diverse, with greater wetland-dryland overlap than macrofloras. It appears that these two floras were coexistent at times on the regional landscape.

Conservatism of Late Pennsylvanian vegetational patterns during short-term cyclic and long-term directional environmental change, western equatorial Pangea

PubMed Central

TABOR, NEIL J.; ROMANCHOCK, CHARLES M.; LOOY, CYNTHIA V.; HOTTON, CAROL L.; DIMICHELE, WILLIAM A.; CHANEY, DAN S.

2014-01-01

Patterns of plant distribution by palaeoenvironment were examined across the Pennsylvanian–Permian transition in North–Central Texas. Stratigraphically recurrent packages of distinct lithofacies, representing different habitats, contain qualitatively and quantitatively different macrofloras and microfloras. The species pools demonstrate niche conservatism, remaining closely tied to specific habitats, during both short-term cyclic environmental change and a long-term trend of increasing aridity. The deposits examined principally comprise the terrestrial Markley and its approximate marine equivalent, the Harpersville Formation and parts of lower Archer City Formation. Fossiliferous deposits are lens-like, likely representing fill sequences of channels formed during abandonment phases. Palaeosols, represented by blocky mudstones, comprise a large fraction of the deposits. They suggest progressive climate change from minimally seasonal humid to seasonal subhumid to seasonal dry subhumid. Five lithofacies yielded plants: kaolinite-dominated siltstone, organic shale, mudstone beds within organic shale, coarsening upward mudstone–sandstone interbeds and channel sandstone. Both macro- and microflora were examined. Lithofacies proved compositionally distinct, with different patterns of dominance diversity. Organic shales (swamp deposits), mudstone partings (swamp drainages) and coarsening upward mudstone–sandstone interbeds (floodplains) typically contain Pennsylvanian wetland vegetation. Kaolinite-dominated siltstones and (to the extent known) sandstones contain taxa indicative of seasonally dry substrates. Some kaolinite-dominated siltstones and organic shales/coals yielded palynomorphs. Microfloras are more diverse, with greater wetland–dryland overlap than macrofloras. It appears that these two floras were coexistent at times on the regional landscape. PMID:25339793

Description and quantitative modeling of oolitic reservoir analogs within the lower Kansas City Group (Pennsylvanian), southeastern Kansas

DOE Office of Scientific and Technical Information (OSTI.GOV)

French, J.A.; Watney, W.L.

A significant number of petroleum reservoirs within the Kansas City Group in central and western Kansas are dominantly oolitic grainstones that cap 10- to 30-m-thick, shallowing-upward, carbonate-rich depositional sequences. Coeval units that occur at and near the surface in southeastern Kansas contain similar porous lithofacies that have been examined in detail via cores, outcrops, and an extensive log database to better understand the equivalent reservoirs. These studies suggest that individual oolitic, reservoir-quality units in the Bethany Falls Limestone (equivalent to the K zone in the subsurface) developed at several relative sea level stands that occurred during development of a highstandmore » systems tract within this depositional sequence. As many as three grain-rich parasequences may occur at a given location. The occurrence of multiple parasequences indicates a relatively complex history of K-zone deposition, which likely resulted in significant effects on reservoir architecture. Two-dimensional forward modeling of this sequence with our interactive, PC-based software has revealed that limited combinations of parameters such as shelf configuration, eustasy, sedimentation rates, and subsidence rates generate strata successions similar to those observed. Sensitivity analysis coupled with regional characterization of processes suggest ranges of values that these parameters could have had during deposition of these units. The ultimate goal of this modeling is to improve our ability to predict facies development in areas of potential and known hydrocarbon accumulations.« less

27nt-RNAs guide histone variant deposition via 'RNA-induced DNA replication interference' and thus transmit parental genome partitioning in Stylonychia.

PubMed

Postberg, Jan; Jönsson, Franziska; Weil, Patrick Philipp; Bulic, Aneta; Juranek, Stefan Andreas; Lipps, Hans-Joachim

2018-06-12

During sexual reproduction in the unicellular ciliate Stylonychia somatic macronuclei differentiate from germline micronuclei. Thereby, programmed sequence reduction takes place, leading to the elimination of > 95% of germline sequences, which priorly adopt heterochromatin structure via H3K27me3. Simultaneously, 27nt-ncRNAs become synthesized from parental transcripts and are bound by the Argonaute protein PIWI1. These 27nt-ncRNAs cover sequences destined to the developing macronucleus and are thought to protect them from degradation. We provide evidence and propose that RNA/DNA base-pairing guides PIWI1/27nt-RNA complexes to complementary macronucleus-destined DNA target sequences, hence transiently causing locally stalled replication during polytene chromosome formation. This spatiotemporal delay enables the selective deposition of temporarily available histone H3.4K27me3 nucleosomes at all other sequences being continuously replicated, thus dictating their prospective heterochromatin structure before becoming developmentally eliminated. Concomitantly, 27nt-RNA-covered sites remain protected. We introduce the concept of 'RNA-induced DNA replication interference' and explain how the parental functional genome partition could become transmitted to the progeny.

Tidal sedimentation from a fluvial to estuarine transition, Douglas Group, Missourian -- Virgilian, Kansas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanier, W.P.; Feldman, H.R.; Archer, A.W.

The Tonganoxie Sandstone Member of the Stranger Formation (Douglas Group, Upper Pennsylvanian, Kansas) was deposited in a funnel-shaped, northeast-southwest-trending paleovalley that was incised during the uppermost Missourian sealevel lowstand and backfilled during the subsequent transgression. Quarry exposures of the Tonganoxie near Ottawa, Kansas, include [approximately] 5 m of sheetlike, vertically accreted siltstones and sandy siltstones, bounded above and below by thin coals with upright plant fossils and paleosols. Strata range from submillimeter-thick, normally graded rhythmites to graded bedsets up to 12.5 cm thick with a vertical sedimentary structure sequence (VSS) consisting of the following intervals: (A) a basal massive tomore » normally graded interval; (B) a parallel-laminated interval; (C) a ripple-cross-laminated interval; and (D) an interval of draped lamination. The Tonganoxie succession has many similarities to fluvial overbank/floodplain deposits: sheetlike geometry, upright plant fossils, lack of bioturbation and body fossils, dominance of silt, and a punctuated style of rapid sedimentation from suspension-laden waning currents. Analysis of stratum-thickness variations through the succession suggests that tides significantly influenced sediment deposition. A fluvial-to-estuarine transitional depositional setting is interpreted for the Tonganoxie by analogy with modern depositional settings that show similar physical and biogenic sedimentary structures, vertical sequences of sedimentary structures, and aggradation rates.« less

The volcanic-sedimentary sequence of the Lousal deposit, Iberian Pyrite Belt (Portugal)

NASA Astrophysics Data System (ADS)

Rosa, Carlos; Rosa, Diogo; Matos, Joao; Relvas, Jorge

2010-05-01

The Iberian Pyrite Belt (IPB) is a massive sulfide province that is located in the south of Portugal and Spain, and hosts more than 90 massive sulfide deposits that amount to more than 1850 million metric tonnes of sulfide ore (Tornos, 2006). The ore deposits size, vary from ~1Mt to >100Mt (e.g. Neves Corvo and Aljustrel in Portugal, and Rio Tinto and Tharsis in Spain). The ore deposits are hosted by a submarine sedimentary and volcanic, felsic dominated, succession that constitutes the Upper Devonian to Lower Carboniferous Volcanic and Sedimentary Complex (VSC). The VSC ranges in thickness from approximately 600 to 1300 m (Tornos 2006). The VSC overlies the Phyllite-Quartzite Group (PQ) (Upper Devonian, base unknown) and is overlain by the Baixo Alentejo Flysch Group (Lower to Upper Carboniferous). The Lousal massive sulfide deposit is located in the western part of the IPB and occurs mostly interbedded with black mudstone. The VSC sequence at Lousal mine consists of a mudstone and quartzite sequence (PQ Group) in the lower part of the succession, over which a thick sequence of rhyolitic lavas (>300 m) occurs. Above the rhyolitic lavas there is a thick sequence of black and grey mudstone that hosts the massive sulfide ore bodies, and a rhyolitic sill. The upper part of the VSC sequence consists of a thick mudstone interval that hosts two thick basaltic units, locally with pillows. The rhyolites have small coherent cores, locally with flow bands, that grade to surrounding massive clastic intervals, with large lateral extent. The clasts show jigsaw-fit arrangement in many places and have planar or curviplanar margins and locally are perlitic at the margin. The top contact of these units is in most locations not exposed, which makes difficult to interpret the mode of emplacement. However, the thick clastic intervals, above described, are in accordance with quenching of volcanic glass with abundant water and therefore indicate that quenching of the rhyolites was the dominant fragmentation mechanism. Unlike many locations of the IPB, fiamme-rich pyroclastic units were not identified at Lousal. The ore deposits occur in close proximity with this volcanic centre that may have driven hydrothermal circulation that led to ore formation. The volcanic rocks show intense chloritic alteration, indicating that the mineralizing event occurred after most of the rhyolitic units have emplaced. The massive sulfides show abundant sedimentary structures which is not typical in the massive sulfide deposits of the IPB. The Lousal 50 Mt massive sulfide deposit consists of at least 11 ore bodies and was exploited until 1988 mainly for pyrite. The ores mined averaged 0.7% Cu, 0.8%Pb e 1.4%Zn (Strauss, 1971). These relatively low base metal grades led to an evaluation of the contents and distribution of high-tech element in the ore bodies, which would improve the economic viability of mining the deposit. This evaluation is currently focusing on the distribution and mineralogy of selenium, as ores mined in the past were known to be rich in this element. This work benefits from research projects INCA (PTDC/CTE-GIN/67027/2006; Characterization of crucial mineral resources for the development of renewable energy technologies: The Iberian Pyrite Belt ores as a source of indium and other high-technology elements) and project ARCHYMEDES II (POCTI/CTA/45873/2002), both funded by the Fundação para a Ciência e Tecnologia. REFERENCES Strauss, G.K., 1970. Sobre la geologia de la provincia piritifera del Suroeste de la Peninsula Iberica y sus yacimientos, en especial sobre la mina de pirita de Lousal (Portugal): Memoria del IGME 77, 1-266. Tornos, F., 2006. Environment of formation and styles of volcanogenic massive sulfides: The Iberian Pyrite Belt. Ore Geology Reviews 28, 259-307.

Insilico profiling of microRNAs in Korean ginseng (Panax ginseng Meyer)

PubMed Central

Mathiyalagan, Ramya; Subramaniyam, Sathiyamoorthy; Natarajan, Sathishkumar; Kim, Yeon Ju; Sun, Myung Suk; Kim, Se Young; Kim, Yu-Jin; Yang, Deok Chun

2013-01-01

MicroRNAs (miRNAs) are a class of recently discovered non-coding small RNA molecules, on average approximately 21 nucleotides in length, which underlie numerous important biological roles in gene regulation in various organisms. The miRNA database (release 18) has 18,226 miRNAs, which have been deposited from different species. Although miRNAs have been identified and validated in many plant species, no studies have been reported on discovering miRNAs in Panax ginseng Meyer, which is a traditionally known medicinal plant in oriental medicine, also known as Korean ginseng. It has triterpene ginseng saponins called ginsenosides, which are responsible for its various pharmacological activities. Predicting conserved miRNAs by homology-based analysis with available expressed sequence tag (EST) sequences can be powerful, if the species lacks whole genome sequence information. In this study by using the EST based computational approach, 69 conserved miRNAs belonging to 44 miRNA families were identified in Korean ginseng. The digital gene expression patterns of predicted conserved miRNAs were analyzed by deep sequencing using small RNA sequences of flower buds, leaves, and lateral roots. We have found that many of the identified miRNAs showed tissue specific expressions. Using the insilico method, 346 potential targets were identified for the predicted 69 conserved miRNAs by searching the ginseng EST database, and the predicted targets were mainly involved in secondary metabolic processes, responses to biotic and abiotic stress, and transcription regulator activities, as well as a variety of other metabolic processes. PMID:23717176

Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mead, David; Lucas, Susan; Copeland, A

2012-01-01

Paenibacillus speciesY412MC10 was one of a number of organisms initially isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA. The isolate Y412MC10 was initially classified as a Geobacillus sp. based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species and not Geobacillus; the 16S rRNA analysis indicated the organism was a strain of Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute.more » The genome of Paenibacillus lautus strain Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. The Paenibacillus sp.Y412MC10 genome sequence was deposited at the NCBI in October 2009 (NC{_}013406). Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other Paenibacilli. Over 25% of the proteins predicted by the Y412MC10 genome share no identity with the closest sequenced Paenibacillus species; most of these are predicted hypothetical proteins and their specific function in the environment is unknown.« less

Sedimentary processes on the Storfjorden trough-mouth fan during last deglaciation phase: the role of subglacial meltwater plumes on continental margin sedimentation

NASA Astrophysics Data System (ADS)

Lucchi, Renata G.; Camerlenghi, Angelo; Colmenero-Hidalgo, Elena; Sierro, Francisco J.; Bárcena, Maria Angeles; Flores, José-Abel; Urgeles, Roger; Macrı, Patrizia; Sagnotti, Leonardo; Caburlotto, Andrea

2010-05-01

The continental margin of the Southern Storfjorden trough-mouth fan was investigated within the SVAIS project (BIO Hesperides cruise, August 2007) as a Spanish contribution to IPY Activity N. 367 (Neogene ice streams and sedimentary processes on high- latitude continental margins - NICE STREAMS). The objectives were to investigate the glacially-dominated late-Neogene-Quaternary sedimentary architecture of the NW Barents Sea continental margin and reconstruct its sedimentary system in response to natural climate change. The paleo-ice streams in Storfjorden had a small catchment area draining ice from the southern Spitsbergen and Bear Island. The short distance from the ice source to the calving front produced a short residence time of ice, and therefore a rapid response to climatic changes. Here ground truthing recovered the last few thousands years sedimentary sequence thought to represent last deglaciation phase. Detailed palaeostratigraphic investigations together with paleomagnetic and rock magnetic analyses and AMS dating define the constraints for high-resolution inter-core correlation and dating. Most of the cores contain at the base gravity-mass deposits including debris flows and over-consolidated glacigenic diamicton. Mass deposits are overlain by an oxidized interval originated at the release and sink of fresh, cold and oxygenated melt-waters at the inception of the deglaciation phase. On the upper slope the oxidized interval is overlain by several meters of finely-stratified sediments composed of sandy-silt layers cyclically recurring within finer-grained laminated silty-clay sediments. Textural and compositional analyses suggest preferential deposition by settling from meltwater sediment-laden plumes (plumites) occurred during deglaciation with coarser layers representing episodes of subglacial meltwater discharge (glacial hyperpycnal flows) accompanying the ice streams retreat. The laminated sequence is truncated at uppermost part by a more recent gravity-mass deposit that possibly removed part of the younger sequence. In the deeper part of the slope the plumites consist of crudely laminated, terrigenous and almost barren sediments. Here the sedimentary sequence is topped by intensively bioturbated, bioclasts-bearing silty-clays representing the most recent interglacial sedimentation. On the continental shelf, the upper sedimentary sequence contains dispersed cm-thick bivalve's shells suggesting an oxygenated and nutrient-rich environment (interglacial) overlaying an interval of terrigenous, barren sediments (deglaciation). Here the short core's length suggests the presence of stiffer/coarser sediments at the base that could not be sampled. The seismic stratigraphy indicates that the slope is formed by alternating debris flow deposits and layered sediments corresponding into our cores to the fast-deposited, low-density, terrigenous plumites. Bathymetric and seismic data revealed the presence of widespread submarine landslides restricted to the southernmost part of Storfjorden continental slope. Geotechnical investigation are in progress in order to understand if such layered deposits can act on the slope as a possible preferential weak horizon favoring sediment failure.

SEXCMD: Development and validation of sex marker sequences for whole-exome/genome and RNA sequencing.

PubMed

Jeong, Seongmun; Kim, Jiwoong; Park, Won; Jeon, Hongmin; Kim, Namshin

2017-01-01

Over the last decade, a large number of nucleotide sequences have been generated by next-generation sequencing technologies and deposited to public databases. However, most of these datasets do not specify the sex of individuals sampled because researchers typically ignore or hide this information. Male and female genomes in many species have distinctive sex chromosomes, XX/XY and ZW/ZZ, and expression levels of many sex-related genes differ between the sexes. Herein, we describe how to develop sex marker sequences from syntenic regions of sex chromosomes and use them to quickly identify the sex of individuals being analyzed. Array-based technologies routinely use either known sex markers or the B-allele frequency of X or Z chromosomes to deduce the sex of an individual. The same strategy has been used with whole-exome/genome sequence data; however, all reads must be aligned onto a reference genome to determine the B-allele frequency of the X or Z chromosomes. SEXCMD is a pipeline that can extract sex marker sequences from reference sex chromosomes and rapidly identify the sex of individuals from whole-exome/genome and RNA sequencing after training with a known dataset through a simple machine learning approach. The pipeline counts total numbers of hits from sex-specific marker sequences and identifies the sex of the individuals sampled based on the fact that XX/ZZ samples do not have Y or W chromosome hits. We have successfully validated our pipeline with mammalian (Homo sapiens; XY) and avian (Gallus gallus; ZW) genomes. Typical calculation time when applying SEXCMD to human whole-exome or RNA sequencing datasets is a few minutes, and analyzing human whole-genome datasets takes about 10 minutes. Another important application of SEXCMD is as a quality control measure to avoid mixing samples before bioinformatics analysis. SEXCMD comprises simple Python and R scripts and is freely available at https://github.com/lovemun/SEXCMD.

[Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing].

PubMed

Karaevskaia, E S; Demchenko, L S; Demidov, N É; Rivkina, E M; Bulat, S A; Gilichinskiĭ, D A

2014-01-01

Archaeal communities of permafrost deposits of King George Island and Bunger Hills Oasis (Antarctica) differing in the content of biogenic methane were analyzed using clone libraries of two 16S rRNA gene regions. Phylotypes belonging to methanogenic archaea were identified in all horizons.

Subsurface dolomite formation during post-depositional flow of sulphate-bearing fluids from underlying salt giants: Early Pliocene example at DSDP Leg 42A, Site 374, Ionian Abyssal Plain

NASA Astrophysics Data System (ADS)

McKenzie, Judith A.; Evans, Nick; Hodell, David; Aloisi, Giovanni; Vasconcelos, Crisogono

2017-04-01

Deciphering exact mechanisms for the formation of massive dolomite deposits has long been an enigma in sedimentary geology. The recognition that microbes can play a role in the dolomite precipitation process has added a new dimension to the study of the origin of dolomite formations in both shallow and deep-water environments. This scientific advance has evolved, particularly, through the investigation of dolomite-containing, organic-rich hemipelagic sediments cored on various continental margins during DSDP and ODP drilling campaigns, as well as intensive evaluations of modern hypersaline dolomite-precipitating environments with complementary culture experiments conducted in the laboratory. For example, the association of an active subsurface microbial community in contact with underlying brines of unknown origin leading to in situ dolomite precipitation has been observed in a Quaternary sequence of hemi-pelagic, organic carbon-rich sediments drilled on the Peru Margin, ODP Leg 201, Site 1229 (1). Specifically, it can be concluded that the long-term activity of subsurface microbes can be maintained by post-depositional flow of sulfate-bearing fluids from underlying large-scale evaporite deposits, or salt giants, promoting in situ dolomite precipitation. Another example of dolomite precipitation directly associated with the underlying Messinian salt giant was found at DSDP Leg 42A, Site 374 in the Ionian Abyssal Plain. Deep-sea drilling recovered a lowermost Pliocene sequence of diagenetically altered sediment (Unit II) separating the overlying Pliocene open-marine deposits (Unit I) and the underlying end Messinian dolomitic mudstone with gypsum layers (Unit III). The lower portion of this altered interval contained in Core 11, Section 2 (378.0 - 381.5 mbsf) comprises a dolomicrite with an unusual crystal morphology (2). The original interstitial water geochemical profiles indicate that a saline brine is diffusing upwards from below and into the dolomicrite sequence. There appears to be on-going bacterial sulfate reduction in this boundary zone between the evaporitic and normal pelagic sediments with a significant decrease in sulfate concentrations, whereas the chloride profile remains constant. It was concluded that the earliest Pliocene marine sediments of Unit II had been dolomitized after burial as a consequence of ionic migration across a steep Mg-concentration gradient (3). However, with the addition of a microbial factor into the study of the dolomite precipitation process, an alternate interpretation is possible. We propose that, at the location of DSDP Leg 42A, Site 374, modern subsurface dolomite precipitation is ongoing and the site is a "natural laboratory" in which to investigate the microbial phenomenon in the context of a giant evaporite deposit. This actualistic example may provide a new model for the origin of massive dolomite deposits associated with other salt giants in the rock record. (1) Meister, P., et al., 2007. Sedimentology, 54, 1007-1031. (2) Bernoulli, D. & Mélières, F., 1978. In: Hsü, K., Montadert, L. et al., 1978. Initial Reports of the Deep Sea Drilling Project, Volume 42, Part 1, 621-633. (3) McDuff, R.E., et al., 1978. In: Hsü, K., Montadert, L. et al., 1978. Initial Reports of the Deep Sea Drilling Project, Volume 42, Part 1, 561-568.

Anatomy of a mountain: The Thebes Limestone Formation (Lower Eocene) at Gebel Gurnah, Luxor, Nile Valley, Upper Egypt

NASA Astrophysics Data System (ADS)

King, Christopher; Dupuis, Christian; Aubry, Marie-Pierre; Berggren, William A.; Knox, Robert O.'B.; Galal, Wael Fathi; Baele, Jean-Marc

2017-12-01

We present a detailed geologic study of the Thebes Formation at Gebel Gurnah in its locus typicus on the West Bank (opposite Luxor) of the Nile River in the Upper Nile Valley, Egypt. This is the first detailed measurement and lithologic description of the ∼340 m thick (predominantly) carbonate section. The Thebes Formation is divided into thirteen major lithic units (A to M). We interpret data on the lithologic succession and variations, whole rock/clay mineralogy, and macro/micropaleontology in terms of deposition on a shallow carbonate platform episodically influenced by continental runoff, and describe six depositional sequences that we place in the global framework of Lower Eocene (Ypresian) sequence stratigraphy. We note however significant incompatibilities between the Thebes depositional sequences and the global sequences. We emend the definition of the Thebes Formation by defining its top as corresponding to level 326 m at the top of Nodular Limestone 'L' (NLL), and assigning the overlying beds to the Minia Limestone Formation. New biostratigraphic data and revision of previous studies establish the direct assignment of the Thebes Formation to planktonic foraminiferal Zones E4/P6b (upper part), E5/P7 and (indirectly) Zone E6/P8, and (probably, indirectly) Zone E7a/;P9;, and to calcareous nannofossil Zone NP12 and lower Zone NP13 of the Lower Eocene (Ypresian) and provide a temporal framework spanning ∼ 2.8 Myr from <52.45 to ∼49.6 Ma for the deposition of the Thebes Formation prior to the prominent sea level fall (∼49.6 Ma) towards the end of the Early Eocene. Dominantly carbonate deposition, with a strongly reduced detrital influx, occurred on a very wide shelf (probably) at least ∼ 100 km from the coastline. The thick sedimentary succession and the marked vertical lithologic variations are interpreted as resulting from sea level fluctuations imprinted on a long-term decrease in sea-level associated with rapid subsidence reflecting tectonic relaxation after the major Late Paleocene tectonic reorganization of the Syrian Arc.

Structural, mineralogical and geochemical constraints on the atypical komatiite-hosted Turret deposit in the Agnew-Mt. White district, Western Australia

NASA Astrophysics Data System (ADS)

Voute, F.; Thébaud, N.

2015-08-01

In the Norseman-Wiluna belt, Yilgarn Craton, the Agnew-Mt. White district is the host of many gold deposits. Located in the hinge of the regional Lawlers anticline, the Turret gold deposit is structurally controlled by the Table Hill shear zone that transects the Agnew Ultramafic unit. Geochemistry, coupled with petrographic data, allowed the delineation of the paragenetic sequence associated with gold mineralisation and include (1) a pervasive talc-carbonate alteration assemblage, (2) a pre-mineralisation stage associated with pervasive arsenopyrite + chalcopyrite + pyrrhotite + pyrite alteration, followed by (3) a late deformation event along a dilatational segment of the main Table Hill shear zone, leading to the formation of a breccia hosting a Cu-Bi-Mo-Au (± Ag ± Zn ± Te ± W) metal assemblage. The presence of Au-Ag-Cu alloys, native bismuth, chalcopyrite and other Bi-Te-S phases in the mineralisation stage suggest that gold may have been scavenged from the hydrothermal fluids by composite Bi-Te-Cu-Au-Ag-S liquids or melts. Using this mineral paragenetic sequence, together with mineralogical re-equilibration textures observed, we show that the gold deposition at Turret occurred over a temperature range approximately between c. 350 and 270 °C. This temperature range, together with the structural control and typical mesothermal alteration pattern including carbonate-chlorite alteration, shows that the Turret deposit shares common characteristics with the orogenic gold deposit class. However, the metal association of Cu, Au, Bi, and Mo, the quartz-poor, and high copper-sulphide content (up to 15 %) are characteristics that depart from the typical orogenic gold deposit mineralogy. Through comparison with similar deposits in the Yilgarn Craton and worldwide, we propose that the Turret deposit represents an example of a porphyry-derived Au-Cu-Bi-Mo deposit.

Stratigraphy and Facies of Cretaceous Schrader Bluff and Prince Creek Formations in Colville River Bluffs, North Slope, Alaska

USGS Publications Warehouse

Flores, Romeo M.; Myers, Mark D.; Houseknecht, David W.; Stricker, Gary D.; Brizzolara, Donald W.; Ryherd, Timothy J.; Takahashi, Kenneth I.

2007-01-01

Stratigraphic and sedimentologic studies of facies of the Upper Cretaceous rocks along the Colville River Bluffs in the west-central North Slope of Alaska identified barrier shoreface deposits consisting of vertically stacked, coarsening-upward parasequences in the Schrader Bluff Formation. This vertical stack of parasequence deposits represents progradational sequences that were affected by shoaling and deepening cycles caused by fluctuations of sea level. Further, the vertical stack may have served to stabilize accumulation of voluminous coal deposits in the Prince Creek Formation, which formed braided, high-sinuosity meandering, anastomosed, and low-sinuosity meandering fluvial channels and related flood plain deposits. The erosional contact at the top of the uppermost coarsening-upward sequence, however, suggests a significant drop of base level (relative sea level) that permitted a semiregional subaerial unconformity to develop at the contact between the Schrader Bluff and Prince Creek Formations. This drop of relative sea level may have been followed by a relative sea-level rise to accommodate coal deposition directly above the unconformity. This rise was followed by a second drop of relative sea level, with formation of incised valley topography as much as 75 ft deep and an equivalent surface of a major marine erosion or mass wasting, or both, either of which can be traced from the Colville River Bluffs basinward to the subsurface in the west-central North Slope. The Prince Creek fluvial deposits represent late Campanian to late Maastrichtian depositional environments that were affected by these base level changes influenced by tectonism, basin subsidence, and sea-level fluctuations.

Characterizing avulsion stratigraphy in ancient alluvial deposits

NASA Astrophysics Data System (ADS)

Jones, H. L.; Hajek, E. A.

2007-11-01

Guidelines for identifying ancient avulsion deposits were set forth by Kraus and Wells [Kraus, M.J., Wells, T.M., 1999. Recognizing avulsion deposits in the ancient stratigraphical record. In: Smith, N.D., Rogers, J. (Eds.), Fluvial Sedimentology VI, Special Publication of the International Association of Sedimentologists, vol. 28, pp. 251-268], building on the study by Smith et al. [Smith, N.D., Cross, T.A., Dufficy, J.P., Clough, S.R., 1989. Anatomy of an avulsion. Sedimentology 36, 1-23] of the modern Saskatchewan River system (Cumberland Marshes, central Canada), and serve to characterize avulsion depositional sequences in the ancient Willwood and Fort Union Formations (Paleogene, Bighorn Basin, NW Wyoming, USA). We recognize, however, that the model is not universally applicable to avulsion-dominated successions, specifically systems which lack defining "heterolithic avulsion deposits", set forth by Kraus and Wells [Kraus, M.J., Wells, T.M., 1999. Recognizing avulsion deposits in the ancient stratigraphical record. In: Smith, N.D., Rogers, J. (Eds.), Fluvial Sedimentology VI, Special Publication of the International Association of Sedimentologists, vol. 28, pp. 251-268]. Observations in several fluvial intervals suggest that the avulsion stratigraphy outlined by Kraus and Wells [Kraus, M.J., Wells, T.M., 1999. Recognizing avulsion deposits in the ancient stratigraphical record. In: Smith, N.D., Rogers, J. (Eds.), Fluvial Sedimentology VI, Special Publication of the International Association of Sedimentologists, vol. 28, pp. 251-268] represents one category of avulsion stratigraphy found in the rock record, but does not capture the nature of avulsion deposits everywhere. Based on observations (using measured sections, outcrop photo-panels, and aerial photographs) in the Willwood Formation (Eocene, Wyoming) and Ferris Formation (Cretaceous/Paleogene, Wyoming), we present two end-member categories of avulsion stratigraphy in ancient deposits; stratigraphically abrupt, when a main paleochannel is stratigraphically juxtaposed directly atop floodplain/overbank deposits, and stratigraphically transitional, where crevasse splays and other non-floodplain/-overbank deposits stratigraphically precede a main paleochannel. This characterization provides a broader, more inclusive way to recognize and describe avulsion stratigraphy in ancient deposits and may be an important factor to consider when modeling connectivity in fluvial reservoirs. Furthermore, our observations show that one type of avulsion channel stratigraphy may prevail over another within an ancient basin, suggesting that system-wide factors such as splay-proneness or avulsion style (i.e. aggradational, incisional, etc.; [Slingerland, R., Smith, N.D., 2004. River avulsions and their deposits. Annual Review of Earth and Planetary Sciences 32, 257-285]) may be primary controls on the type of avulsion stratigraphy deposited and preserved in ancient basin-fills.

Algeria: structural evolution and hydrocarbon potential of a complicated Tectonic province

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knudsen, H.W.

1985-02-01

During most of the pre-Carboniferous, Algeria was part of a stable foreland platform on which a thick clastic sequence was deposited. Caledonian tectonics were primarily epeirogenic, but they established structural alignments that were further reinforced by the much stronger movements of the Carboniferous Hercynian orogeny. In northern and eastern Algeria, a variable basal sandstone and a thick sequence of Triassic and Lower Jurassic evaporites were deposited over the eroded Hercynian surface. This provided a seal for subsequent hydrocarbon migration from the underlying Silurian and Devonian source rocks. Important epeirogenic events and tensional faulting occurred during the Jurassic and Cretaceous. Compressionalmore » forces in the tertiary culminated in the Alpine orogeny. A broad zone of uplift and southward-directed imbricate thrusting formed along the northern margins of Algeria obscuring much of the sub-Tertiary depositional and structural features. Hydrocarbon accumulation in Algeria has been predominantly controlled by the relationships among the Silurian-Devonian source rocks, the Hercynian unconformity, and the distribution of the overlying Triassic clastic and evaporite sequence. More than 65% of the recoverable oil reserves and 90% of the gas reserves are trapped immediately below or above the Hercynian unconformity, with the evaporites providing the seal. Heretofore, the complex geology of the Tertiary overthrust zone has been a deterrent to exploration in both the autochthonous Miocene basins and the sub-Tertiary sequence. However, improved seismic techniques and renewed interest in the potential of overthrust provinces point to increased activity in this area.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mello, M.R.; Soldan, A.L.; Maxwell, J.R.

A geochemical and biological marker investigation of a variety of oils from offshore Brazil and west Africa, ranging in age from Lower Cretaceous to Tertiary, has been done, with the following aims: (1) assessing the depositional environment of source rocks, (2) correlating the reservoired oils, (3) comparing the Brazilian oils with their west African counterparts. The approach was based in stable isotope data; bulk, elemental, and hydrous pyrolysis results; and molecular studies involving quantitative geological marker investigations of alkanes using GC-MS and GC-MS-MS. The results reveal similarities between groups of oils from each side of the Atlantic and suggest anmore » origin from source rocks deposited in five types of depositional environment: lacustrine fresh water, lacustrine saline water, marine evaporitic/carbonate, restricted marine anoxic, and marine deltaic. In west Africa, the Upper Cretaceous marine anoxic succession (Cenomanian-Santonian) appears to be a major oil producer, but in Brazil it is generally immature. The Brazilian offshore oils have arisen mainly from the pre-salt sequence, whereas the African oils show a balance between origins from the pre-salt and marine sequences. The integration of the geochemical and geological data indicate that new frontiers of hydrocarbon exploration in the west African basins must consider the Tertiary reservoirs in the offshore area of Niger Delta, the reservoirs of the rift sequences in the shallow-water areas of south Gabon, Congo, and Cuanza basins, and the reservoirs from the drift sequences (post-salt) in the deep-water areas of Gabon, Congo Cabinda, and Cuanza basins.« less

Early rifting deposition: examples from carbonate sequences of Sardinia (Cambrian) and Tuscany (Triassic-Jurassic), Italy: an analogous tectono-sedimentary and climatic context

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cocozza, T.; Gandin, A.

Lower Cambrian Ceroide Limestone (Sardinia) and Lower Jurassic Massiccio Limestone (Tuscany) belong to sequences deposited in analogous tectono-sedimentary context: the former linked to the Caledonian Sardic Phase, the latter to the Alpine Orogeny. Both units consist of massive pure limestone characterized by marginal and lagoonal sequences repeatedly interfingering in the same geological structure. This distribution indicates a morphology of the platforms composed of banks (marginal facies) and shallow basins (lagoonal facies) comparable with a Bahamian complex. Dolomitization affects patchily the massive limestone bodies, and karstic features, breccias, and sedimentary dikes occur at their upper boundary. Both units overlie early dolomitemore » and evaporites (sabkha facies) containing siliciclastic intercalations in their lower and/or upper part and are unconformably covered by open-shelf red (hematitic), nodular limestone Ammonitico Rosso facies). The sedimentary evolution of the two sequences appears to have been controlled by synsedimentary tectonics whose major effects are the end of the terrigenous input, the bank-and-basin morphology of the platform, the irregular distribution of the dolomitization, and the nodular fabric of the overlying facies. The end of the Bahamian-type system is marked by the karstification of the emerged blocks and is followed by their differential sinking and burial under red-nodular facies. From a geodynamic viewpoint, sequences composed of Bahamian-like platform carbonates followed by Ammonitico Rosso facies imply deposition along continental margins subjected to block-faulting during an extensional regime connected with the beginning of continental rifting. Moreover, the variation from sabkha to Bahamian conditions suggests the drifting of the continent from arid to humid, tropical areas.« less

Geology of natural gas reservoir: Upper Travis Peak Formation, western flank of Sabine Uplift, east Texas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fracasso, M.A.

The Travis Peak Formation (Lower Cretaceous) in the eastern East Texas basin represents a sand-rich, fluvial-deltaic depositional system. This lobate, high-constructive deltaic system prograded radially to the southeast from an Upshur County locus. Regional studies of the Travis Peak established a threefold internal stratigraphic framework: a middle sand-rich fluvial and delta-plain sequence is gradationally overlain and underlain by a marine-influenced delta-fringe zone with a higher mud content. The entire Travis Peak succession thins over the Bethany dome on the western flank of the Sabine uplift. However, the delta-fringe sequences are relatively thicker over the structure because of a disproportionately greatermore » thinning of the middle sandy fluvial-deltaic sequence. Lesser sand deposition over the Bethany dome reflects an active structural control over facies distribution. Gas production in the Bethany field and surrounding area is concentrated in thin zones (5-15 ft) of the upper delta-fringe sequence. This distribution probably reflects the increased abundance of mudstone beds in the upper delta-fringe interval, which may have served as source rocks or barriers to upward gas migration, or as both. The predominant trapping mechanism in this region is stratigraphic sand pinch-out in a structurally updip direction on the flanks of major structures. Studies of core and closely spaced electric logs west of the Bethany dome help define the depositional systems in the upper delta-fringe producing interval. This sequence comprises a complex mosaic of continental and marine facies, and exhibits an overall upward trend of increasing marine influence that spans a gradual transition into transgressive carbonates of the Sligo Formation.« less

The draft genome sequence and annotation of the desert woodrat Neotoma lepida.

PubMed

Campbell, Michael; Oakeson, Kelly F; Yandell, Mark; Halpert, James R; Dearing, Denise

2016-09-01

We present the de novo draft genome sequence for a vertebrate mammalian herbivore, the desert woodrat (Neotoma lepida). This species is of ecological and evolutionary interest with respect to ingestion, microbial detoxification and hepatic metabolism of toxic plant secondary compounds from the highly toxic creosote bush (Larrea tridentata) and the juniper shrub (Juniperus monosperma). The draft genome sequence and annotation have been deposited at GenBank under the accession LZPO01000000.

Status of the Microbial Census

PubMed Central

Schloss, Patrick D.; Handelsman, Jo

2004-01-01

Over the past 20 years, more than 78,000 16S rRNA gene sequences have been deposited in GenBank and the Ribosomal Database Project, making the 16S rRNA gene the most widely studied gene for reconstructing bacterial phylogeny. While there is a general appreciation that these sequences are largely unique and derived from diverse species of bacteria, there has not been a quantitative attempt to describe the extent of sequencing efforts to date. We constructed rarefaction curves for each bacterial phylum and for the entire bacterial domain to assess the current state of sampling and the relative taxonomic richness of each phylum. This analysis quantifies the general sense among microbiologists that we are a long way from a complete census of the bacteria on Earth. Moreover, the analysis indicates that current sampling strategies might not be the most effective ones to describe novel diversity because there remain numerous phyla that are globally distributed yet poorly sampled. Based on the current level of sampling, it is not possible to estimate the total number of bacterial species on Earth, but the minimum species richness is 35,498. Considering previous global species richness estimates of 107 to 109, we are certain that this estimate will increase with additional sequencing efforts. The data support previous calls for extensive surveys of multiple chemically disparate environments and of specific phylogenetic groups to advance the census most rapidly. PMID:15590780

Developing a post-fire flood chronology and recurrence probability from alluvial stratigraphy in the Buffalo Creek watershed, Colorado, USA

USGS Publications Warehouse

Elliott, J.G.; Parker, R.S.

2001-01-01

Stratigraphic and geomorphic evidence indicate floods that occur soon after forest fires have been intermittent but common events in many mountainous areas during the past several thousand years. The magnitude and recurrence of these post-fire flood events reflects the joint probability between the recurrence of fires and the recurrence of subsequent rainfall events of varying magnitude and intensity. Following the May 1996 Buffalo Creek, Colorado, forest fire, precipitation amounts and intensities that generated very little surface runoff outside of the burned area resulted in severe hillslope erosion, floods, and streambed sediment entrainment in the rugged, severely burned, 48 km2 area. These floods added sediment to many existing alluvial fans, while simultaneously incising other fans and alluvial deposits. Incision of older fans revealed multiple sequences of fluvially transported sandy gravel that grade upward into charcoal-rich, loamy horizons. We interpret these sequences to represent periods of high sediment transport and aggradation during floods, followed by intervals of quiescence and relative stability in the watershed until a subsequent fire occurred. An alluvial sequence near the mouth of a tributary draining a 0??82 km2 area indicated several previous post-fire flood cycles in the watershed. Dendrochronologic and radiocarbon ages of material in this deposit span approximately 2900 years, and define three aggradational periods. The three general aggradational periods are separated by intervals of approximately nine to ten centuries and reflect a 'millennium-scale' geomorphic response to a closely timed sequence of events: severe and intense, watershed-scale, stand-replacing fires and subsequent rainstorms and flooding. Millennium-scale aggradational units at the study site may have resulted from a scenario in which the initial runoff from the burned watershed transported and deposited large volumes of sediment on downstream alluvial surfaces and tributary fans. Subsequent storm runoff may have produced localized incision and channelization, preventing additional vertical aggradation on the sampled alluvial deposit for several centuries. Two of the millennium-scale aggradational periods at the study site consist of multiple gravel and loam sequences with similar radiocarbon ages. These closely dated sequences may reflect a 'multidecade-scale' geomorphic response to more frequent, but aerially limited and less severe fires, followed by rainstorms of relatively common recurrence. Published in 2001 by John Wiley and Sons, Ltd.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE PAGES

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian; ...

2017-03-06

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

Neural correlates of nesting behavior in zebra finches (Taeniopygia guttata).

PubMed

Hall, Zachary J; Bertin, Marion; Bailey, Ida E; Meddle, Simone L; Healy, Susan D

2014-05-01

Nest building in birds involves a behavioral sequence (nest material collection and deposition in the nest) that offers a unique model for addressing how the brain sequences motor actions. In this study, we identified brain regions involved in nesting behavior in male and female zebra finches (Taeniopygia guttata). We used Fos immunohistochemistry to quantify production of the immediate early gene protein product Fos (a molecular indicator of neuronal activity) in the brain correlated this expression with the variation in nesting behavior. Using this technique, we found that neural circuitry involved in motor sequencing, social behavior, reward and motivation were active during nesting. Within pairs of nesting birds, the number of times a male picked up or deposited nesting material and the amount of time a female spent in the nest explained the variation in Fos expression in the anterior motor pathway, social behavior network, and reward neural circuits. Identification of the brain regions that are involved in nesting enables us to begin studying the roles of motor sequencing, context, and reward in construction behavior at the neural level. Copyright © 2014 Elsevier B.V. All rights reserved.

Neural correlates of nesting behavior in zebra finches (Taeniopygia guttata)

PubMed Central

Hall, Zachary J.; Bertin, Marion; Bailey, Ida E.; Meddle, Simone L.; Healy, Susan D.

2014-01-01

Nest building in birds involves a behavioral sequence (nest material collection and deposition in the nest) that offers a unique model for addressing how the brain sequences motor actions. In this study, we identified brain regions involved in nesting behavior in male and female zebra finches (Taeniopygia guttata). We used Fos immunohistochemistry to quantify production of the immediate early gene protein product Fos (a molecular indicator of neuronal activity) in the brain correlated this expression with the variation in nesting behavior. Using this technique, we found that neural circuitry involved in motor sequencing, social behavior, reward and motivation were active during nesting. Within pairs of nesting birds, the number of times a male picked up or deposited nesting material and the amount of time a female spent in the nest explained the variation in Fos expression in the anterior motor pathway, social behavior network, and reward neural circuits. Identification of the brain regions that are involved in nesting enables us to begin studying the roles of motor sequencing, context, and reward in construction behavior at the neural level. PMID:24508238

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential.

PubMed

Reitschuler, Christoph; Spötl, Christoph; Hofmann, Katrin; Wagner, Andreas O; Illmer, Paul

2016-04-01

(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.

Accumulation and erosion of Mars' south polar layered deposits.

PubMed

Seu, Roberto; Phillips, Roger J; Alberti, Giovanni; Biccari, Daniela; Bonaventura, Francesco; Bortone, Marco; Calabrese, Diego; Campbell, Bruce A; Cartacci, Marco; Carter, Lynn M; Catallo, Claudio; Croce, Anna; Croci, Renato; Cutigni, Marco; Di Placido, Antonio; Dinardo, Salvatore; Federico, Costanzo; Flamini, Enrico; Fois, Franco; Frigeri, Alessandro; Fuga, Oreste; Giacomoni, Emanuele; Gim, Yonggyu; Guelfi, Mauro; Holt, John W; Kofman, Wlodek; Leuschen, Carlton J; Marinangeli, Lucia; Marras, Paolo; Masdea, Arturo; Mattei, Stefania; Mecozzi, Riccardo; Milkovich, Sarah M; Morlupi, Antonio; Mouginot, Jérémie; Orosei, Roberto; Papa, Claudio; Paternò, Tobia; Persi del Marmo, Paolo; Pettinelli, Elena; Pica, Giulia; Picardi, Giovanni; Plaut, Jeffrey J; Provenziani, Marco; Putzig, Nathaniel E; Russo, Federica; Safaeinili, Ali; Salzillo, Giuseppe; Santovito, Maria Rosaria; Smrekar, Suzanne E; Tattarletti, Barbara; Vicari, Danilo

2007-09-21

Mars' polar regions are covered with ice-rich layered deposits that potentially contain a record of climate variations. The sounding radar SHARAD on the Mars Reconnaissance Orbiter mapped detailed subsurface stratigraphy in the Promethei Lingula region of the south polar plateau, Planum Australe. Radar reflections interpreted as layers are correlated across adjacent orbits and are continuous for up to 150 kilometers along spacecraft orbital tracks. The reflectors are often separated into discrete reflector sequences, and strong echoes are seen as deep as 1 kilometer. In some cases, the sequences are dipping with respect to each other, suggesting an interdepositional period of erosion. In Australe Sulci, layers are exhumed, indicating recent erosion.

Off-platform Silurian sequences in the Ambler River quadrangle: A section in Geologic studies in Alaska by the U.S. Geological Survey during 1987

USGS Publications Warehouse

Dumoulin, Julie A.; Harris, Anita G.

1988-01-01

Lithofacies changes in coeval upper Paleozoic rocks have been used to unravel the tectonic history of northern Alaska (for example, Mayfield and others, 1983). Conodont biostratigraphy and detailed petrologic studies are now revealing facies differences in lower Paleozoic rocks that can also be used to constrain their tectono-sedimentary framework (Dumoulin and Harris, 1987). A basic element of basin analysis is the discrimination of shallow-water shelf and platform sequences from deeper water slope and basinal deposits. This report documents several new localities of deeper water, off-platform Silurian deposits in the Ambler River quadrangle and briefly outlines some of their paleogeographic implications.

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.

PubMed

Liu, Xia; Zhao, Bo; Zheng, Hua-Jun; Hu, Yan; Lu, Gang; Yang, Chang-Qing; Chen, Jie-Dan; Chen, Jun-Jian; Chen, Dian-Yang; Zhang, Liang; Zhou, Yan; Wang, Ling-Jian; Guo, Wang-Zhen; Bai, Yu-Lin; Ruan, Ju-Xin; Shangguan, Xiao-Xia; Mao, Ying-Bo; Shan, Chun-Min; Jiang, Jian-Ping; Zhu, Yong-Qiang; Jin, Lei; Kang, Hui; Chen, Shu-Ting; He, Xu-Lin; Wang, Rui; Wang, Yue-Zhu; Chen, Jie; Wang, Li-Jun; Yu, Shu-Ting; Wang, Bi-Yun; Wei, Jia; Song, Si-Chao; Lu, Xin-Yan; Gao, Zheng-Chao; Gu, Wen-Yi; Deng, Xiao; Ma, Dan; Wang, Sen; Liang, Wen-Hua; Fang, Lei; Cai, Cai-Ping; Zhu, Xie-Fei; Zhou, Bao-Liang; Jeffrey Chen, Z; Xu, Shu-Hua; Zhang, Yu-Gao; Wang, Sheng-Yue; Zhang, Tian-Zhen; Zhao, Guo-Ping; Chen, Xiao-Ya

2015-09-30

Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11-20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

Metazen – metadata capture for metagenomes

DOE PAGES

Bischof, Jared; Harrison, Travis; Paczian, Tobias; ...

2014-12-08

Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack themore » appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.« less

Metazen – metadata capture for metagenomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bischof, Jared; Harrison, Travis; Paczian, Tobias

Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack themore » appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.« less

Characterisation of a novel Bacillus sp. SJ-10 β-1,3-1,4-glucanase isolated from jeotgal, a traditional Korean fermented fish.

PubMed

Kim, Yu-Ri; Kim, Eun-Young; Lee, Jong Min; Kim, Joong Kyun; Kong, In-Soo

2013-06-01

A novel β-1,3-1,4-glucanase gene was identified in Bacillus sp. SJ-10 (KCCM 90078) isolated from jeotgal, a traditional Korean fermented fish. We analysed the β-1,3-1,4-glucanase gene sequence and examined the recombinant enzyme. The open reading frame of the gene encoded 244 amino acids. The sequence was not identical to any β-glucanases deposited in GenBank. The gene was cloned into pET22b(+) and expressed in Escherichia coli BL21. Purification of recombinant β-1,3-1,4-glucanase was conducted by affinity chromatography using a Ni-NTA column. Enzyme specificity of β-1,3-1,4-glucanase was confirmed based on substrate specificity. The optimal temperature and pH of the purified enzyme towards barley β-glucan were 50 °C and pH 6, respectively. More than 80 % of activity was retained at temperatures of 30-70 °C and pH values of 4-9, which differed from all other bacterial β-1,3-1,4-glucanases. The degradation products of barley β-glucan by β-1,3-1,4-glucanase were analysed using thin-layer chromatography, and ultimately glucose was produced by treatment with cellobiase.

Draft genome sequence of Anoxybacillus flavithermus KU2-6-11 isolated from hot-spring in Uzon caldera (Kamchatka, Russia).

PubMed

Rozanov, Aleksey S; Korzhuk, Anton V; Bryanskaya, Alla V; Peltek, Sergey E

2018-02-01

The Anoxybacillus flavithermus KU2-6-11 was isolated from sediments of a nameless hot spring. The hot spring is located in Uzon caldera (Kamchatka, Russia). The sequenced and annotated genome is 2,646,305 bp and encodes 2787genes. The draft genome sequence of the Anoxybacillus flavithermus KU2-6-11 has been deposited at DDBJ/EMBL/GenBank under the accession PEDM01000000 and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/nuccore/PEDM01000000.

Composition and origin of Early Cambrian Tiantaishan phosphorite-Mn carbonate ores, Shaanxi Province, China

USGS Publications Warehouse

Hein, J.R.; Fan, D.; Ye, J.; Liu, T.; Yeh, H.-W.

1999-01-01

The Tiantaishan phosphorite-Mn carbonate ores occur in the Early Cambrian Tananpo Formation in complexly folded and faulted rocks located in southern Shaanxi Province. About 65 x 106 tonnes of 17% P2O5 ore reserves exist and Mn-ore reserves are about 8.3 x 106 tonnes of +18% Mn. The stratigraphic sequence in ascending order consists of black phyllite, black to gray phosphorite ore, black phyllite, rhodochrostone ore, Mn mixed-carbonates, and dolostone. Data are presented from microprobe mineral chemistry, whole-rock chemistry, stable isotopes of carbonates, X-ray mineralogy, petrographic and SEM observations, and statistical analysis of chemical data. The dominant ore-forming minerals are hydroxy- and carbonate fluorapatite and Ca rhodochrosite, with Mg kutnahorite and dolomite comprising the Mn mixed-carbonate section. Pyrite occurs in all rock types and alabandite (MnS) occurs throughout the rhodochrostone section. The mean P2O5 content of phosphorite is 31% and argillaceous phosphorite is 16%, while the mean MnO content of rhodochrostone ore is 37%. Phosphorite ores are massive, spheroidal, laminated, and banded, while rhodochrostone ores have oolitic, spheroidal, and granular fabrics. The most distinguishing characteristics of the ores are high total organic carbon (TOC) contents (mean 8.4%) in the phosphorite and high P2O5 contents (mean 2.7%) in the rhodochrostone ore. The atypically high TOC contents in the Tiantaishan phosphorite probably result from very strong productivity leading to high sedimentation rates accompanied by weak reworking of sediments; poor utilization of the organic matter by bacteria; and/or partial replacement of bacterial or algal mats by the apatite. The depositional setting of the ores was the margin of an epicontinental seaway created as a direct consequence of global processes that included break-up of a supercontinent, formation of narrow seaways, creation of extensive continental shelves, overturn of stagnant, metal-rich deep-ocean waters, and marine transgression. Water depth increased from deposition of the black phyllite sequence through deposition of the Mn mixed-carbonate sequence, then shallowed again during deposition of the overlying dolostone sequence. Bottom waters were mostly dysoxic to suboxic, but fluctuated from oxic to anoxic. Productivity was high during deposition of the black phyllite sequence, increased during precipitation of phosphorite, and then decreased to moderate levels during precipitation of rhodochrostone ores. Biosilica contributions occur in each lithology, but are greatest in rhodochrostone. Changes in sedimentation were determined by changes in water depth, productivity, upwelling, sea-level change, and ventilation of the depositional basin. The source of the phosphorus was organic matter produced in great quantities during deposition of the black phyllite and phosphorite sequences in a zone of coastal upwelling. Organic matter accumulation was rapid. Globally, Mn was supplied by overturn of stagnant, metal-rich deep-ocean waters, which were redistributed to areas of coastal upwelling and seaways; that process may have been initiated by latest Proterozoic glaciations which would have promoted density stratification and accumulation and storage of metals. Regionally, Mn was supplied by terrigenous input into the shallow seaway and hydrothermal input into the deeper water parts of that seaway. Locally, Mn sources included leaching and transport of metals from the sediment column. Manganese was stored locally in low-oxygen (not anoxic) seawater prior to Mn-ore formation. The source of the carbon in the Mn carbonates and dolostones was predominantly seawater bicarbonate and secondarily CO2 derived from the oxidation of organic matter in the bacterially mediated diagenetic zone of sulfate reduction.

Hydrologic framework of Long Island, New York

USGS Publications Warehouse

Smolensky, Douglas A.; Buxton, Herbert T.; Shernoff, Peter K.

1990-01-01

Long Island, N.Y., is underlain by a mass of unconsolidated geologic deposits of clay, silt, sand, and gravel that overlie southward-sloping consolidated bedrock. These deposits are thinnest in northern Queens County (northwestern Long Island), where bedrock crops out, and increase to a maximum thickness of 2,000 ft in southeastern Long Island. This sequence of unconsolidated deposits consists of several distinct geologic units ranging in age from late Cretaceous through Pleistocene, with some recent deposits near shores and streams. These units are differentiated by age, depositional environment, and lithology in table 1. Investigations of ground-water availability and flow patterns may require information on the internal geometry of the hydrologic system that geologic correlations and interpretation alone cannot provide; hydrologic interpretations in which deposits are differentiated on the basis of water-transmitting properties are generally needed also. This set of maps and vertical sections depicts the hydrogeologic framework of the unconsolidated deposits that form Long Island's ground-water system. These deposits can be classified into eight major hydrogeologic units (table 1). The hydrogeologic interpretations presented herein are not everywhere consistent with strict geologic interpretation owing to facies changes and local variations in the water-transmitting properties within geologic units. These maps depict the upper-surface altitude of seven of the eight hydrogeologic units, which, in ascending order, are: consolidated bedrock, Lloyd aquifer, Raritan confining unit, Magothy aquifer, Monmouth greensand, Jameco aquifer, and Gardiners Clay. The upper glacial aquifer—the uppermost unit—is at land surface over most of Long Island and is, therefore, not included. The nine north-south hydrogeologic sections shown below depict the entire sequence of unconsolidated deposits and, together with the maps, provide a detailed three-dimensional interpretation of Long Island's hydrogeologic framework. The structure-contour map that shows the upper-surface altitude of the Cretaceous deposits is included to illustrate the erosional unconformity between the Cretaceous and overlying Pleistocene deposits. Pleistocene erosion played a major role in determining the shape and extent of the Lloyd aquifer, the Raritan confining unit, and the Magothy aquifer, and thus partly determined their hydrogeologic relation with subsequent (post-Cretaceous) deposits.

Lipid biomarker and compound-specific isotope analysis of cave sediments: a new approach to investigating past vegetation change

NASA Astrophysics Data System (ADS)

Blyth, A.; Griffiths, T.; Robson, S.

2009-12-01

Caves are vital archives for records of terrestrial palaeoenvironmental change, as they form sheltered sediment traps capable of preserving long environmental sequences. Due to their unique role in the landscape, they are also intimately connected to the archaeology and palaeoecology of the parent region. Chemical proxy records preserved in speleothems (chemically precipitated cave deposits) have long been used as a tool in palaeoclimatic research, but clastic sediments deposited by air, water, and breakdown of the surrounding rock also have much to contribute. However, although well researched in a sedimentary context, the geochemical records contained in these deposits, especially organic parameters, have been less well-studied. Here we present the first in-depth study of the organic geochemistry of cave sediment sequences, using samples from two south-east Asian caves, and focusing on plant-derived lipid biomarkers and their associated compound-specific carbon isotope records. The work aimed to establish: whether routine extraction and analysis of compounds was feasible in this context at acceptable sample sizes; whether there was a significant vegetation-derived contribution to the record; whether the depositional mode of the sediment (colluvium, midden, channel fill etc) affects the organic composition; and whether the records show coherent and interpretable variation through time. Two sites were studied: Niah Cave in Borneo, where the sediments recovered are a mixture of colluvium and channel fill and date back to >40 ka; and Hang Boi in Vietnam, where the principal deposit is a Holocene occupation midden dominated by land-snail shells. To recover the lipid fraction 7 g aliquots of freeze-dried sediment were extracted by sonication in 95:5 dichloromethane:methanol. Excess solvent was then removed via rotary evaporation and the extracts derivatised with BF3-Methanol and BSTFA prior to analysis by GC-MS. The lipid extracts contain a range of compounds including sterols, triterpenoids, and homologous series of n-alkanes, n-fatty acids, n-alkanols, n-alkan-2-ones, and ω-hydroxy acids. There is a clear and strong plant derived signal, with a high carbon preference index and odd-over-even predominance in the n-alkanes, and a large high molecular weight component with even-over-odd chain length predominance in the n-fatty acids and n-alkanols. The sediments from Niah Cave have a generally lower relative plant-derived contribution than those from Hang Boi, which we suggest results from the large amount of swift guano present in the former cave. When considered as time-series, considerable variation is seen in both sites, with the Niah material in particular showing interpretable co-variation betweeen proxies, which indicates that changes in organic matter source are being recorded. The results from this work show that abundant and measurable lipids are recoverable from cave sediments, and a strong plant-derived signal is seen. This indicates that the technique has considerable potential in terrestrial palaeoenvironmental research.

Layered Deposits of Arabia Terra and Meridiani Planum: Keys to the Habitability of Ancient Mars

NASA Technical Reports Server (NTRS)

Allen, Carlton C.; Oehler, Dorothy Z.; Paris, Kristen N.; Venechuk, Elizabeth M.

2006-01-01

Understanding the habitability of ancient Mars is a key goal in the exploration of that planet. Evidence for conditions favorable to early life must be sought in ancient sedimentary rocks, such as those of Arabia Terra and Meridiani Planum. Arabia Terra, the northernmost extension of the ancient highlands, is dominated by cratered plains and minor ridged units. These plains extend south into the adjacent Meridiani Planum. The Opportunity rover landed in northern Meridiani, close to the border with Arabia. High resolution MOC images reveal extensive layered sequences across much of the Arabia and Meridiani region. These layers have been interpreted as eroded remnants of sedimentary rock deposits (Edgett, 2005). The layered sequences are concentrated in the SW quadrant of Arabia and in northern Meridiani. Preliminary mapping by Edgett (2005) distinguished four large scale layered sequences in the Arabia and Meridiani region. These have dimensions of hundreds to more than 1,000 km. MOLA altimetry shows that each of the sequences can attain a thickness of 200 to 400 m, with a total thickness greater than 1 km. The sequences are generally flat lying, with regional slopes of a few degrees. Much finer layering is evident within a number of craters. The plains and ridged units of the Arabia and Meridiani region were originally mapped as Noachian based on crater statistics, particularly the number of large craters (Scott and Carr, 1978). The layered sequences in the current study postdate many, but not all, of these large craters. The layered sequences have partially or totally filled a number of craters with diameters ranging from 20 to over 50 km. The topmost layered sequence, as well as the lower two sequences, have intermediate thermal inertia, as derived from THEMIS, indicative of moderate induration. The TES spectra from the lower sequences include features indicative of basalt. Some areas of the topmost sequence, which includes the Opportunity landing site, have TES spectra dominated by hematite. Just below this topmost sequence lies a sequence with higher thermal inertia, indicative of more indurated or coarser grained material. The TES spectra of this sequence lack distinctive mineral features, and the rocks may be obscured by a thin coating of dust. The layers have been extensively eroded. The uppermost sequences are characterized by deeply scalloped boundaries. Filled craters have been partially exhumed. Finely layered deposits within craters have been strongly dissected. Landforms uniquely attributable to wind erosion are rare, but erosive styles and geomorphology characteristic of water and possibly ice are present. The layered sequences in Arabia Terra and Meridiani Planum likely reflect an epoch when the planet was much more habitable than it is today. Several areas in these layered sequences are under intensive study as candidate landing sites for the 2009 Mars Science Laboratory.

Sedimentary paleoenvironments of fossil platyrrhine localities, Miocene Pinturas Formation, Santa Cruz Province, Argentina

USGS Publications Warehouse

Bown, T.M.

1990-01-01

The Pinturas Formation is a pyroclastic and epiclastic aeolian deposit of Miocene age lying discordantly upon Jurassic rocks in the elevated Andean precordillera of northwest Santa Cruz Province, Argentina. The history of development of the Pinturas Formation was significantly affected by the gradual, though sporadic, draping of this aeolian sediment across a profound, slowly filling paleotopography. The Pinturas depositional cycle consisted of: (1) minor aeolian deposition followed by soil formation, and (2) major aeolian deposition followed by intervals of regional erosion. Fluvial action seems to have been almost wholly confined to intraformational erosion, and two significant intraformational erosional unconformities divide the Pinturas Formation into three sequences. The lower sequence is dominated by pyroclastic mudrocks upon which were formed very mature, probably mollic, paleosols; the middle sequence is composed largely of epiclastic sand occurring as barchanoid paleodunes; and the upper sequence consists of massive, poorly bedded pyroclastic mudrocks. Many Pinturas lacunae were reconstructed on the basis of locally preserved strata, and a novel method of holostrome reconstruction using relative paleosol maturities places Pinturas sedimentation in a more accurate temporal light. It also indicates: (1) that the Pinturas sediment accumulation rate increased with time; (2) that regional erosive intervals are correlated directly with major influxes of pyroclastic material; and (3) that the introduction of the Pinturas platyrrhine primates occurred in the sequence:Carlocebus carmenensis, C. intermedius andSoriacebus ameghinorum. Soriacebus adrianae. Pinturas paleosols appear to have formed under moist conditions, and both mature and immature varieties yield a host of ichnofossils. These include the burrows and nests of bees, scarabeid beetles, termites, and at least two different kinds of colonial rodents, in addition to rhizoliths and the calcified boles and root systems of trees. A fossil nest of a nasutitermitine termite in the lower sequence of the formation indicates the presence of tropical forest. Climatic conditions may have been drier during deposition of the barchanoid paleodunes in early late Pinturas time, or the dunes might reflect drier source areas or have simply encroached on areas of highland forest. Fossil mammals are abundant in Pinturas sediments, and attritional concentrations of them were recognized in the upper parts of paleosols and on the floors of erosional scours. Radiometric dates indicate that the fossil mammals (including platyrrhine primates) occurring in the lower and middle parts of the formation may range in age from about 16-6 to younger than 13-3 Ma (million years ago) (Santacrucian and, almost certainly, Friasian land-mammal ages). This age range is somewhat younger than previous estimates, and suggests that the Pinturas faunas correlate broadly with those from the type Santa Cruz Formation, with the presumed position of the type Friasian, and with the base of the marine Gaiman Formation in the lower valley of the Rio Chubut.

Astronomical forcing of a Middle Permian chert sequence in Chaohu, South China

NASA Astrophysics Data System (ADS)

Yao, Xu; Zhou, Yaoqi; Hinnov, Linda A.

2015-07-01

Astronomical forcing has been shown to be a fundamental driver of climate change through geological time. Pelagic, bedded cherts deposited in Mesozoic ocean basins with chert-mudstone cycles have been shown to contain the imprint of Milankovitch astronomical climate forcing. In the Chaohu region, South China, we studied a Middle Permian radiolarian chert sequence (Gufeng Formation) with chert-mudstone couplets reminiscent of the Mesozoic cherts, but deposited on a continental shelf. Spectral analysis of lithologic bed thickness data from two sections of this chert sequence reveals that 13 cm to 20 cm chert-mudstone cycles in the stratigraphic domain match theoretical 32-kyr Middle Permian obliquity cycling, together with a hierarchy of other cycles with 12 cm, 9 cm, 7 cm, 6.6 cm and 5.4 cm wavelengths. Tuning the 13 cm to 20 cm stratigraphic cycles to Earth's obliquity cycle periodicity indicates that the cm-scale cycles are precession-scale variations with a strong ∼400 kyr amplitude modulation. Tuning to theoretical precession terms provides further support for the astronomical forcing of the chert sequence. We propose that monsoon-controlled upwelling contributed to the development of the chert-mudstone cycles. A seasonal monsoon controlled by astronomical forcing (i.e., insolation) influenced the intensity of upwelling. Stronger upwelling increased radiolarian productivity in the surface ocean, increasing silica deposition. Glacio-eustatic oscillations from ice sheet dynamics in southern Gondwana modulated terrigenous mud flux to the basin. The two processes jointly contributed to the astronomical rhythms of these tropical chert-mudstone sequences, which are characterized by comparably strong obliquity and precession responses. Subsequent diagenesis distorted the chert and mudstone layering, but not enough to destroy the original stratigraphic patterns. The resulting astronomical time scale (ATS) assumes a Roadian/Wordian boundary age of 268.8 Ma for the onset of the first chert layer at the base of the sequence and ends at 264.1 Ma, for a total duration of 4.7 myr.

Quaternary geology of the DFDP-2 drill holes, Alpine Fault, New Zealand

NASA Astrophysics Data System (ADS)

Upton, P.; Cox, S.; Howarth, J. D.; Sutherland, R.; Langridge, R.; Barth, N. C.; Atkins, C.

2015-12-01

A 240 m-thick Quaternary sediment sequence in Whataroa Valley was much thicker than predicted before drilling. DFDP-2A and DFDP-2B were mostly drilled through the sequence by dual-rotary method using air or water circulation, returning cuttings bagged at 1 or 2 m sample intervals. Some sorting/bias and contamination occurred. Core was retrieved in DFDP-2A from 125-160 m, with highly variable recovery (0-100%) and mixed preservation/quality. The sequence is interpreted to comprise: fluvial-glacial gravels (0-58 m); grading downward into sandy lake delta sediments (59-77 m); overlying a monotonous sequence of lake mud and silts, with rare pebble-cobble diamictite (77-206 m); with a basal unit (206-240 m) containing coarse cobbles and boulders that may represent a distinct till/diamictite. Evidence has yet to be found for any marine influence in lowermost sediments, despite deposition at least 120 m below present day sea level, and potentially 200 m bsl if uplift has occurred on the Alpine Fault. When corrected for uplift the lacustrine sequence broadly correlates to those in present Lakes Rotokina and Wahapo, suggesting a substantial (~100 km2) pro-glacial lake once covered the area. Radiocarbon dating of plant fragments indicate 70 m of upper lacustrine and deltaic sediments (129-59 m) were deposited rapidly between 16350-15800 Cal BP. Overlying alluvial gravels are much younger (<1 ka), but potentially also involved pulses of rapid aggradation. The sequence provides a record of sedimentation on the Alpine Fault hanging wall following late-glacial ice retreat up Whataroa Valley, with uplift and erosion followed by Holocene alluvial gravel deposition. Future work will address: (1) the nature and history of sedimentation, including the lithology and origin of sediments; (2) what, if any, geological record of tectonics (movement) or Alpine Fault earthquakes (shaking) the sediments contain.

Erosion and deposition on a debris-flow fan

NASA Astrophysics Data System (ADS)

Densmore, A. L.; Schuerch, P.; Rosser, N. J.; McArdell, B. W.

2011-12-01

The ability of a debris flow to entrain or deposit sediment controls the downstream evolution of flow volume, and ultimately dictates both the geomorphic impact of the flow and the potential hazard that it represents. Our understanding of the patterns of, and controls on, such flow volume changes remains extremely limited, however, partly due to a poor mechanistic grasp of the interactions between debris flows and their bed and banks. In addition, we lack a good understanding of the cumulative long-term effects of sequences of flows in a single catchment-fan system. Here we begin to address these issues by using repeated terrestrial laser scanning (TLS) to characterize the detailed surface change associated with the passage of multiple debris flows on the Illgraben fan, Switzerland. We calculate surface elevation change along a 300 m study reach, and from this derive the downfan rate of flow volume change, or lag rate; for comparison, we also derive the spatially-averaged lag rate over the entire ~2 km length of the fan. Lag rates are broadly comparable over both length scales, indicating that flow behavior does not vary significantly across the fan for most flows, but importantly we find that flow volume at the fan head is a poor predictor of volume at the fan toe. The sign and magnitude of bed elevation change scale with local flow depth; at flow depths < 2 m, erosion and deposition are approximately equally likely, but erosion becomes increasingly dominant for flow depths > 2 m. On the Illgraben fan, this depth corresponds to a basal shear stress of 3-4 kPa. Because flow depth is in part a function of channel cross-sectional topography, which varies strongly both within and between flows, this result indicates that erosion and deposition are likely to be highly dynamic. The dependence of flow volume change on both the channel topography and the flow history may thus complicate efforts to predict debris-flow inundation areas by simple flow routing. We then apply a 2d numerical model of debris-flow fan evolution to explore the key controls on debris-flow routing and topographic development over sequences of multiple flows. We find that fan topographic roughness plays an important role in both channel development and fan surface stability. We also find that, while first-order fan shape is largely insensitive to the input flow sequence, second-order variables such as the pattern of surface exposure ages and the distribution of channel characteristics hold more promise as robust recorders of past flow conditions. Further work is needed to understand the degree to which the TLS-derived (and Illgraben-specific) relationship between bed elevation change and flow depth can be applied in different settings, and to elucidate the role played by coarse debris in controlling patterns of erosion and deposition.

Glaciotectonic deformation and reinterpretation of the Worth Point stratigraphic sequence: Banks Island, NT, Canada

NASA Astrophysics Data System (ADS)

Vaughan, Jessica M.; England, John H.; Evans, David J. A.

2014-05-01

Hill-hole pairs, comprising an ice-pushed hill and associated source depression, cluster in a belt along the west coast of Banks Island, NT. Ongoing coastal erosion at Worth Point, southwest Banks Island, has exposed a section (6 km long and ˜30 m high) through an ice-pushed hill that was transported ˜ 2 km from a corresponding source depression to the southeast. The exposed stratigraphic sequence is polydeformed and comprises folded and faulted rafts of Early Cretaceous and Late Tertiary bedrock, a prominent organic raft, Quaternary glacial sediments, and buried glacial ice. Three distinct structural domains can be identified within the stratigraphic sequence that represent proximal to distal deformation in an ice-marginal setting. Complex thrust sequences, interfering fold-sets, brecciated bedrock and widespread shear structures superimposed on this ice-marginally deformed sequence record subsequent deformation in a subglacial shear zone. Analysis of cross-cutting relationships within the stratigraphic sequence combined with OSL dating indicate that the Worth Point hill-hole pair was deformed during two separate glaciotectonic events. Firstly, ice sheet advance constructed the hill-hole pair and glaciotectonized the strata ice-marginally, producing a proximal to distal deformation sequence. A glacioisostatically forced marine transgression resulted in extensive reworking of the strata and the deposition of a glaciomarine diamict. A readvance during this initial stage redeformed the strata in a subglacial shear zone, overprinting complex deformation structures and depositing a glaciotectonite ˜20 m thick. Outwash channels that incise the subglacially deformed strata record a deglacial marine regression, whereas aggradation of glaciofluvial sand and gravel infilling the channels record a subsequent marine transgression. Secondly, a later, largely non-erosive ice margin overrode Worth Point, deforming only the most surficial units in the section and depositing a capping till. The investigation of the Worth Point stratigraphic sequence provides the first detailed description of the internal architecture of a polydeformed hill-hole pair, and as such provides an insight into the formation and evolution of an enigmatic landform. Notably, the stratigraphic sequence documents ice-marginal and subglacial glaciotectonics in permafrost terrain, as well as regional glacial and relative sea level histories. The reinterpreted stratigraphy fundamentally rejects the long-established paleoenvironmental history of Worth Point that assumed a simple ‘layer-cake’ stratigraphy including the type-site for an organically rich, preglacial interval (Worth Point Fm).

Cyclicity in Upper Mississippian Bangor Limestone, Blount County, Alabama

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bronner, R.L.

1988-01-01

The Upper Mississippian (Chesterian) Bangor Limestone in Alabama consists of a thick, complex sequence of carbonate platform deposits. A continuous core through the Bangor on Blount Mountain in north-central Alabama provides the opportunity to analyze the unit for cyclicity and to identify controls on vertical facies sequence. Lithologies from the core represent four general environments of deposition: (1) subwave-base, open marine, (2) shoal, (3) lagoon, and (4) peritidal. Analysis of the vertical sequence of lithologies in the core indicates the presence of eight large-scale cycles dominated by subtidal deposits, but defined on the basis of peritidal caps. These large-scale cyclesmore » can be subdivided into 16 small-scale cycles that may be entirely subtidal but illustrate upward shallowing followed by rapid deepening. Large-scale cycles range from 33 to 136 ft thick, averaging 68 ft; small-scale cycles range from 5 to 80 ft thick and average 34 ft. Small-scale cycles have an average duration of approximately 125,000 years, which is compatible with Milankovitch periodicity. The large-scale cycles have an average duration of approximately 250,000 years, which may simply reflect variations in amplitude of sea level fluctuation or the influence of tectonic subsidence along the southeastern margin of the North American craton.« less

Sequence stratigraphy and hydrocarbon potential of the Phu Khanh Basin offshore central Vietnam, South China Sea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, G.H.; Watkins, J.S.

1996-12-31

The Phu Khanh Basin offshore central Vietnam is one of the few untested basins on the Vietnam margin of the South China Sea. Analysis of over 1,600 km of multi-channel seismic reflection data indicates that the Phu Khanh Basin follows a typical rift-margin order: faulted basement, synrift sedimentation, a breakup unconformity, and postrift sedimentation. Postrift sedimentation consists of a transgressive phase characterized by ramp-like depositional geometries followed by a regressive phase characterized by prograding sequences. An early middle Miocene unconformity separates these two phases. During the transgressive phase rising sea level provided favorable conditions for carbonate buildup development. The regressivemore » interval contains a number of third-order depositional sequences composed of seismically resolvable lowstand, highstand, and rarely, transgressive systems tracts. Lacustrine sediments deposited in graben and half-graben lakes during the rifting stage are probably the principal source rocks. Fractured and/or weathered basement, carbonate complexes, basinfloor fans, and shallows water sands may have good reservoir quality. Potential traps include basement hills, carbonate complexes, fault taps, and stratigraphic traps within lowstand systems tracts. Hydrocarbon indicators such as flat spots, bright spots, gas chimneys with gas mounds on the seafloor occur at a number of locations.« less

Sequence stratigraphy and hydrocarbon potential of the Phu Khanh Basin offshore central Vietnam, South China Sea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, G.H.; Watkins, J.S.

1996-01-01

The Phu Khanh Basin offshore central Vietnam is one of the few untested basins on the Vietnam margin of the South China Sea. Analysis of over 1,600 km of multi-channel seismic reflection data indicates that the Phu Khanh Basin follows a typical rift-margin order: faulted basement, synrift sedimentation, a breakup unconformity, and postrift sedimentation. Postrift sedimentation consists of a transgressive phase characterized by ramp-like depositional geometries followed by a regressive phase characterized by prograding sequences. An early middle Miocene unconformity separates these two phases. During the transgressive phase rising sea level provided favorable conditions for carbonate buildup development. The regressivemore » interval contains a number of third-order depositional sequences composed of seismically resolvable lowstand, highstand, and rarely, transgressive systems tracts. Lacustrine sediments deposited in graben and half-graben lakes during the rifting stage are probably the principal source rocks. Fractured and/or weathered basement, carbonate complexes, basinfloor fans, and shallows water sands may have good reservoir quality. Potential traps include basement hills, carbonate complexes, fault taps, and stratigraphic traps within lowstand systems tracts. Hydrocarbon indicators such as flat spots, bright spots, gas chimneys with gas mounds on the seafloor occur at a number of locations.« less

Comparative community structure of archaea in rumen of buffaloes and cattle.

PubMed

Paul, Shyam S; Dey, Avijit; Baro, Daoharu; Punia, Balbir S

2017-08-01

Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank. Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P < 0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P < 0.05) in cattle than in buffaloes. This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor V.; Baker, Scott E.; Andersen, Mikael R.

2011-04-28

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compels additional exploration. We therefore undertook whole genome sequencing of the acidogenic A. niger wild type strain (ATCC 1015), and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence and half the telomeric regionsmore » have been elucidated. Moreover, sequence information from ATCC 1015 was utilized to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 megabase of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis revealed up-regulation of the electron transport chain, specifically the alternative oxidative pathway in ATCC 1015, while CBS 513.88 showed significant up-regulation of genes relevant to glucoamylase A production, such as tRNA-synthases and protein transporters. Our results and datasets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.[Supplemental materials (10 figures, three text documents and 16 tables) have been made available. The whole genome sequence for A. niger ATCC 1015 is available from NBCI under acc. no ACJE00000000. The up-dated sequence for A. niger CBS 513.88 is available from EMBL under acc. no AM269948-AM270415. The sequence data from the phylogeny study has been submitted to NCBI (GU296686-296739). Microarray data from this study is submitted to GEO as series GSE10983. Accession for reviewers is possible through: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi token GSE10983] The dsmM_ANIGERa_coll511030F library and platform information is deposited at GEO under number GPL6758« less

20th-century glacial-marine sedimentation in Vitus Lake, Bering Glacier, Alaska, U.S.A.

USGS Publications Warehouse

Molnia, B.F.; Post, A.; Carlson, P.R.

1996-01-01

Vitus Lake, the ice-marginal basin at the southeastern edge of Bering Glacier, Alaska, U.S.A., is a site of modern, rapid, glacial-marine sedimentation. Rather than being a fresh-water lake, Vitus Lake is a tidally influenced, marine to brackish embayment connected to the Pacific Ocean by an inlet, the Seal River. Vitus Lake consists of five deep bedrock basins, separated by interbasinal highs. Glacial erosion has cut these basins as much as 250 m below sea level. High-resolution seismic reflection surveys conducted in 1991 and 1993 of four of Vitus Lake's basins reveal a complex, variable three-component acoustic stratigraphy. Although not fully sampled, the stratigraphy is inferred to be primarily glacial-marine units of (1) basal contorted and deformed glacial-marine and glacial sediments deposited by basal ice-contact processes and submarine mass-wasting; (2) acoustically well-stratified glacial-marine sediment, which unconformably overlies the basal unit and which grades upward into (3) acoustically transparent or nearly transparent glacial-marine sediment. Maximum thicknesses of conformable glacial-marine sediment exceed 100 m. All of the acoustically transparent and stratified deposits in Vitus Lake are modern in age, having accumulated between 1967 and 1993. The basins where these three-part sequences of "present-day" glacial-marine sediment are accumulating are themselves cut into older sequences of stratified glacial and glacial-marine deposits. These older units outcrop on the islands in Vitus Lake. In 1967, as the result of a major surge, glacier ice completely filled all five basins. Subsequent terminus retreat, which continued through August 1993, exposed these basins, providing new locations for glacial-marine sediment accumulation. A correlation of sediment thicknesses measured from seismic profiles at specific locations within the basins, with the year that each location became ice-free, shows that the sediment accumulation at some locations exceeds 10 m year-1.

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit.

PubMed

Diaby, N; Dold, B; Rohrbach, E; Holliger, C; Rossi, P

2015-11-15

Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands. Copyright © 2015 Elsevier B.V. All rights reserved.

Mixtures of Sulfates in Melas Chasma

NASA Image and Video Library

2017-09-04

In this image from NASA's Mars Reconnaissance Orbiter, layering within the light-toned sulfate deposit is the result of different states of hydration. Some of the layers have sulfates with little water (known as monohydrated sulfates) whereas other layers have higher amounts of water (called polyhydrated sulfates). The different amounts of water within the sulfates may reflect changes in the water chemistry during deposition of the sulfates, or may have occurred after the sulfates were laid down when heat or pressure forced the water out of some layers, causing a decrease in the hydration state. Many locations on Mars have sulfates, which are sedimentary rocks formed in water. Within Valles Marineris, the large canyon system that cuts across the planet, there are big and thick sequences of sulfates. The CRISM instrument on MRO is crucial for telling scientists which type of sulfate is associated with each layer, because each hydration state will produce a spectrum with absorptions at specific wavelengths depending upon the amount of water contained within the sulfate. https://photojournal.jpl.nasa.gov/catalog/PIA21935

Geologic map of the Bonners Ferry 30' x 60' quadrangle, Idaho and Montana

USGS Publications Warehouse

Miller, Fred K.; Burmester, Russell F.

2003-01-01

This data set maps and describes the geology of the Bonners Ferry 30' x 60' quadrangle, Idaho and Montana. The bedrock geology of the Bonners Ferry quadrangle consists of sedimentary, metamorphic, and granitic rocks ranging in age from Middle Proterozoic to Eocene. Bedrock units include rocks of (1) the Middle Proterozoic Belt Supergroup (2) the Middle Proterozoic Deer Trail Group, (3) the Late Proterozoic Windermere Group, (4) miogeoclinal or shelf facies lower Paleozoic rocks, and (5) Mesozoic and Tertiary granitic rocks. The Belt Supergroup, a thick sequence of argillite, siltite, quartzite, and impure carbonate rocks up to 9,000 m thick, occurs in two non-contiguous sequences in the quadrangle: (1) the Clark Fork-Eastport Sequence east of the Purcell trench and (2) the Newport Sequence in the hanging wall of the Newport Fault. Only the two lowest Belt formations of the Newport Sequence are found in the Bonners Ferry quadrangle, but these two units are part of a continuous section, which extends southwestward to the town of Newport. Belt Supergroup rocks of the Clark Fork-Eastport Sequence are separated from those of the Newport Sequence by the Newport Fault, Priest River Complex, and Purcell Trench Fault. Some formations of the Belt Supergroup show differences in thickness and (or) lithofacies from one sequence to the other that are greater than those predicted from an empirical depositional model for the distances currently separating the sequences. These anomalous thickness and facies differences suggest that there has been a net contraction along structures separating the sequences despite Eocene extension associated with emplacement of the Priest River Complex. In addition to these two Belt sequences, probable Belt rocks are present in the Priest River Complex as high metamorphic grade crystalline schist and gneiss. Northwest of the Newport Sequence of Belt Supergroup is the Deer Trail Group, a distinct Middle Proterozoic sequence of argillite, siltite, quartzite, and carbonate rocks lithostratigraphically similar to the Belt Supergroup, but separated from all Belt Supergroup rocks by the Jumpoff Joe Fault. Rocks of the Deer Trail Group are pervasively phyllitic and noticeably more deformed than rocks in the Belt Supergroup sequences. Lithostratigraphically the Deer Trail Group is equivalent to part of the upper part of the Belt Supergroup. Differences in lithostratigraphy and thickness between individual Deer Trail and Belt units and between the Deer Trail and Belt sequences as a whole indicate that they were probably much farther apart when they were deposited. The Windermere Group is a lithologically varied sequence of volcanic rocks and coarse-grained, mostly immature, clastic sedimentary rocks up to 8,000 m thick. It is characterized by extreme differences in thickness and lithofacies over short distances caused by syndepositional faulting associated with initial stages of continental rifting in the Late Proterozoic. Strata of the Windermere Group unconformably overlie only the Deer Trail Group, and are nowhere found in depositional contact with Belt Supergroup rocks. Paleozoic rocks in the Bonners Ferry quadrangle consist of a thin, fault-bounded remnant preserved within the Clark Fork-Eastport Belt Supergroup Sequence. Mesozoic granitic rocks underlie at least 50 percent of the Bonners Ferry quadrangle. They fall into two petrogenetic suites, hornblende-biotite plutons and muscovite-biotite (two-mica) plutons, most of which are Cretaceous in age. Both suites are represented in the mid-crustal Priest River Complex and in the higher level plutons that flank the complex; by far the majority of the Priest River Complex are Cretaceous, two-mica bodies. Tertiary rocks are restricted to a single small stock, numerous hypabyssal dikes that are too small to show at the scale of the map, and to cataclastic rocks related to the Newport Fault. Quaternary deposits include unconsolidated to poorl

Interglacial-glacial cycles recorded in the deposit sequence at Kruzhyky on the Dniester River (East Carpathian Foreland)

NASA Astrophysics Data System (ADS)

Łanczont, Maria; Boguckyj, Aandrij; Mroczek, Przemysław; Zieliński, Paweł; Jacyszyn, Andrij; Pidek, Agnieszka I.; Urban, Danuta; Kulesza, Piotr; Hołub, Beata

2010-01-01

Palaeogeographic investigations were carried out in the Kruzhyky site, which is situated in the East Carpathian Foreland, in the Dniester River valley, on the terrace 5 composed of the Mesopleistocene fluvial, glacigenic and aeolian deposits (Figs 1 and 2). These deposits are exposed along the section about 150 m long of the 15-17-metre-high river bank. In the undercutting of the Dniester River high bank the following five deposit complexes were described (Figs 3 and 4): 1. Fluvial complex-gravelly-sandy fining-up sequence. The Carpathian gravels with massive structure or faint horizontal stratification are covered by gravelly sands and sands with trough cross-stratification. They are overlain by sands and silts with ripple lamination merging into flaser lamination. These sediments were deposited as a result of rapid fall of flood in gravel-bed braided river. Gravel fractions represent deposition in longitudinal bars during high-energy flood flows, and sandy-gravelly and sandy-silty fractions-in channels between bars during waning flow (in the lower flow regime), at low river stages. 2. Fluvial-flood complex-package of alternating deformed clays with massive structure or faint lamination and silts with horizontal lamination. A lens, separated by erosion surface, occurs laterally. It is mostly composed of non-carbonate clays with numerous plant macroremnants, strongly gleyed, with interbeddings of sand. The silty-clayey complex was deposited from suspension, most probably after floods in depressions on floodplain. The lens of organogenic material (Fig. 5, Tables 3 and 4) is probably the result of deposition in cut off shallow channel (a kind of muddy depression) with periodically active weak flow. Based on the palaeobiological (pollen, macroremnants, Ostracoda) analyses of the deposits filling the reservoir, we find that it existed in cold climate and was surrounded with scarce sedge vegetation. 3. Proglacial complex-sandy-silty rhythmite composed of sands with horizontal stratification and silts with horizontal or flaser lamination; single small-scale lithofacies of sands with trough cross-stratification occur in places; single gravel grains are numerous. Two deformation horizons are found: the higher one is characterized by the occurrence of folds and flexure deflections, and the lower one-involution structures and casts of ice wedges/fissures. This complex is probably the result of deposition on the distal part of flat, periodically inundated fluvioglacial fan connected with advancing ice sheet. 4. Ablation complex-sandy or sandy-silty diamicton occurring as isolated inserts, lenses or tongues. Its lower boundary is sharp, erosional and uneven (concave). This complex represents flows of supraglacial tills, which strongly deformed the deposits of the underlying complex 3. 5. Aeolian complex-silty (loess) and sandy-silty (Table 1) deposits with distinct traces of intensive, postsedimentary alterations of pedogenesis of different ages (Tables 1 and 2). It is composed of two soil units separated by thin, primary loess layer: a) older, well-developed paleosol with several pedofeatures very typical of the Sokal (Mazovian) soil; b) younger unit developed as pedocomplex consisting of two mature soils, the upper of which ("modern" neosol) is formed in the top of relict and exhumed paleosol. The described paleosols should be recognized as at least two soils of different ages and of interglacial rank, developed in periglacial loess-like deposits. The Kruzhyky profile is unique in the Dniester River valley. On account of its situation, it supplements the former information about the terrace 5 structure, which has been determined in detail in the Halyč site. And what is most important, it is the only site on the terrace 5 where glacial deposits were found. Lithofacial analysis carried out in the profile enables us to reconstruct the following events reflecting interglacial-glacial cycles: 1. The lowest, gravelly-sandy unit indicates the functioning of warm (probably interglacial) braided river flowing from the Carpathians to the east; 2. The continuous clayey-silty-loamy sequence represents periglacial-glacial environment connected with the ice-sheet advance from the west or north-west on the examined area. Based on the presented data, we can only find that the ice-sheet front occurred at a distance of about 4-5 km from the Kruzhyky profile, and it was its maximum extent in Central Europe; 3. The loess-soil sequence of varied structure, which covers older paleorelief, represents two cycles of loess accumulation in periglacial environment and at least two pedogenesis cycles. Based on the described deposit sequence, we can verify the regional stratigraphic scheme (Fig. 6), and especially elaborate anaglacial phase.

Palaeoredox conditions and sequence stratigraphy of the Cretaceous storm-dominated, mixed siliciclastic-carbonate ramp in the Eastern Cordillera Basin (Colombia): Evidence from sedimentary geochemical proxies and facies analysis

NASA Astrophysics Data System (ADS)

Rivera, Huber A.; Le Roux, Jacobus P.; Sánchez, L. Katherine; Mariño-Martínez, Jorge E.; Salazar, Christian; Barragán, J. Carolina

2018-10-01

The Cretaceous black shales of Colombia are among the most important successions in the north of South America and have attracted the attention of many geoscientists and exploration companies over the last few decades, because of their high hydrocarbon potential and the presence of emerald deposits. However, many uncertainties still remain with regard to their tectonic setting, sequence stratigraphy, depositional environments, palaeoxygenation conditions, and organic matter preservation. In order to develop a more integrated picture of these different processes and conditions, we conducted a detailed sedimentological, inorganic geochemical (U, V, Ni, Zn, Mn, Fe, Ti, Mo, Cu, Cr, Cd, Ba) and sequence stratigraphic analysis of the Cretaceous black shales in the Magdalena-Tablazo Sub-Basin (Eastern Cordillera Basin) of Colombia. Eleven lithofacies and five lithofacies associations of a storm-dominated, siliciclastic-carbonate ramp were identified, which range from basin to shallow inner ramp environments. These facies were grouped into six third-order stratigraphic sequences showing high-order cycles of marine transgression with constrained regressive pulses during the late Valanginian to early Coniacian. The black shales succession represents deposition under anoxic bottom water with some intervals representing dysoxic-suboxic conditions. The evolution of the sedimentary environments and their palaeoxygenation history reflect tectonic and eustatic sea-level controls that 1) produced a variable orientation and position of the coastline throughout the Cretaceous; 2) conditioned the low-gradient ramp geometry (<0.3°) and 3) modified the oxygenation conditions in the Magdalena-Tablazo Sub-Basin. An improved understanding of the sedimentary setting during deposition of the Cretaceous black shales in the Magdalena-Tablazo Sub-Basin assists in highlighting the interplay between the mechanism of sedimentation and continuum anoxic conditions prevailing in a basin, as well the important role of nutrient input from continental runoff as a trigger of high productivity and extended anoxia conditions.

Stratigraphy of Pyroclastic Deposits of EL Aguajito Caldera, Baja California Sur, MÉXICO

NASA Astrophysics Data System (ADS)

Osorio Ocampo, L. S.; Macias, J. L.; García Sánchez, L.; Pola, A.; Saucedo, R.; Sánchez, J. M.; Avellán, D. R.; Cardona, S.; Reyes-Agustín, G.; Arce, J. L.

2015-12-01

El Aguajito caldera is located in the State of Baja California Sur, it comprises an area of 450 km2 and sits within the Santa Rosalía Basin which is controlled by NE-SW extensional structures and the NW-SE Cimarron Fault that transects the caldera structure. The oldest rocks are ~90 Ma granodiorites covered by an Oligocene-Miocene volcano-sedimentary sequence, the Miocene Santa Lucia Formation and La Esperanza basalt. Pliocene volcanism is represented by La Reforma caldera, El Aguajito caldera, and the Tres Vírgenes Volcanic complex. This study focuses on the cartography and stratigraphy of area in order to understand the evolution of the volcanic system. The stratigraphy from base to top consists of a series of shallow marine sediments (fossiliferous sandstones) covered by a thick sequence of ignimbrites and pyroclastic flows interbedded with volcaniclastic deposits (Gloria and El Infierno Formations). On top of these deposits is El Aguajito caldera, it consists of a 2 m thick pumice fallout followed by an ignimbrite with three transitional lithofacies: a ≤30-m thick light-pink pyroclastic flow enriched in pumice at the base that gradually becomes enrich in lithics towards the top with the occurrence of degasing pipes. On top rests a 15 m-thick light-purple ignimbrite slightly welded with fiammes and a sequence of pumiceous pyroclastic flows and fallouts. These deposits have been associate to the caldera formation with a collapse diameter of ~8 km marked by rhyolitic domes exposed along a ring collapse crowned the sequence as well as NW-SE aligned rhyolitic domes parallel to the seashore. This cartography allowed to present a preliminary new geological map with four stratigraphic units recognized so far, that were emplaced under subaerial conditions beginning with a Plinian column followed by the emplacement of El Aguajito ignimbrite with its subsequent caldera collapse and finally the extrusion of resurgent domes.

High resolution climatic variations recorded by mollusk fauna at Nussloch (Rhine valley, Germany) during the last glaciation

NASA Astrophysics Data System (ADS)

Moine, O.; Rousseau, D. D.; Antoine, P.

2003-04-01

Between 31 and 19 kyr B.P. important eolian sediments deposited in Western Europe at Nussloch favored by the enhanced atmospheric circulation at mid-latitudes and large areas of deflation providing quantities of material. The 10m-high studied sequence is composed of an alternation of nine gley-loess cycles deposited in a steppic environment. During gley formations, the climate is less windy, colder and more humid, and the malacofaunas have lower diversity and equitability than during the loess deposition. Top of the gleys is characterized by the thaw of the permafrost, when it is present, and by a demographic explosion of the mollusk fauna. Similar lithological alternations have been evidenced in all the Late Pleistocene deposits in Western Europe. They suggest that global climatic variations had a strong influence on the continental domain in Europe during this interval. Using the GRIP timescale, previously adapted to our loess sequence, we showed that the terrestrial mollusk abundance matches with the d18O of the Greenland ice-core. Thus, the high biological abundances regularly occurring in the sequence is interpreted be related to climate ameliorations. Nevertheless, the system is disturbed in the upper part of the sequence due to a strong increase in local moisture indicated by a decrease in both mollusk species richness and in d13C of the organic matter of the soil, restraining the development of the malacofauna during climatic improvements. The comparison with marine proxies indicates that the composition of the assemblages during the Heinrich 3 event had a higher proportion of semi-open environment species than during Heinrich 2 event, that could suggest a less severe climate. Furthermore, Heinrich 3 event is preceding by few particular assemblages typical of a very cold and humid environment. A strong amount of precipitation could have occurred at this time on the European continent, and could explain the important expansion of the Scandinavian ice-sheet southward just before the Last Glacial Maximum.

The influence of delta formation mechanism on geotechnical property sequence of the late Pleistocene-Holocene sediments in the Mekong River Delta.

PubMed

Hoang, Truong Minh; van Lap, Nguyen; Oanh, Ta Thi Kim; Jiro, Takemura

2016-11-01

The aim of the study was to characterize a variety of microstructure development-levels and geotechnical property sequences of the late Pleistocene-Holocene deposits in the Mekong River delta (MRD), and the paper furthermore discusses the influences of delta formation mechanisms on them. The survey associated the geotechnical engineering and the sedimentary geology of the late Pleistocene-Holocene deposits at five sites and also undifferentiated Pleistocene sediments. A cross-section which was rebuilt in the delta progradation-direction and between the Mekong and Bassac rivers represents the stratigraphy. Each sedimentary unit was formed under a different delta formation mechanism and revealed a typical geotechnical property sequence. The mechanical behaviors of the sediment succession in the tide-dominated delta with significant fluvial-activity and material source tend to be more cohesionless soils and strengths than those in the tide- and wave-dominated delta and even the coast. The particular tendency of the mechanical behavior of the deposit succession can be reasonably estimated from the delta formation mechanism. The characteristics of the clay minerals from the Mekong River produced the argillaceous soil which does not have extremely high plasticity. The microstructure development-levels are low to very high indicating how to choose hydraulic conductivity value, k, for estimating overconsolidation ratio, OCR, by the piezocone penetration tests (CPTU). The OCR of sediments in the delta types strangely change with depth but none less than 1. The post-depositional processes significantly influenced the microstructure development, particularly the dehydrating and oxidizing processes.

Paleoseismology of a possible fault scarp in Wenas Valley, central Washington

USGS Publications Warehouse

Sherrod, Brian L.; Barnett, Elizabeth A.; Knepprath, Nichole; Foit, Franklin F.

2013-01-01

In October 2009, two trenches excavated across an 11-kilometer-long scarp at Wenas Valley in central Washington exposed evidence for late Quaternary deformation. Lidar imagery of the Wenas Valley illuminated the west-northwest-trending, 2- to 8-meter-high scarp as it bisected alluvial fans developed at the mouths of canyons along the south side of Umtanum Ridge. The alignment of the scarp and aeromagnetic lineaments suggested that the scarp may be a product of and controlled by the same tectonic structure that produced the magnetic lineaments. Several large landslides mapped in the area demonstrated the potential for large mass-wasting events in the area. In order to test whether the scarp was the result of an earthquake-generated surface rupture or a landslide, trenches were excavated at Hessler Flats and McCabe Place. The profiles of bedrock and soil stratigraphy that underlie the scarp in each trench were photographed, mapped, and described, and a sequence of depositional and deformational events established for each trench. The McCabe Place trench exposed a sequence of volcaniclastic deposits overlain by soils and alluvial deposits separated by three unconformities. Six normal faults and two possible reverse faults deformed the exposed strata. Crosscutting relations indicated that up to five earthquakes occurred on a blind reverse fault, and a microprobe analysis of lapilli suggested that the earliest faulting occurred after 47,000 years before present. The Hessler Flat trench exposure revealed weathered bedrock that abuts loess and colluvium deposits and is overlain by soil, an upper sequence of loess, and colluvium. The latter two units bury a distinctive paloesol.

Novel in situ resistance measurement for the investigation of CIGS growth in a selenization process

NASA Astrophysics Data System (ADS)

Liu, Wei; Tian, Jian-Guo; Li, Zu-Bin; He, Qing; Li, Feng-Yan; Li, Chang-Jian; Sun, Yun

2009-03-01

During the selenization process of CIGS thin films, the relation between the element loss rate and the precursor depositions are analyzed. The growth of the CIGS thin films during the selenization process is investigated by the novel in situ resistance measurement, by which the formation of compound semiconductors can be observed directly and simultaneously. Their structures, phase evolutions and element losses are analyzed by XRD and XRF. Based on the experimental results, it can be concluded that the phase transforms have nothing to do with the deposition sequences of precursors, while the element loss rates are related to the deposition sequences in this process. In addition, element loss mechanisms of CIGS thin films prepared by the selenization process are analyzed by the phase evolutions and chemical combined path in the In, Ga-Se reaction processes. Moreover it is verified that the element losses are depressed by increasing the ramping-up rate finally. The results provide effective methods to fabricate high-quality CIGS thin films with low element losses.

Biotic association and palaeoenvironmental reconstruction of the "Loma del Pterodaustro" fossil site (Early Cretaceous, Argentina)

USGS Publications Warehouse

Chiappe, L.; Rivarola, D.; Cione, A.; Fregenal-Martinez, M.; Sozzi, H.; Buatois, L.; Gallego, O.; Laza, J.; Romero, E.; Lopez-Arbarello, A.; Buscalioni, A.; Marsicano, C.; Adamonis, S.; Ortega, F.; McGehee, S.; Di, Iorio O.

1998-01-01

A sedimentological analysis of the basal section of the Early Cretaceous, lacustrine Lagarcito Formation at "Loma del Pterodaustro" (San Luis, Argentina) and a summary of its biological components are presented. Three sedimentological facies can be recognized in the basal sequence of the Lagarcito Formation. Fossil remains are particularly abundant in laminated claystones of a facies interpreted as deposits formed in offshore areas of the lake. The preservation of delicate structures allows recognition of these deposits as a Konservat Lagersta??tte. Up to now, rocks at "Loma del Pterodaustro" have yielded plants, conchostracans, semionotid and pleuropholid fishes, pterodactyloid pterosaurs, and a variety of invertebrate traces. The chronology of the Lagarcito Formation is discussed and it is concluded that this unit is of Albian age. The palaeoenvironment of deposition of the basal sequence of the Lagarcito Formation at "Loma del Pterodaustro" is interpreted as a perennial, shallow lake developed within an alluvial plain, under semiarid climatic conditions.

Speleology and magnetobiostratigraphic chronology of the GD 2 locality of the Gondolin hominin-bearing paleocave deposits, North West Province, South Africa.

PubMed

Herries, Andy I R; Adams, Justin W; Kuykendall, Kevin L; Shaw, John

2006-12-01

Speleological, paleomagnetic, mineral magnetic, and biochronological analyses have been undertaken at the Gondolin hominin-bearing paleocave, North West Province, South Africa. Two fossiliferous but stratigraphically separate sequences, GD2 and GD1/3, which were once part of a large cavern system, have been identified. Although some comparative paleomagnetic samples were taken from the GD 1, 3, and 4 localities that are currently under investigation, the research presented here focuses on the fossil-rich, in situ deposits at locality GD 2, excavated by E.S. Vrba in 1979. The GD 2 deposits are dominated by normal-polarity calcified clastic deposits that are sandwiched between clastic-free flowstone speleothems. The lower flowstone has a sharp contact with the red siltstone deposits and is of reversed polarity. The capping flowstone shows a change from normal to reversed polarity, thereby preserving a polarity reversal. While the paleomagnetic work indicates that the GD 2 fossil material was deposited during a normal-polarity period, the shortness of the sequence made matching of the magnetostratigraphy to the geomagnetic polarity time scale (GPTS) impossible without the aid of biochronology. While lacking multiple time-sensitive taxa, the recovery of specimens attributable to Stage III Metridiochoerus andrewsi is consistent with a deposition date between 1.9 and 1.5 Ma. A comparison of the magnetostratigraphy with the GPTS therefore suggests that the fauna-bearing siltstone of GD 2 date to the Olduvai normal-polarity event, which occurred between 1.95 and 1.78 Ma, and that the reversal from normal to reversed polarity identified in the capping flowstone dates to 1.78 Ma. The main faunal layers therefore date to slightly older than 1.78 Ma. Deposits from the GD 1 locality are dominated by reversed directions of magnetization, which show that this deposit is not of the same age as the faunal layers from the GD 2 locality.

Quantitative controls on location and architecture of carbonate depositional sequences: Upper miocene, cabo de gata region, SE Spain

USGS Publications Warehouse

Franseen, E.K.; Goldstein, R.H.; Farr, M.R.

1997-01-01

Sequence stratigraphy, pinning-point relative sea-level curves, and magnetostratigraphy provide the quantitative data necessary to understand how rates of sea-level change and different substrate paleoslopes are dominant controls on accumulation rate, carbonate depositional sequence location, and internal architecture. Five third-order (1-10 my) and fourth-order (0.1-1.0 my) upper Miocene carbonate depositional sequences (DS1A, DS1B, DS2, DS3, TCC) formed with superimposed higher-frequency sea-level cycles in an archipelago setting in SE Spain. Overall, our study indicates when areas of high substrate slope (> 15??) are in shallow water, independent of climate, the location and internal architecture of carbonate deposits are not directly linked to sea-level position but, instead, are controlled by location of gently sloping substrates and processes of bypass. In contrast, if carbonate sediments are generated where substrates of low slope ( 15.6 cm/ky to ??? 2 cm/ky and overall relative sea level rose at rates of 17-21.4 cm/ky. Higher frequency sea-level rates were about 111 to more than 260 cm/ky, producing onlapping, fining- (deepening-) upward cycles. Decreasing accumulation rates resulted from decreasing surface area for shallow-water sediment production, drowning of shallow-water substrates, and complex sediment dispersal related to the archipelago setting. Typical systems tract and parasequence development should not be expected in "bypass ramp" settings; facies of onlapping strata do not track base level and are likely to be significantly different compared to onlapping strata associated with coastal onlap. Basal and upper DS2 reef megabreccias (indicating the transition from cool to warmer climatic conditions) were eroded from steep upslope positions and redeposited downslope onto areas of gentle substrate during rapid sea-level falls (> 22.7 cm/ky) of short duration. Such rapid sea-level falls and presence of steep slopes are not conducive to formation of forced regressive systems tracts composed of down-stepping reef clinoforms. The DS3 reefal platform formed where shallow water coincided with gently sloping substrates created by earlier deposition. Slow progradation (0.39-1.45 km/my) is best explained by the lack of an extensive bank top, progressively falling sea level, and low productivity resulting from siliciclastic debris and excess nutrients shed from nearby volcanic islands. Although DS3 strata were deposited during a third-order relative sea-level cycle, a typical transgressive systems tract is not recognizable, indicating that the initial relative rise in sea level was too rapid (??? 19 cm/ky). Downstepping reefs, forming a forced regressive systems tract, were deposited during the relative sea-level fall at the end of DS3, indicating that relatively slow rates of fall (10 cm/ky or less) over favorable paleoslope conditions are conducive to generation of forced regressive systems tracts consisting of downstepping reef clinoforms. The TCC sequence consists of four shallow-water sedimentary cycles that were deposited during a 400 ky to 100 ky time span. Such shallow-water cycles, typical of many platforms, form only where shallow water intersects gently sloping substrates. The relative thicknesses of cycles (< 2 m to 15 m thick), magnitudes of relative sea-level fluctuations associated with each cycle (25-30 m), high rates of relative sea-level fluctuations (minimum of 25-120 cm/ky), and the widespread distribution of similar TCC cycles in the Mediterranean and elsewhere are supportive of a glacio-eustatic

Quantitative controls on location and architecture of carbonate depositional sequences: upper miocene, cabo de gata region, se Spain

USGS Publications Warehouse

Franseen, E.K.; Goldstein, R.H.; Farr, M.R.

1998-01-01

Sequence stratigraphy, pinning-point relative sea-level curves, and magnetostratigraphy provide the quantitative data necessary to understand how rates of sea-level change and different substrate paleoslopes are dominant controls on accumulation rate, carbonate depositional sequence location, and internal architecture. Five third-order (1-10 my) and fourth-order (0.1-1.0 my) upper Miocene carbonate depositional sequences (DS1A, DS1B, DS2, DS3, TCC) formed with superimposed higher-frequency sea-level cycles in an archipelago setting in SE Spain. Overall, our study indicates when areas of high substrate slope (> 15??) are in shallow water, independent of climate, the location and internal architecture of carbonate deposits are not directly linked to sea-level position but, instead, are controlled by location of gently sloping substrates and processes of bypass. In contrast, if carbonate sediments are generated where substrates of low slope ( 15.6 cm/ky to ??? 2 cm/ky and overall relative sea level rose at rates of 17-21.4 cm/ky. Higher frequency sea-level rates were about 111 to more than 260 cm/ky, producing onlapping, fining- (deepening-) upward cycles. Decreasing accumulation rates resulted from decreasing surface area for shallow-water sediment production, drowning of shallow-water substrates, and complex sediment dispersal related to the archipelago setting. Typical systems tract and parasequence development should not be expected in "bypass ramp" settings; facies of onlapping strata do not track base level and are likely to be significantly different compared to onlapping strata associated with coastal onlap. Basal and upper DS2 reef megabreccias (indicating the transition from cool to warmer climatic conditions) were eroded from steep upslope positions and redeposited downslope onto areas of gentle substrate during rapid sea-level falls (> 22.7 cm/ky) of short duration. Such rapid sea-level falls and presence of steep slopes are not conducive to formation of forced regressive systems tracts composed of downstepping reef clinoforms. The DS3 reefal platform formed where shallow water coincided with gently sloping substrates created by earlier deposition. Slow progradation (0.39-1.45 km/my) is best explained by the lack of an extensive bank top, progressively falling sea level, and low productivity resulting from siliciclastic debris and excess nutrients shed from nearby volcanic islands. Although DS3 strata were deposited during a third-order relative sea-level cycle, a typical transgresse??e systems tract is not recognizable, indicating that the initial relative rise in sea level was too rapid (??? 19 cm/ky). Downstepping reefs, forming a forced regressive systems tract, were deposited during the relative sea-level fall at the end of DS3, indicating that relatively slow rates of fall (10 cm/ky or less) over favorable paleoslope conditions are conducive to generation of forced regressive systems tracts consisting of downstepping reef clinoforms. The TCC sequence consists of four shallow -water sedimentary cycles that were deposited during a 400 ky to 100 ky time span. Such shallow-water cycles, typical of many platforms, form only where shallow water intersects gently sloping substrates. The relative thicknesses of cycles (< 2 m to 15 m thick), magnitudes of relative sea-level fluctuations associated with each cycle (25-30 m), high rates of relative sea-level fluctuations (minimum of 25-120 cm/ky), and the widespread distribution of similar TCC cycles in the Mediterranean and elsewhere are supportive of a glacio-eustati

Depositional environments of the Rock Springs Formation, southwest flank of the Rock Springs Uplift, Wyoming.

USGS Publications Warehouse

Kirschbaum, M.A.

1986-01-01

This deltaic Upper Cretaceous Rock Springs Formation of the Mesaverde Group was deposited during early Campanian time near the end of the regressive phase of the Niobrara cyclothem. On the southwest end of the Uplift, part of the delta system is exposed near the seaward edge of a series of transgressive/regressive sequences, which consist of intertonguing prodelta, delta-front, and delta-plain deposits. Eight major delta-front sandstones are vertically stacked and laterally continuous throughout the main study area.-from Author

Melanin deposition ruled out as cause of color changes in the red-eared sliders (Trachemys scripta elegans).

PubMed

Cao, Dainan; Gong, Shiping; Yang, Jiangbo; Li, Weiye; Ge, Yan; Wei, Yufeng

2018-03-01

Animal coloration primarily depends on the presence of pigments and the mixing ratio of eumelanin and pheomelanin. The color of red-eared slider's carapace varies with age, from an olive green to a yellow green, and then to a yellow brown in juveniles, generally. The purpose of the present study was to investigate whether this color change is related to the difference in melanin expression. Melanin deposition levels were examined in the carapace, skin, eye and muscle of the three color-types using hematoxylin and eosin staining. Moreover, the full-length coding sequence (CDS) of red-eared slider turtle melanin biosynthesis regulatory genes TYR, TYRP1, MITF and SLC24A5 were cloned, sequenced and quantitatively analyzed. Both histological view of melanin deposition and quantitative real-time PCR test of melanin-regulated gene expressions showed that there are significant differences among different tissues of red-eared slider, but no significant difference among different color-types, indicating that melanin deposition is not associated with ontogenetic color change in the carapace of red-eared slider. This study initially explore the melanin deposition and the mRNA expression of melanin biosynthesis regulatory genes in red-eared slider, which serve as a foundation for further insight into the pigmentation patterns and the mechanism of body color change in turtles. Copyright © 2017 Elsevier Inc. All rights reserved.

Depositional facies and sequence stratigraphy of a Lower Carboniferous bryozoan-crinoidal carbonate ramp in the Illinois Basin, mid-continent USA

USGS Publications Warehouse

Lasemi, Z.; Norby, R.D.; Treworgy, J.D.

1998-01-01

The Lower Carboniferous Fort Payne and Ullin Formations in the Illinois Basin form the transgressive and highstand systems tracts that were deposited in a carbonate ramp setting. During deposition of the Ullin Limestone, biotic communities dominated by fenestrate bryozoans and echinoderms (primarily crinoids) proliferated, possibly in response to global tectonic, biological, and oceanographic events that affected bathymetry and nutrient supply. The Fort Payne Formation consists of a dark grey-brown, siliceous and argillaceous lime mudstone in the lower part (transgressive systems tract) and a very fine-grained wackestone to packstone with rare mud mounds in the upper part (early high-stand), and was deposited in an outer ramp to basinal environment. During deposition of the lower Ullin Limestone (mostly early highstand), bryozoan-crinoidal build-ups accreted both laterally and vertically into several relatively large carbonate banks, which were partly surrounded by siliceous Fort Payne sea. Bryozoans (primarily fenestrates) were especially prevalent during the late stage of bank development and formed mud-free bioherms up to 120 m thick. In places, carbonate mud mounds also formed during the early stage of bank deposition. Bioherm development declined during deposition of the upper Ullin Limestone (late highstand), and a broad, storm-dominated carbonate ramp was established that became the site for widespread deposition of bryozoan-crinoidal sandwaves. Gradual shallowing led to ooid formation at the end of Ullin deposition. This sequence was terminated by a relative rise in sea level that resulted in deposition of the transgressive facies of the lower part of the overlying Salem Limestone. The depositional style and the nature of skeletal material of the Fort Payne and Ullin Formations are similar to those of cool-water carbonates. A deep-water setting along with upwelling of cool, nutrient-rich oceanic waters may have been responsible for the proliferation of bryozoans and crinoids at this time. The deep-water setting and abundant nutrient supply also may have restricted the formation of ooids and proliferation of shallow-water calcareous organisms.

Eustatic and far-field tectonic control on the development of an intra-platform carbonate-shoal complex: upper tongue of the Tanglewood Member, Upper Ordovician Lexington Limestone, central Kentucky, U.S.A.

NASA Astrophysics Data System (ADS)

Koirala, Dibya Raj; Ettensohn, Frank R.; Clepper, Marta L.

2016-11-01

The Lexington or Trenton Limestone is an Upper Ordovician (Chatfieldian-Edenian; upper Sandbian-lower Katian), temperate-water unit, averaging about 60-m thick, that was deposited in relatively shallow waters across the Lexington Platform in east-central United States during the Taconian Orogeny. Lexington/Trenton shallow-water deposition ended across most of the platform in late Chatfieldian time and from that point deepened upward into the more shale-rich Clays Ferry, Point Pleasant and Kope formations due to apparent sea-level rise. In central Kentucky, however, deposition of the Lexington Limestone continued into early Edenian time and includes up to 50 m of additional coarse calcarenites and calcirudites at the top, which form the Tanglewood buildup and reflect locally regressive conditions, apparently related to local structural uplift. Consequently, in central Kentucky, the Lexington is more than 100-m thick, and Lexington deposition on the buildup continued into early Edenian time as an intra-platform shoal complex that tongues out into deeper-water units in all directions. In an attempt to understand how this shoal complex developed, we examined the last major body of coarse skeletal sands in the central Kentucky Lexington Limestone, the upper tongue of the Tanglewood Member, a 12-m-thick succession of fossiliferous calcarenite and calcirudite that occurs across an area of 5200 km2 near the center of the Lexington Platform. Although relatively homogeneous, the upper Tanglewood is divisible into five, small-scale, fining-upward, sequence-like cycles, which contain prominent, widespread deformed horizons. Facies analysis indicates that four lithofacies, which reflect distinct depositional environments, comprise the sequences across the shoal complex. Lithofacies were correlated across the shoal complex by integrating cyclicity and widespread deformed horizons in order to delineate the locations of major depositional environments. Facies analysis shows that the thickest and coarsest parts of each sequence, and the shallowest depositional environments, coincide with basement fault blocks, which are known to have experienced uplift during earlier Lexington Limestone deposition. The occurrence of thick, coarse facies on the same blocks suggests that the blocks continued to experience uplift into shallow water, where tides and waves redistributed sediments during upper Tanglewood deposition. Although eustasy apparently controlled cyclicity, Taconian far-field forces generated by orogeny in the east seem to have influenced facies distribution in each cycle through reactivation of basement fault zones as synsedimentary growth faults. The example of the upper Tanglewood Member shows that tectonic far-field forces can exert important influences on the development of carbonate depositional environments, even in distal intracratonic settings like the Lexington Platform.

Geochemical and Sulfur-Isotopic Signatures of Volcanogenic Massive Sulfide Deposits on Prince of Wales Island and Vicinity, Southeastern Alaska

USGS Publications Warehouse

Slack, John F.; Shanks, Wayne C.; Karl, Susan M.; Gemery, Pamela A.; Bittenbender, Peter E.; Ridley, W. Ian

2007-01-01

Stratabound volcanogenic massive sulfide (VMS) deposits on Prince of Wales Island and vicinity, southeastern Alaska, occur in two volcanosedimentary sequences of Late Proterozoic through Cambrian and of Ordovician through Early Silurian age. This study presents geochemical data on sulfide-rich samples, in situ laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) of sulfide minerals, and sulfur-isotopic analyses of sulfides and sulfates (barite) for identifying and distinguishing between primary sea-floor signatures and later regional metamorphic overprints. These datasets are also used here in an attempt to discriminate the VMS deposits in the older Wales Group from those in the younger Moira Sound unit (new informal name). The Wales Group and its contained VMS deposits have been multiply deformed and metamorphosed from greenschist to amphibolite grade, whereas the Moira Sound unit and related VMS deposits are less deformed and generally less metamorphosed (lower to middle greenschist grade). Variations in the sulfide mineral assemblages and textures of the VMS deposits in both sequences reflect a combination of processes, including primary sea-floor mineralization and sub-sea-floor zone refining, followed by metamorphic recrystallization. Very coarse grained (>1 cm diam) sulfide minerals and abundant pyrrhotite are restricted to VMS deposits in a small area of the Wales Group, at Khayyam and Stumble-On, which record high-grade metamorphism of the sulfides. Geochemical and sulfur-isotopic data distinguish the VMS deposits in the Wales Group from those in the Moira Sound unit. Although base- and precious-metal contents vary widely in sulfide-rich samples from both sequences, samples from the Moira Sound generally have proportionately higher Ag contents relative to base metals and Au. In situ LA-ICP-MS analysis of trace elements in the sulfide minerals suggests that primary sea-floor hydrothermal signatures are preserved in some samples (for example, Mn, As, Sb, and Tl in pyrite from the Moira Sound unit), whereas in other samples the signatures are varyingly annealed, owing to metamorphic overprinting. A limited LA-ICP-MS database for sphalerite indicates that low-Fe sphalerite is preferentially associated with the most Au rich deposits, the Niblack and Nutkwa. Sulfur-isotopic values for sulfide minerals in the VMS deposits in the Wales Group range from 5.9 to 17.4 permil (avg 11.5?2.7 permil), about 5 to 6 permil higher than those in the Moira Sound unit, which range from -2.8 to 10.4 permil (avg 6.1?4.0 permil). This difference in 34Ssulfide values reflects a dominantly seawater sulfate source of the sulfides and is linked to the 34S values of contemporaneous seawater sulfate, which were slightly higher during the Late Proterozoic through Cambrian than during the Ordovician through Early Silurian.

The status of the species Enterobacter siamensisKhunthongpan et al. 2014. Request for an Opinion.

PubMed

Kämpfer, Peter; Doijad, Swapnil; Chakraborty, Trinad; Glaeser, Stefanie P

2016-01-01

In the course of a taxonomic study describing novel species of the genus Enterobacter it was found that the 16S rRNA gene sequence of the type strain of Enterobacter siamensis, obtained both directly from the authors of the publication on Enterobacter siamensis and from the Korean Collection for Type Cultures (C2361T and KCTC 23282T, respectively), was not congruent with the 16S rRNA gene sequence deposited in the GenBank database under the accession number HQ888848, which was applied for phylogenetic analysis in the species proposal. The remaining deposit in the Japanese type culture collection, NBRC 107138T, showed an identical 16S rRNA gene sequence to the other two cultures and overall, this sequence differed at 35 positions in comparison with the 1429 bp sequence published under the accession number HQ888848.Therefore, the type strain of this species cannot be included in any further scientific comparative study. It is proposed that the Judicial Commission of the International Committee on Systematics of Prokaryotes place the name Enterobacter siamensis on the list of rejected names, if a suitable replacement for the type strain is not found or a neotype strain is not proposed within two years following the publication of this Request for an Opinion.

Progradational sequences in Miocene shoreline deposits, southeastern Caliente Range, California

USGS Publications Warehouse

Clifton, H. Edward

1981-01-01

An exceptionally well exposed marine-nonmarine transition in middle Miocene strata exists in the southeastern Caliente Range, California. About 50 individual progradational sequences form a succession that ranges in thickness from approximately 1000 m (where predominantly nonmarine) to more than 2500 m (where predominantly marine). Paleogreographic evidence in basalt flows near the top of the succession and in overlying fluvial deposists indicates that these middle Miocene strata were deposited across a north-northwest trending shoreline.A complete progradational sequence typically is several meters to a few tens of meters thick and includes strata that represent three intertonguing stratigraphic units. Individual sequences generally rest on a thin gravel deposit interpreted as a transgressive lag on an erosional surface. The gravel is overlain by structureless siltstone or fine-grained sandstone deposited at water depths where the rate of faunal mixing exceeded that of production of structures by physical processes. These rocks grade upward into bedded fine sandstone deposited closer to shore where physical processes exceeded bioturbation. Crossbedded lenses of coarse sand or fine gravel in the upper part of this facies suggest the presence of failry long-period surface waves. The bedded fine sandstone is sharply overlain by a crossbedded coarse sandstone facies that is interpreted as a combined offshore bar-rip channel-surf zone assemblage. Cross-strata dip dominantly offshore, suggesting substantial deposition from rip currents. A secondary, shore=parallel mode of cross-strata direction suggests longshore currents produced by surface waves from the northwest. The crossbedded coarse-grained sandstone grades upward into planar-bedded medium-grained sandstone that is interpreted as a beach foreshore. This facies grades upward through structureless medium-grained sandstone into nonmarine or lagoonal red and green mudstone of the Caliente Formation.The middle Miocene succession was deposited in a subsiding basin that was otherwise remarkably stable tectonically; the position of the strand line differed no more than a few kilometers through a period of 1 to 3 m.y. The average duration of the transgressive-regressive cycles, a few tens of thousands of years, together with their distribution in groups of three or four in the lower two-thirds of the succession, is consistent with the pattern of long-term climatic cycles produced by periodicity of the earth's solar orbit and may be related to eustatic sea level changes attendant to the development of the Antarctic ice cap. Changes in the pattern of progradation in the upper part of the succession and nearby basaltic eruptions may hav been precursors to the onset of movement along the San Andreas fault in this area 12-14 m.y. ago.

Fabrication of Ternary AgPdAu Alloy Nanoparticles on c-Plane Sapphire by the Systematical Control of Film Thickness and Deposition Sequence

NASA Astrophysics Data System (ADS)

Kunwar, Sundar; Pandey, Puran; Sui, Mao; Bastola, Sushil; Lee, Jihoon

2018-06-01

In this work, a systematic study on the fabrication of ternary AgPdAu alloy nanoparticles (NPs) on c-plane sapphire (0001) is presented and the corresponding structural and optical characteristics are demonstrated. The metallic trilayers of various thicknesses and deposition orders are annealed in a controlled manner (400 °C to 900 °C) to induce the solid-state dewetting that yields the various structural configurations of AgPdAu alloy NPs. The dewetting of relatively thicker trilayers (15 nm) is gradually progressed with void nucleation, growth, and coalescence, isolated NP formation, and shape transformation, along with the temperature control. For 6 nm thickness, owing to the sufficient dewetting of trilayers along with enhanced diffusion, dense and small spherical alloy NPs are fabricated. Depending on the specific growth condition, the surface diffusion and interdiffusion of metal atoms, surface and interface energy minimization, Rayleigh instability, and equilibrium configuration are correlated to describe the fabrication of ternary alloy NPs. Ternary alloy NPs exhibit morphology-dependent ultraviolet-visible-near infrared (UV-VIS-NIR) reflectance properties such as the inverse relationship of average reflectance with the surface coverage, absorption enhancement in specific regions, and reflectance maxima in UV and NIR regions. In addition, Raman spectra depict the six active phonon modes of sapphires and their intensity and position modulation by the alloy NPs.

Dakota sandstone facies, western Oklahoma panhandle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atalik, E.; Mansfield, C.F.

The Cretaceous Dakota Sandstone in Cimarron County comprised three sandstone units and intervening mudrocks; it overlies the Kiowa Shale Member of the Purgatoire Formation. Deposits include shoreface, beach (foreshore) and dune, estuarine and tidal channel, marine marginal bay and swamp/marsh in a generally progradational sequences associated with marine regression in the Western Interior. The shoreface sand, characterized by ripple lamination, bioturbation and the trace fossils Teichichnus and Thalassinoides, is fine-grained, 5-10 m (15-30 ft) thick and grades into the underlying Kiowa Shale. Beach and associated dune deposits are 2-5 m (6-16 ft) thick, medium to fine-grained, medium to thick-bedded, tabular-planarmore » cross-bedded, and lenticular; cross-bed paleocurrent headings are northeasterly and northwesterly. Estuarine channel deposits are 3-5 m (10 to 16 ft) thick, trough to tabular-planar cross-bedded, and medium to coarse-grained with local conglomerate overlying the scoured base which commonly cuts into the Kiowa Shale or overlying shoreface sandstone; rip-up clasts and wood pieces are common but trace fossils are rare; southeasterly and southwesterly paleocurrents predominate. Tidal channel deposits are thinner (up to 2 m of 6 ft) and finer grained (medium to fine-grained) that the estuarine channel deposits; they occur within fine-grained sandstone and mudrock sequences, are trough cross-bedded, and commonly contain trace fossils (e.g., Skolithos) and wood fragments. Marine marginal (tidal flat or bay.) deposits comprise fine-grained sandstone, siltstone and interbedded shale, that are 1-3m (3-10 ft) thick with abundant burrows, small ripple marks, and parallel lamination. These grade into the fine to very fine-grained sandstones, siltstones, shales, and coals of the swamp/marsh deposits that are 1-5m (3-16 ft) thick and contain ripple marks, burrows, other trace fossils, and parallel lamination.« less

Sedimentological imprints of environmental variability at the Balkan Peninsula on the sediment sequence of Lake Ohrid (Macedonia, Albania) between the Mid Pleistocene Transition and present days: The ICDP SCOPSCO project

NASA Astrophysics Data System (ADS)

Francke, Alexander; Wagner, Bernd; Leicher, Niklas; Raphael, Gromig; Leng, Melanie; Lacey, Jack; Vogel, Hendrik; Baumgarten, Henrike; Thomas, Wonik; Zanchetta, Giovanni; Roberto, Sulpizio; Krastel, Sebastian; Lindhorst, Katja

2015-04-01

The UNESCO World Heritage site of Lake Ohrid in the Balkans is thought to be the oldest, continuously existing lake in Europe. In order to unravel the geological and evolutionary history of the lake, a deep drilling campaign was conducted in spring 2013 under the umbrella of the ICDP SCOPSCO project. At the coring site "DEEP" in central parts of the lake, more than 1,500 m of sediments were recovered down to a penetration depth of 569 m blf. This sediment sequence is assumed to be more than 1.2 Ma old and likely covers the entire lacustrine deposits of the Lake Ohrid Basin. Currently, an age model for the upper 260m of the DEEP- site sequence is available. This age model is based on chronological tie points (tephrochronology), and wiggle matching of down hole logging data and (bio-)geochemistry data (XRF, TIC, TOC) from the core sequence to the global benthic stack LR04 and local insolation patterns. The data suggests that the upper 260 m of the DEEP-site sequence corresponds to the time period between the Mid Pleistocene Transition (MPT) and present days. During this period, the sedimentological properties of the sediments show a strong dependency on environmental variability in the area. Interglacial deposits appear massive or marbled, contain up to 80 % of CaCO3 (high TIC), high amounts of organic matter (high TOC) and biogenic silica (high BSi), and low contents of clastic material. Glacial deposits are predominantly marbled and calcite is generally absent. Similarly, the amounts of organic matter and biogenic silica are low, and glacial sediments predominately consist of clastic matter. Distinct layers of siderite and uniformly distributed Fe- or Mn- oxides occur in the glacial deposits, vivianite concretions occur in both the glacial and interglacial periods. High CaCO3 contents in deposits formed during warm (interglacial) periods are also known from studies on short pilot cores from Lake Ohrid and are triggered by increased productivity in the lake, such as also indicated by enhanced contents of organic matter and biogenic silica. Thereby, CaCO3 precipitation is caused by photosynthesis induced calcite precipitation during algae blooms in spring and early summer. Negligible contents of TIC in deposits formed during glacial periods can be explained by an overall low productivity (low TOC and BSi) and, in addition, by dilution of CaCO3. Dilution of CaCO3 might be a result of more acid bottom water conditions, triggered by improved mixing conditions (less thermal stratification), oxidation of OM and CO2 release from the surface sediments. Oxygenated surface sediments and degradation of organic matter are indicated by the marbled structure of the glacial sediments implying intensive bioturbation, and by TOC/TN ratios around 4, respectively. The high amount of clastic material in deposits from cold (glacial) periods can be a result of mutual dilution with calcite, organic matter and biogenic silica, but might also indicate more intensive erosion in the catchment due to a less dense vegetation cover.

Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

USGS Publications Warehouse

Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

1998-01-01

The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (<20 m) in this supposedly ice-free world because Eocene sequence boundaries also appear to correlate with minor ??18O increases. Subsidence estimates (backstripping) indicate amplitudes of short-term (million-year scale) lowerings that are consistent with estimates derived from ??18O studies (25-50 m in the Oligocene-middle Miocene and 10-20 m in the Eocene) and a long-term lowering of 150-200 m over the past 65 myr, consistent with estimates derived from volume changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and high pelagic input associated with warm climates resulted in widespread carbonate deposition and thin sequences. Late middle Eocene and earliest Oligocene cooling events curtailed carbonate deposition in the coastal plain and slope, respectively, resulting in a switch to siliciclastic sedimentation. In onshore areas, Oligocene sequences are thin owing to low siliciclastic and pelagic input, and their distribution is patchy, reflecting migration or progradation of depocenters; in contrast, Miocene onshore sequences are thicker, reflecting increased sediment supply, and they are more complete downdip owing to simple tectonics. We conclude that the New Jersey margin provides a natural laboratory for unraveling complex interactions of eustasy, tectonics, changes in sediment supply, and climate change.

Responses of soil N-fixing bacteria communities to invasive plant species under different types of simulated acid deposition

NASA Astrophysics Data System (ADS)

Wang, Congyan; Zhou, Jiawei; Jiang, Kun; Liu, Jun; Du, Daolin

2017-06-01

Biological invasions have incurred serious threats to native ecosystems in China, and soil N-fixing bacteria communities (SNB) may play a vital role in the successful plant invasion. Meanwhile, anthropogenic acid deposition is increasing in China, which may modify or upgrade the effects that invasive plant species can cause on SNB. We analyzed the structure and diversity of SNB by means of new generation sequencing technology in soils with different simulated acid deposition (SAD), i.e., different SO4 2- to NO3 - ratios, and where the invasive ( Amaranthus retroflexus L.) and the native species ( Amaranthus tricolor L.) grew mixed or isolated for 3 months. A. retroflexus itself did not exert significant effects on the diversity and richness of SNB but did it under certain SO4 2- to NO3 - ratios. Compared to soils where the native species grew isolated, the soils where the invasive A. retroflexus grew isolated showed lower relative abundance of some SNB classes under certain SAD treatments. Some types of SAD can alter soil nutrient content which in turn could affect SNB diversity and abundance. Specifically, greater SO4 2- to NO3 - ratios tended to have more toxic effects on SNB likely due to the higher exchange capacity of hydroxyl groups (OH-) between SO4 2- and NO3 -. As a conclusion, it can be expected a change in the structure of SNB after A. retroflexus invasion under acid deposition rich in sulfuric acid. This change may create a plant soil feedback favoring future A. retroflexus invasions.

Responses of soil N-fixing bacteria communities to invasive plant species under different types of simulated acid deposition.

PubMed

Wang, Congyan; Zhou, Jiawei; Jiang, Kun; Liu, Jun; Du, Daolin

2017-06-01

Biological invasions have incurred serious threats to native ecosystems in China, and soil N-fixing bacteria communities (SNB) may play a vital role in the successful plant invasion. Meanwhile, anthropogenic acid deposition is increasing in China, which may modify or upgrade the effects that invasive plant species can cause on SNB. We analyzed the structure and diversity of SNB by means of new generation sequencing technology in soils with different simulated acid deposition (SAD), i.e., different SO 4 2- to NO 3 - ratios, and where the invasive (Amaranthus retroflexus L.) and the native species (Amaranthus tricolor L.) grew mixed or isolated for 3 months. A. retroflexus itself did not exert significant effects on the diversity and richness of SNB but did it under certain SO 4 2- to NO 3 - ratios. Compared to soils where the native species grew isolated, the soils where the invasive A. retroflexus grew isolated showed lower relative abundance of some SNB classes under certain SAD treatments. Some types of SAD can alter soil nutrient content which in turn could affect SNB diversity and abundance. Specifically, greater SO 4 2- to NO 3 - ratios tended to have more toxic effects on SNB likely due to the higher exchange capacity of hydroxyl groups (OH - ) between SO 4 2- and NO 3 - . As a conclusion, it can be expected a change in the structure of SNB after A. retroflexus invasion under acid deposition rich in sulfuric acid. This change may create a plant soil feedback favoring future A. retroflexus invasions.

Depositional environments of some Pleistocene coastal terrace deposits, southwestern Oregon - case history of progradational beach and dune sequence.

USGS Publications Warehouse

Hunter, R.E.

1980-01-01

These deposits comprise a basal gravelly unit and 3 overlying sandy units, each with mud beds, a paleosol, or the modern soil in its uppermost part. The gravelly unit is interpreted as a progradational deposit. The main parts of the sandy units are made up of 1) a crossbedded sand facies, the dominant structure in which is medium-scale crossbedding (interpreted as the product of small eolian dunes), and 2) an irregularly bedded sand facies, which is locally pebbly and is dominated by scour-and-fill structures, interpreted as deposits of interdune ephemeral streams, ephemeral ponds, and wet to dry subaerial flats. The mud beds and paleosols represent times of temporary stabilization of the dune field.- from Author

Investigation of the poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene]/indium tin oxide interface using photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Lägel, B.; Beerbom, M. M.; Doran, B. V.; Lägel, M.; Cascio, A.; Schlaf, R.

2005-07-01

The interface between the luminescent polymer poly [2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) and sputter-cleaned indium tin oxide (ITO) was investigated using photoemission spectroscopy in combination with in situ thin film deposition. MEH-PPV was deposited in high vacuum directly from toluene solution on the ITO substrate using a home-built electrospray thin-film deposition system. The deposition was carried out in multiple steps without breaking the vacuum. In between deposition steps the sample was characterized with x-ray and ultraviolet photoemission spectroscopy. The evaluation of the spectra sequence allowed the determination of the orbital lineup (charge injection barriers) at the interface, as well as the MEH-PPV growth mode at the interface.

Dzhezkazgan and associated sandstone copper deposits of the Chu-Sarysu basin, Central Kazakhstan

USGS Publications Warehouse

Box, Stephen E.; Seltmann, Reimar; Zientek, Michael L.; Syusyura, Boris; Creaser, Robert A.; Dolgopolova, Alla

2012-01-01

Sandstone-hosted copper (sandstone Cu) deposits occur within a 200-km reach of the northern Chu-Sarysu basin of central Kazakhstan (Dzhezkazgan and Zhaman-Aibat deposits, and the Zhilandy group of deposits). The deposits consist of Cu sulfide minerals as intergranular cement and grain replacement in 10 ore-bearing members of sandstone and conglomerate within a 600- to 1,000-m thick Pennsylvanian fluvial red-bed sequence. Copper metal content of the deposits ranges from 22 million metric tons (Mt, Dzehzkazgan) to 0.13Mt (Karashoshak in the Zhilandy group), with average grades of 0.85 to 1.7% Cu and significant values for silver (Ag) and rhenium (Re). Broader zones of iron reduction (bleaching) of sandstones and conglomerates of the red-bed sequence extend over 10 km beyond each of the deposits along E-NE-trending anticlines, which began to form in the Pennsylvanian. The bleached zones and organic residues within them are remnants of ormer petroleum fluid accumulations trapped by these anticlines. Deposit sites along these F1anticlines are localized at and adjacent to the intersections of nearly orthogonal N-NW-trending F2synclines. These structural lows served to guide the flow of dense ore brines across the petroleum-bearing anticlines, resulting in ore sulfide precipitation where the two fluids mixed. The ore brine was sourced either from the overlying Early Permian lacustrine evaporitic basin, whose depocenter occurs between the major deposits, or from underlying Upper Devonian marine evaporites. Sulfur isotopes indicate biologic reduction of sulfate but do not resolve whether the sulfate was contributed from the brine or from the petroleum fluids. New Re-Os age dates of Cu sulfides from the Dzhezkazgan deposit indicate that mineralization took place between 299 to 309 Ma near the Pennsylvanian-Permian age boundary. At the Dzhezkazgan and some Zhilandy deposits, F2fold deformation continued after ore deposition. Copper orebodies in Lower Permian shale near the Zhaman-Aibat deposit indicate that at least some of the mineralization there is younger than at Dzhezkazgan, consistent with the Re-Os age and with differences in their ore Pb isotopes.

Incised valley fill interpretation for Mississippian Black Hand Sandstone, Appalachian Basin, USA: Implications for glacial eustasy at Kinderhookian-Osagean (Tn2-Tn3) boundary

USGS Publications Warehouse

Matchen, D.L.; Kammer, T.W.

2006-01-01

Lower Mississippian strata of east-central Ohio are predominantly fine-grained marine deposits of the Cuyahoga and Logan formations. Within these sediments is the Black Hand Sandstone of the Cuyahoga Formation. The Black Hand Sandstone is a multistory, crossbedded, coarse-grained conglomeratic sandstone. The contact between the Black Hand Sandstone and the subjacent Cuyahoga Formation is sharp and scoured, with intraclasts of the Cuyahoga Formation incorporated into the basal Black Hand Sandstone. The Black Hand Sandstone was previously thought to represent a distributary channel deposit; however, the combination of lithofacies and architectural elements indicates deposition in a braided stream setting. The Cuyahoga Formation was deposited in a shallow marine setting. The erosional basal contact of the Black Hand Sandstone and the juxtaposition of fluvial and marine sediments suggests a sequence boundary. The geographic distribution of the Black Hand Sandstone combined with the evidence for a sequence boundary suggests deposition in an incised valley. The age of the Black Hand Sandstone is key to inferring the causes of valley incision. The Black Hand Sandstone is nearly devoid of body fossils, necessitating a biostratigraphic analysis of the surrounding Cuyahoga and Logan formations. Analysis indicates the Logan Formation is early Osagean age. Data from the Cuyahoga Formation suggest a Kinderhookian age with a possible transition to the Osagean in the uppermost Cuyahoga Formation. This constrains the age of the Black Hand Sandstone to the transition at the Kinderhookian-Osagean boundary. Recent reports indicate late Kinderhookian (Tournaisian, Tn2) Gondwanan glaciation based upon tillites and sharp excursions in stable-isotope curves. A glacio-eustatic fall in sea level is inferred to have caused incision of the Cuyahoga Formation, followed by deposition of the Black Hand Sandstone and Logan Formation during the subsequent sea level rise. The associated unconformity correlates to the sequence boundary at the Kinderhookian-Osagean boundary in the stratotype area of North America, and the correlative Tn2-Tn3 boundary worldwide, supporting the hypothesis of a global eustatic event at this time. ?? 2006 Elsevier B.V. All rights reserved.

Draft genome sequence of Mycobacterium tuberculosis strain B9741 of Beijing B0/W lineage from HIV positive patient from Siberia.

PubMed

Shur, K V; Zaychikova, M V; Mikheecheva, N E; Klimina, K M; Bekker, O B; Zhdanova, S N; Ogarkov, O B; Danilenko, V N

2016-12-01

We report a draft genome sequence of Mycobacterium tuberculosis strain B9741 belonging to Beijing B0/W lineage isolated from a HIV patient from Siberia, Russia. This clinical isolate showed MDR phenotype and resistance to isoniazid, rifampin, streptomycin and pyrazinamide. We analyzed SNPs associated with virulence and resistance. The draft genome sequence and annotation have been deposited at GenBank under the accession NZ_LVJJ00000000.

Geologic and Fossil Locality Maps of the West-Central Part of the Howard Pass Quadrangle and Part of the Adjacent Misheguk Mountain Quadrangle, Western Brooks Range, Alaska

USGS Publications Warehouse

Dover, James H.; Tailleur, Irvin L.; Dumoulin, Julie A.

2004-01-01

The map depicts the field distribution and contact relations between stratigraphic units, the tectonic relations between major stratigraphic sequences, and the detailed internal structure of these sequences. The stratigraphic sequences formed in a variety of continental margin depositional environments, and subsequently underwent a complexde formational history of imbricate thrust faulting and folding. A compilation of micro and macro fossil identifications is included in this data set.

Genome sequence of Bradyrhizobium sp. LMTR 3, a diazotrophic symbiont of Lima bean (Phaseolus lunatus).

PubMed

Ormeño-Orrillo, Ernesto; Rey, Luis; Durán, David; Canchaya, Carlos A; Zúñiga-Dávila, Doris; Imperial, Juan; Martínez-Romero, Esperanza; Ruiz-Argüeso, Tomás

2017-09-01

Bradyrhizobium sp. LMTR 3 is a representative strain of one of the geno(species) of diazotrophic symbionts associated with Lima bean ( Phaseolus lunatus ) in Peru. Its 7.83 Mb genome was sequenced using the Illumina technology and found to encode a complete set of genes required for nodulation and nitrogen fixation, and additional genes putatively involved in root colonization. Its draft genome sequence and annotation have been deposited at GenBank under the accession number MAXC00000000.

Whole genome sequences and annotation of Micrococcus luteus SUBG006, a novel phytopathogen of mango.

PubMed

Rakhashiya, Purvi M; Patel, Pooja P; Thaker, Vrinda S

2015-12-01

Actinobaceria, Micrococcus luteus SUBG006 was isolated from infected leaves of Mangifera indica L. vr. Nylon in Rajkot, (22.30°N, 70.78°E), Gujarat, India. The genome size is 3.86 Mb with G + C content of 69.80% and contains 112 rRNA sequences (5S, 16S and 23S). The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JOKP00000000.

Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China.

PubMed

Lee, Kwok-Ho; Wang, Yong-Feng; Li, Hui; Gu, Ji-Dong

2014-12-01

Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases.

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing.

PubMed

Jeong, Hyeonsoo; Song, Ki-Duk; Seo, Minseok; Caetano-Anollés, Kelsey; Kim, Jaemin; Kwak, Woori; Oh, Jae-Don; Kim, EuiSoo; Jeong, Dong Kee; Cho, Seoae; Kim, Heebal; Lee, Hak-Kyo

2015-08-20

Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data. We generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism. Results revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.

Draft genome sequence of the docosahexaenoic acid producing thraustochytrid Aurantiochytrium sp. T66.

PubMed

Liu, Bin; Ertesvåg, Helga; Aasen, Inga Marie; Vadstein, Olav; Brautaset, Trygve; Heggeset, Tonje Marita Bjerkan

2016-06-01

Thraustochytrids are unicellular, marine protists, and there is a growing industrial interest in these organisms, particularly because some species, including strains belonging to the genus Aurantiochytrium, accumulate high levels of docosahexaenoic acid (DHA). Here, we report the draft genome sequence of Aurantiochytrium sp. T66 (ATCC PRA-276), with a size of 43 Mbp, and 11,683 predicted protein-coding sequences. The data has been deposited at DDBJ/EMBL/Genbank under the accession LNGJ00000000. The genome sequence will contribute new insight into DHA biosynthesis and regulation, providing a basis for metabolic engineering of thraustochytrids.

Mammalian prions: tolerance to sequence changes-how far?

PubMed

Salamat, Muhammad Khalid; Munoz-Montesino, Carola; Moudjou, Mohammed; Rezaei, Human; Laude, Hubert; Béringue, Vincent; Dron, Michel

2013-01-01

Upon prion infection, abnormal prion protein (PrP (Sc) ) self-perpetuate by conformational conversion of α-helix-rich PrP (C) into β sheet enriched form, leading to formation and deposition of PrP (Sc) aggregates in affected brains. However the process remains poorly understood at the molecular level and the regions of PrP critical for conversion are still debated. Minimal amino acid substitutions can impair prion replication at many places in PrP. Conversely, we recently showed that bona fide prions could be generated after introduction of eight and up to 16 additional amino acids in the H2-H3 inter-helix loop of PrP. Prion replication also accommodated the insertions of an octapeptide at different places in the last turns of H2. This reverse genetic approach reveals an unexpected tolerance of prions to substantial sequence changes in the protease-resistant part which is associated with infectivity. It also demonstrates that conversion does not require the presence of a specific sequence in the middle of the H2-H3 area. We discuss the implications of our findings according to different structural models proposed for PrP (Sc) and questioned the postulated existence of an N- or C-terminal prion domain in the protease-resistant region.

Genomic and Proteomic Characterization of Bacteriocin-Producing Leuconostoc mesenteroides Strains Isolated from Raw Camel Milk in Two Southwest Algerian Arid Zones

PubMed Central

Benmechernene, Zineb; Fernández-No, Inmaculada; Quintela-Baluja, Marcos; Kihal, Mebrouk; Calo-Mata, Pilar; Barros-Velázquez, Jorge

2014-01-01

Information on the microbiology of camel milk is very limited. In this work, the genetic characterization and proteomic identification of 13 putative producing bacteriocin Leuconostoc strains exhibiting antilisterial activity and isolated from camel milk were performed. DNA sequencing of the 13 selected strains revealed high homology among the 16S rRNA genes for all strains. In addition, 99% homology with Leuconostoc mesenteroides was observed when these sequences were analysed by the BLAST tool against other sequences from reference strains deposited in the Genbank. Furthermore, the isolates were characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDITOF MS) which allowed for the identification of 2 mass peaks 6242 m/z and 5118 m/z that resulted to be specific to the species L. mesenteroides. Remarkably, the phyloproteomic tree provided more intraspecific information of L. mesenteroides than phylogenetic analysis. Accordingly, phyloproteomic analysis grouped L. mesenteroides strains into different subbranches, while all L. mesenteroides isolates were grouped in the same branch according to phylogenetic analysis. This study represents, to our knowledge, the first report on the use of MALDI-TOF MS on the identification of LAB isolated from camel milk. PMID:24809059

Vitellogenesis in Bufo arenarum: Identification, characterization and immunolocalization of high molecular mass lipovitellin during oogenesis

PubMed Central

O’Brien, Emma D.; Salicioni, Ana M.; Cabada, Marcelo O.; Arranz, Silvia E.

2009-01-01

Vitellogenin (Vtg), a large lipoglycophosphoprotein, is the most important precursor of the yolk proteins, and the major source of nutrients for the developing embryo in oviparous species. After its uptake by the oocytes, Vtg is converted into lipovitellins (high and light) and phosvitin, which are deposited into crystalline yolk platelets. We describe here the presence of two high molecular mass lipovitellins isoforms in Bufo arenarum mature oocytes with masses of 113 and 100 kDa, respectively. The amino acid sequence analysis of p113 and p100 peptides showed a high sequence homology between both polypeptides and the complete reported sequences of Xenopus laevis vitellogenin. Using specific antibodies, we determined that the Vtg uptake begins early during oogenesis, at the previtellogenic stage, and continues until oocytes have reached their mature status. In addition, we found that large endocytic vesicles mediate Vtg uptake in stage I oocytes, and that the size of the endocytic vesicles declines with oogenesis progression. In terms of the Vtg protein trafficking, we detected the Vtg precursor (190 kDa) in the liver of estradiol-injected females. Finally, we propose a subclassification of B. arenarum stage-II oocytes into three physiologically and morphologically distinct periods (early, mid and late). PMID:19932187

Vitellogenesis in Bufo arenarum: identification, characterization and immunolocalization of high molecular mass lipovitellin during oogenesis.

PubMed

O'Brien, Emma D; Salicioni, Ana M; Cabada, Marcelo O; Arranz, Silvia E

2010-03-01

Vitellogenin (Vtg), a large lipoglycophosphoprotein, is the most important precursor of the yolk proteins, and the major source of nutrients for the developing embryo in oviparous species. After its uptake by the oocytes, Vtg is converted into lipovitellins (high and light) and phosvitin, which are deposited into crystalline yolk platelets. We describe here the presence of two high molecular mass lipovitellin isoforms in Bufo arenarum mature oocytes with masses of 113 and 100 kDa, respectively. The amino acid sequence analysis of p113 and p100 peptides showed a high sequence homology between both polypeptides and the complete reported sequences of Xenopus laevis vitellogenin. Using specific antibodies, we determined that the Vtg uptake begins early during oogenesis, at the previtellogenic stage, and continues until oocytes have reached their mature status. In addition, we found that large endocytic vesicles mediate Vtg uptake in stage I oocytes, and that the size of the endocytic vesicles declines with oogenesis progression. In terms of the Vtg protein trafficking, we detected the Vtg precursor (190 kDa) in the liver of estradiol-injected females. Finally, we propose a subclassification of B. arenarum stage II oocytes into three physiologically and morphologically distinct periods (early, mid and late). 2009 Elsevier Inc. All rights reserved.

Isolation of genes from female sterile flowers in Medicago sativa.

PubMed

Capomaccio, Stefano; Barone, Pierluigi; Reale, Lara; Veronesi, Fabio; Rosellini, Daniele

2009-06-01

A better knowledge of female sporogenesis and gametogenesis could have several practical applications, from commercial hybrid seed production to gene containment in GM crops. With the purpose of isolating genes involved in the megasporogenesis process, the cDNA-AFLP technique was employed to isolate transcript-derived fragments (TDF) differentially expressed between female-fertile and female-sterile full-sib alfalfa plants. This female sterility trait involves female-specific arrest of sporogenesis at early prophase associated with ectopic, massive callose deposition within the nucellus. Ninety-six TDFs were generated and BLAST analyses revealed similarities with genes involved in different Gene Ontology categories. Three TDFs were selected based on their putative functions: showing high similarity to a soybean flower-expressed beta 1,3-glucanase, to an Arabidopsis thaliana MAPKKK, and to an A. thaliana eukaryotic initiation translation factor eIF4G III, respectively. The full length mRNA sequences were obtained. RT-PCR and in situ hybridizations were performed to confirm differential expression during flower development. The genomic organization of the three genes was assessed through sequencing and Southern experiments. Sequence polymorphisms were found between sterile and fertile plants. Our approach based on differential display and bulked segregant analysis was successful in isolating genes that were differentially expressed between fertile and sterile alfalfa plants.

DNA microdevice for electrochemical detection of Escherichia coli 0157:H7 molecular markers.

PubMed

Berganza, J; Olabarria, G; García, R; Verdoy, D; Rebollo, A; Arana, S

2007-04-15

An electrochemical DNA sensor based on the hybridization recognition of a single-stranded DNA (ssDNA) probe immobilized onto a gold electrode to its complementary ssDNA is presented. The DNA probe is bound on gold surface electrode by using self-assembled monolayer (SAM) technology. An optimized mixed SAM with a blocking molecule preventing the nonspecific adsorption on the electrode surface has been prepared. In this paper, a DNA biosensor is designed by means of the immobilization of a single stranded DNA probe on an electrochemical transducer surface to recognize specifically Escherichia coli (E. coli) 0157:H7 complementary target DNA sequence via cyclic voltammetry experiments. The 21 mer DNA probe including a C6 alkanethiol group at the 5' phosphate end has been synthesized to form the SAM onto the gold surface through the gold sulfur bond. The goal of this paper has been to design, characterise and optimise an electrochemical DNA sensor. In order to investigate the oligonucleotide probe immobilization and the hybridization detection, experiments with different concentration of DNA and mismatch sequences have been performed. This microdevice has demonstrated the suitability of oligonucleotide Self-assembled monolayers (SAMs) on gold as immobilization method. The DNA probes deposited on gold surface have been functional and able to detect changes in bases sequence in a 21-mer oligonucleotide.

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps

PubMed Central

Meola, Marco; Lazzaro, Anna; Zeyer, Josef

2015-01-01

Deposition of Sahara dust (SD) particles is a frequent phenomenon in Europe, but little is known about the viability and composition of the bacterial community transported with SD. The goal of this study was to characterize SD-associated bacteria transported to the European Alps, deposited and entrapped in snow. During two distinct events in February and May 2014, SD particles were deposited and promptly covered by falling snow, thus preserving them in distinct ochre layers within the snowpack. In June 2014, we collected samples at different depths from a snow profile at the Jungfraujoch (Swiss Alps; 3621 m a.s.l.). After filtration, we performed various microbiological and physicochemical analyses of the snow and dust particles therein that originated in Algeria. Our results show that bacteria survive and are metabolically active after the transport to the European Alps. Using high throughput sequencing, we observed distinct differences in bacterial community composition and structure in SD-layers as compared to clean snow layers. Sporulating bacteria were not enriched in the SD-layers; however, phyla with low abundance such as Gemmatimonadetes and Deinococcus-Thermus appeared to be specific bio-indicators for SD. Since many members of these phyla are known to be adapted to arid oligotrophic environments and UV radiation, they are well suited to survive the harsh conditions of long-range airborne transport. PMID:26733988

eSensor®: A Microarray Technology Based on Electrochemical Detection of Nucleic Acids and Its Application to Cystic Fibrosis Carrier Screening

NASA Astrophysics Data System (ADS)

Reed, Michael R.; Coty, William A.

We have developed a test for identification of carriers for cystic fibrosis using the eSensor® DNA detection technology. Oligonucleotide probes are deposited within self-assembled monolayers on gold electrodes arrayed upon printed circuit boards. These probes allow sequence-specific capture of amplicons containing a panel of mutation sites associated with cystic fibrosis. DNA targets are detected and mutations genotyped using a “sandwich” assay methodology employing electrochemical detection of ferrocene-labeled oligonucleotides for discrimination of carrier and non-carrier alleles. Performance of the cystic fibrosis application demonstrates sufficient accuracy and reliability for clinical diagnostic use, and the procedure can be performed by trained medical technologists available in the hospital laboratory.

Middle Pleistocene infill of Hinkley Valley by Mojave River sediment and associated lake sediment: Depositional architecture and deformation by strike-slip faults

USGS Publications Warehouse

Miller, David; Haddon, Elizabeth; Langenheim, Victoria; Cyr, Andrew J.; Wan, Elmira; Walkup, Laura; Starratt, Scott W.

2018-01-01

Hinkley Valley in the Mojave Desert, near Barstow about 140 km northeast of Los Angeles and midway between Victorville Valley and the Lake Manix basin, contains a thick sedimentary sequence delivered by the Mojave River. Our study of sediment cores drilled in the valley indicates that Hinkley Valley was probably a closed playa basin with stream inflow from four directions prior to Mojave River inflow. The Mojave River deposited thick and laterally extensive clastic wedges originating from the southern valley that rapidly filled much of Hinkley Valley. Sedimentary facies representing braided stream, wetland, delta, and lacustrine depositional environments all are found in the basin fill; in some places, the sequence is greater than 74 m (245 ft) thick. The sediment is dated in part by the presence of the ~631 ka Lava Creek B ash bed low in the section, and thus represents sediment deposition after Victorville basin was overtopped by sediment and before the Manix basin began to be filled. Evidently, upstream Victorville basin filled with sediment by about 650 ka, causing the ancestral Mojave River to spill to the Harper and Hinkley basins, and later to Manix basin.Initial river sediment overran wetland deposits in many places in southern Hinkley Valley, indicating a rapidly encroaching river system. These sediments were succeeded by a widespread lake (“blue” clay) that includes the Lava Creek B ash bed. Above the lake sediment lies a thick section of interlayered stream sediment, delta and nearshore lake sediment, mudflat and/or playa sediment, and minor lake sediment. This stratigraphic architecture is found throughout the valley, and positions of lake sediment layers indicate a successive northward progression in the closed basin. A thin overlapping sequence at the north end of the valley contains evidence for a younger late Pleistocene lake episode. This late lake episode, and bracketing braided stream deposits of the Mojave River, indicate that the river avulsed through the valley, rather than continuing toward Lake Manix, during the late Pleistocene. Two dextral strike-slip fault zones, the Lockhart and the Mt. General, fold and displace the distinctive stratigraphic units, as well as surficial late Pleistocene and Holocene deposits. The sedimentary architecture and the two fault zones provide a framework for evaluating groundwater flow in Hinkley Valley.

Sedimentology and sequence stratigraphy of the Cretaceous Nanushuk, Seabee, and Tuluvak formations exposed on Umiat Mountain, north-central Alaska

USGS Publications Warehouse

Houseknecht, David W.; Schenk, Christopher J.

2005-01-01

Upper Cretaceous strata of the upper part of the Nanushuk Formation, the Seabee Formation, and the lower part of the Tuluvak Formation are exposed along the Colville River on the east flank of Umiat Mountain in north-central Alaska. The Ninuluk sandstone, which is the uppermost unit of the Nanushuk Formation, displays a vertical succession of facies indicative of deposition in an upward-deepening estuarine through shoreface setting. A marine-flooding surface lies between the Ninuluk sandstone and organic-rich shale of the basal part of the Seabee Formation. The Ninuluk sandstone and the lower part of the Seabee Formation are interpreted as components of a transgressive-systems tract. The lowest, well-exposed strata in the Seabee Formation are a succession of shoreface sandstone beds in the middle of the formation. Integration of outcrop information and the Umiat No. 11 well log suggests that this sandstone succession rests on a sequence boundary and is capped by a marine-flooding surface. The sandstone succession is interpreted as a lowstand-systems tract. The upper part of the Seabee Formation includes a thick interval of organic-rich shale deposited in a dysaerobic offshore environment, and the gradational Seabee-Tuluvak contact is a coarsening-upward shale-to-sandstone succession deposited in a prodelta/delta-front environment. The observation that the upper part of the Seabee Formation correlates with seismic clinoforms suggests that dysaerobic conditions extended well up onto the prodelta slope during intervals of transgression and highstand. Correlation of the Umiat Mountain outcrop section with well logs and seismic data suggests that sequence boundaries and lowstand shoreface deposits may be common in the Seabee Formation and that wave action may have been important in transporting sand to the paleoshelf margin. These conclusions may contribute to an enhanced understanding of sand distribution in prospective lowstand turbidite deposits in the subsurface of the central North Slope of Alaska.

Dictionary-driven protein annotation.

PubMed

Rigoutsos, Isidore; Huynh, Tien; Floratos, Aris; Parida, Laxmi; Platt, Daniel

2002-09-01

Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/ bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were released publicly after we built the Bio-Dictionary that is used in our experiments. Finally, we have computed the annotations of more than 70 complete genomes and made them available on the World Wide Web at http://cbcsrv.watson.ibm.com/Annotations/.

Occurrence model for volcanogenic beryllium deposits: Chapter F in Mineral deposit models for resource assessment

USGS Publications Warehouse

Foley, Nora K.; Hofstra, Albert H.; Lindsey, David A.; Seal, Robert R.; Jaskula, Brian W.; Piatak, Nadine M.

2012-01-01

Current global and domestic mineral resources of beryllium (Be) for industrial uses are dominated by ores produced from deposits of the volcanogenic Be type. Beryllium deposits of this type can form where hydrothermal fluids interact with fluorine and lithophile-element (uranium, thorium, rubidium, lithium, beryllium, cesium, tantalum, rare earth elements, and tin) enriched volcanic rocks that contain a highly reactive lithic component, such as carbonate clasts. Volcanic and hypabyssal high-silica biotite-bearing topaz rhyolite constitutes the most well-recognized igneous suite associated with such Be deposits. The exemplar setting is an extensional tectonic environment, such as that characterized by the Basin and Range Province, where younger topaz-bearing igneous rock sequences overlie older dolomite, quartzite, shale, and limestone sequences. Mined deposits and related mineralized rocks at Spor Mountain, Utah, make up a unique economic deposit of volcanogenic Be having extensive production and proven and probable reserves. Proven reserves in Utah, as reported by the U.S. Geological Survey National Mineral Information Center, total about 15,900 tons of Be that are present in the mineral bertrandite (Be4Si2O7(OH)2). At the type locality for volcanogenic Be, Spor Mountain, the tuffaceous breccias and stratified tuffs that host the Be ore formed as a result of explosive volcanism that brought carbonate and other lithic fragments to the surface through vent structures that cut the underlying dolomitic Paleozoic sedimentary rock sequences. The tuffaceous sediments and lithic clasts are thought to make up phreatomagmatic base surge deposits. Hydrothermal fluids leached Be from volcanic glass in the tuff and redeposited the Be as bertrandite upon reaction of the hydrothermal fluid with carbonate clasts in lithic-rich sections of tuff. The localization of the deposits in tuff above fluorite-mineralized faults in carbonate rocks, together with isotopic evidence for the involvement of magmatic water in an otherwise meteoric water-dominated hydrothermal system, indicate that magmatic volatiles contributed to mineralization. At the type locality, hydrothermal alteration of dolomite clasts formed layered nodules of calcite, opal, fluorite, and bertrandite, the latter occurring finely intergrown with fluorite. Alteration assemblages and elemental enrichments in the tuff and surrounding volcanic rocks include regional diagenetic clays and potassium feldspar and distinctive hydrothermal halos of anomalous fluorine, lithium, molybdenum, niobium, tin, and tantalum, and intense potassium feldspathization with sericite and lithium-smectite in the immediate vicinity of Be ore. Formation of volcanogenic Be deposits is due to the coincidence of multiple factors that include an appropriate Be-bearing source rock, a subjacent pluton that supplied volatiles and heat to drive convection of meteoric groundwater, a depositional site characterized by the intersection of normal faults with permeable tuff below a less permeable cap rock, a fluorine-rich ore fluid that facilitated Be transport (for example, BeF42- complex), and the existence of a chemical trap that caused fluorite and bertrandite to precipitate at the former site of carbonate lithic clasts in the tuff.

Clinoforms in Melas Chasma

NASA Image and Video Library

2017-04-10

In this image from NASA's Mars Reconnaissance Orbiter, a group of steeply inclined light-toned layers is bounded above and below by unconformities (sudden or irregular changes from one deposit to another) that indicate a "break" where erosion of pre-existing layers was taking place at a higher rate than deposition of new materials. The layered deposits in Melas Basin may have been deposited during the growth of a delta complex. This depositional sequence likely represents a period where materials were being deposited on the floor of a lake or running river. The map is projected here at a scale of 25 centimeters (9.8 inches) per pixel. [The original image scale is 28.9 centimeters (11.4 inches) per pixel (with 1 x 1 binning); objects on the order of 87 centimeters (34.2 inches) across are resolved.] North is up. https://photojournal.jpl.nasa.gov/catalog/PIA21580

RefSeq microbial genomes database: new representation and annotation strategy.

PubMed

Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris; O'Neill, Kathleen; Tolstoy, Igor

2014-01-01

The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.

Development of Multi-functional Properties on Cotton Fabric by In Situ Application of TiO2 and ZnO Nanoparticles

NASA Astrophysics Data System (ADS)

Butola, B. S.; Garg, Aayush; Garg, Aman; Chauhan, Indu

2018-06-01

Cotton fabrics functionalized with different combinations of TiO2 and ZnO were evaluated for multifunctional properties including UV protection, antimicrobial and self-cleaning. The ZnO nanoparticles synthesized using sol gel method were applied on cotton fabric by pad-dry-cure method and TiO2 was deposited in situ. The deposition of both TiO2 and ZnO was examined and confirmed by SEM and EDX analysis. Application of both metal oxides resulted in good improvement in UV protection of treated fabrics. The fabrics which were finished with combination of both Zinc and Titanium oxides, showed UPF rating of 50+ as compared to UPF rating of untreated cotton, which was only 5. The same fabrics also showed higher self-cleaning extent as compared to untreated cotton fabric. It was found that the sequence of application of ZnO and TiO2 affected the antimicrobial activity of the finished fabric and also the durability. When application of TiO2 was followed by ZnO, the combination resulted in development of excellent antimicrobial property against Escherichia coli ( 99% colony reduction) which was retained after 10 wash cycles. However, when application of ZnO nanoparticles was followed by application of TiO2, the improvement in antimicrobial activity was found to be moderate ( 48% colony reduction) and had poor wash durability. Hence, the specific sequence of application of these metals oxides can be utilized for obtaining good durability of the multifunctional properties on cotton fabric.

Development of Multi-functional Properties on Cotton Fabric by In Situ Application of TiO2 and ZnO Nanoparticles

NASA Astrophysics Data System (ADS)

Butola, B. S.; Garg, Aayush; Garg, Aman; Chauhan, Indu

2018-05-01

Cotton fabrics functionalized with different combinations of TiO2 and ZnO were evaluated for multifunctional properties including UV protection, antimicrobial and self-cleaning. The ZnO nanoparticles synthesized using sol gel method were applied on cotton fabric by pad-dry-cure method and TiO2 was deposited in situ. The deposition of both TiO2 and ZnO was examined and confirmed by SEM and EDX analysis. Application of both metal oxides resulted in good improvement in UV protection of treated fabrics. The fabrics which were finished with combination of both Zinc and Titanium oxides, showed UPF rating of 50+ as compared to UPF rating of untreated cotton, which was only 5. The same fabrics also showed higher self-cleaning extent as compared to untreated cotton fabric. It was found that the sequence of application of ZnO and TiO2 affected the antimicrobial activity of the finished fabric and also the durability. When application of TiO2 was followed by ZnO, the combination resulted in development of excellent antimicrobial property against Escherichia coli ( 99% colony reduction) which was retained after 10 wash cycles. However, when application of ZnO nanoparticles was followed by application of TiO2, the improvement in antimicrobial activity was found to be moderate ( 48% colony reduction) and had poor wash durability. Hence, the specific sequence of application of these metals oxides can be utilized for obtaining good durability of the multifunctional properties on cotton fabric.

Paleogeographic evolution of carbonate reservoirs: geological and geophysical analysis at the Albian Campos Basin, Brazil

NASA Astrophysics Data System (ADS)

Castillo Vincentelli, Maria Gabriela; Favoreto, Julia; Roemers-Oliveira, Eduardo

2018-02-01

An integrated geophysical and geological analysis of a carbonate reservoir can offer an effective method to better understand the paleogeographical evolution and distribution of a geological reservoir and non-reservoir facies. Therefore, we propose a better method for obtaining geological facies from geophysical facies, helping to characterize the permo-porous system of this kind of play. The goal is to determine the main geological phases from a specific hydrocarbon producer (Albian Campos Basin, Brazil). The applied method includes the use of a petrographic and qualitative description from the integrated reservoir with seismic interpretation of an attribute map (energy, root mean square, mean amplitude, maximum negative amplitude, etc), all calculated at the Albian level for each of the five identified phases. The studied carbonate reservoir is approximately 6 km long with a main direction of NE-SW, and it was sub-divided as follows (from bottom to top): (1) the first depositional sequence of the bank was composed mainly of packstone, indicating that the local structure adjacent to the main bank is protected from environmental conditions; (2) characterized by the presence of grainstone developed at the higher structure; (3) the main sequence of the peloidal packstone with mudstones oncoids; (4) corresponds to the oil production of carbonate reservoirs formed by oolitic grainstone deposited at the top of the carbonate bank; at this phase, rising sea levels formed channels that connected the open sea shelf with the restricted circulation shelf; and (5) mudstone and wackestone represent the system’s flooding phase.

Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

PubMed

Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W

2013-04-11

Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments.

Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

PubMed

Fazal, Mohammed-Abbas; Alexander, Sarah; Burnett, Edward; Deheer-Graham, Ana; Oliver, Karen; Holroyd, Nancy; Parkhill, Julian; Russell, Julie E

2016-11-03

Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939. © Crown copyright 2016.

Sr-87/Sr-86 isotopic age determination of upper Cretaceous Santonian, Campanian and Maastrichtian chondrichthyan teeth of the Atlantic and Eastern Gulf Coastal Plains: Implications for sea level cyclicity and macrofossil time-averaging in depositional sequence lag deposits

NASA Astrophysics Data System (ADS)

Becker, Martin Andrew

1997-11-01

Unconformities and fossil rich layers are common elements in the stratigraphic architecture of upper Cretaceous sediments exposed on both the Atlantic and Eastern Gulf Coastal Plains. Contacts between the Eutaw Formation and Tombigbee Sands Member in Alabama, the Blufftown Formation and Cusseta Sands in Georgia and the Wenonah- Mt. Laurel and Navesink Formations in New Jersey are marked by erosional surfaces with overlying blankets and lenses of macrofossil residuum. These contacts correspond to bounding unconformities and transgressive lags separating Santonian-Campanian, lower Campanian-upper Campanian and Campanian-Maastrichtian depositional sequences. Regression and subsequent transgression of sea level at the top of these depositional sequences resulted in hydrodynamic sorting of sediments and fossils that had previously accumulated in shelf and lower shoreface paleoenvironments. Remobilization of sediments by shoreface retreat reworked fossil hard-parts which became concentrated above erosional surfaces as sea level rose. Because of the abundance of chondrichthyan, pelecypod and ammonite fossils, these lags have great biostratigraphic significance and provide a basis for examining time averaging in macrofossil zonation. Chondrichthyan teeth are composed of extremely durable and highly insoluble, biogenic apatite. This tooth apatite accurately records the Sr87/Sr86 isotopic signature of seawater, from which the numerical age of the teeth can be calculated using published age/concentration data. Teeth (e.g. Squalicorax kaupi, Scapanorhynchus texanus) from Santonian-Campanian lag deposits at the contact of the Eutaw Formation and Tombigbee Sands Member in Alabama yield approximate ages of 85-81 Ma. Teeth from lower-upper Campanian lag deposits at the contact of the Blufftown Formation and Cusseta Sands in Georgia yield approximate ages of 83-75 Ma. Teeth from Campanian-Maastrichtian lag deposits at the contact of the Wenonah-Mt. Laurel and Navesink Formations in New Jersey yield approximate ages of 80-76 Ma. Isotopic age determination from these chondrichthyan teeth indicate average hiatus of approximately 3-7 million years occur during the development of lag accumulations and transgressive unconformities. Santonian, Campanian and Maastrichtian macrofossils analyzed in this study are hydrodynamically stable components representing time-averaged fossil assemblages sorted together by physical processes and are not life cohorts. Abrupt appearance and disappearance of organisms found in upper Cretaceous lag deposits of the Atlantic and Eastern Gulf Coastal Plains are artifacts of a physical sorting processes associated with sea-level cyclicity.

Titanium mineral resources of the western U.S.: an update

USGS Publications Warehouse

Force, Eric R.; Creely, Scott

2000-01-01

Thirteen deposits or districts in the western U.S. have been examined in which titaniummineral resources have been reported or implied. These deposits are of the following general types (in probable order of importance): 1) Cretaceous shoreline placer deposits, 2) silica-sand deposits of California, 3) fluvial monazite placers of Idaho, 4) anorthositerelated deposits, and 5) clay and bauxite deposits of the northwestern U.S. Relative to previous reports, this one shows some greater and some lesser resources (table 1). In any case, titanium-mineral resources of the western U.S. (west of 103° longitude) remain modest at world scale except as unconventional (especially perovskite) and by-product (especially porphyry) resources. Some deposits, however, have enhanced value to the titanium explorationist for the geologic relations they illustrate. Among the new conclusions are: a) Loci of Cretaceous shoreline placers form linear patterns, nested as a function of age, that can be traced for thousands of kilometers, permitting focused exploration in whole new mountain ranges. b) Medial hematite-ilmenite solid-solution, which is highly magnetic, is a major carrier of TiO2 values in the Cretaceous deposits of Wyoming. This phase was previously thought to be relatively rare. c) Regressive shoreline placer deposits in indurated Cretaceous sequences expose intricate facies relations, such as the construction of shoreface sequences by long-shore drift over tidal-channel fill, without much loss of paleogeographic information. d) Due to deep weathering, virtually every Eocene sediment that accumulated in the Ione basin at the foot of the Sierra Nevada has economic value, permitting recovery of altered ilmenite and zircon along with silica, clay, coal, and gold. Ilmenite is most abundant in newly recognized shoreline sands. e) Upper Tertiary fluvial placers of Idaho formed in and filled fault-bounded basins and thus are far more voluminous than deposits in the modern valley system. Previously reported resources are thus far too low. f) Mafic igneous rocks of Proterozoic age near Bagdad, Arizona are of ophiolitic affinity, but contain nelsonitic ilmenite enrichments associated with anorthositic layers.

Growth of the Zagros Fold-Thrust Belt and Foreland Basin, Northern Iraq, Kurdistan

NASA Astrophysics Data System (ADS)

Koshnaw, Renas; Horton, Brian; Stockli, Daniel; Barber, Douglas; Ghalib, Hafidh; Dara, Rebwar

2016-04-01

The Zagros orogenic belt in the Middle Eastern segment of the Alpine-Himalayan system is among the youngest seismically active continental collision zones on Earth. However, due to diachronous and incremental collision, the precise ages and kinematics of shortening and deposition remain poorly understood. The Kurdistan region of the Zagros fold-thrust belt and foreland basin contains well-preserved Neogene wedge-top and foredeep deposits that include clastic nonmarine fill of the Upper Fars, Lower Bakhtiari, and Upper Bakhtiari Formations. These deposits record significant information about orogenic growth, fold-thrust dynamics, and advance of the deformation front. Thermochronologic and geochronologic data from thrust sheets and stratigraphic archives combined with local earthquake data provide a unique opportunity to address the linkages between surface and subsurface geologic relationships. This research seeks to constrain the timing and geometry of exhumation and deformation by addressing two key questions: (1) Did the northwestern Zagros fold-thrust belt evolve from initial thin-skinned shortening to later thick-skinned deformation or vice-versa? (2) Did the fold-thrust belt advance steadily under critical/supercritical wedge conditions involving in-sequence thrusting or propagate intermittently under subcritical conditions with out-of-sequence deformation? From north to south, apatite (U-Th)/He ages from the Main Zagros Thrust, the Mountain Front Flexure (MFF), and additional frontal thrusts suggest rapid exhumation by ~10 Ma, ~5 Ma, and ~8 Ma respectively. Field observations and seismic sections indicate progressive tilting and development of growth strata within the Lower Bakhtiari Formation adjacent to the frontal thrusts and within the Upper Bakhtiari Formation near the MFF. In the Kurdistan region of Iraq, a regional balanced cross section constrained by new thermochronometric results, proprietary seismic reflection profiles, and earthquake hypocenters suggest prolonged thin-skinned shortening in sequence from north to south followed by a thick-skinned out-of-sequence MFF deformation and intermittent hinterland uplift postdating initial collision. Magnetostratigraphic analyses of Dinarta wedge-top deposits and Kifri foredeep deposits constrain accumulation of the Upper Fars-Lower Bakhtiari synorogenic succession to 12.5-5 Ma. These findings suggest that temporal and spatial shifts in upper-crustal modes of deformation in the Kurdistan segment of the Zagros orogenic belt strongly influenced patterns of topographic growth, landscape development, and resulting foreland basin stratigraphy.

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales.

PubMed

Neave, Matthew J; Rachmawati, Rita; Xun, Liping; Michell, Craig T; Bourne, David G; Apprill, Amy; Voolstra, Christian R

2017-01-01

Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.

Compilation of Mineral Resource Data for Mississippi Valley-Type and Clastic-Dominated Sediment-Hosted Lead-Zinc Deposits

USGS Publications Warehouse

Taylor, Ryan D.; Leach, David L.; Bradley, Dwight C.; Pisarevsky, Sergei A.

2009-01-01

This report contains a global compilation of the mineral resource data for sediment-hosted lead-zinc (SH Pb-Zn) deposits. Sediment-hosted lead-zinc deposits are historically the most significant sources of lead and zinc, and are mined throughout the world. The most important SH Pb-Zn deposits are hosted in clastic-dominated sedimentary rock sequences (CD Pb-Zn) that are traditionally called sedimentary exhalative (SEDEX) deposits, and those in carbonate-dominated sequences that are known as Mississippi Valley-type (MVT) Pb-Zn deposits. In this report, we do not include sandstone-Pb, sandstone-hosted Pb, or Pb-Zn vein districts such as those in Freiberg, Germany, or Coeur d'Alene, Idaho, because these deposits probably represent different deposit types (Leach and others, 2005). We do not include fracture-controlled deposits in which fluorite is dominant and barite typically abundant (for example, Central Kentucky; Hansonburg, N. Mex.) or the stratabound fluorite-rich, but also lead- and zinc-bearing deposits, such as those in southern Illinois, which are considered a genetic variant of carbonate-hosted Pb-Zn deposits (Leach and Sangster, 1993). This report updates the Pb, Zn, copper (Cu), and silver (Ag) grade and tonnage data in Leach and others (2005), which itself was based on efforts in the Canadian Geological Survey World Minerals Geoscience Database Project (contributions of D.F. Sangster to Sinclair and others, 1999). New geological or geochronological data, classifications of the tectonic environment in which the deposits formed, and key references to the geology of the deposits are presented in our report. Data for 121 CD deposits, 113 MVT deposits, and 6 unclassified deposits that were previously classified as either SEDEX or MVT in the Leach and others (2005) compilation, are given in appendix table A1. In some cases, mineral resource data were available only for total district resources, but not for individual mines within the district. For these districts, the resource data are presented in appendix table A2. In addition, numerous figures (appendix figures B1-B9) displaying important grade-tonnage and geologic features are included. These mineral deposit resource data are important for exploration targeting and mineral resource assessments. There is significant variability in the resource data for these deposit types, and ore controls vary from one region to another. Therefore, grade-tonnage estimations are best evaluated as subsets of the data in appendix table A1 where local mineralization styles and ore controls characterize the region being evaluated for grade-tonnage relations. Furthermore, consideration should also be given to the tendency for MVT resources to occur in large mineralized regions.

Depositional and diagenetic models of some miocene evaporites on the Red Sea coast, Egypt

NASA Astrophysics Data System (ADS)

El Sayed A. A., Youssef

1986-06-01

The Miocene evaporites on the Red Sea coast, Egypt, are interpreted as a sabkha-chenier complex, which includes deposition in shallow water as well as in supratidal environments Costal sabkhas and shallow subaqueous evaporite sequences are recognised. The subaqueous sequence is represented by nodular mosaic and massive crystalline gypsum covered by a surface layer of nodular, white, dense powdery anhydrite. The sabkha sequences are represented by (a) small mounds overlying the older rock unit (Gebel El Rusas Formation) composed of fenestral stromatolitic and nodular dolomites overlain by a dolomitic limestone layer, (b) thin layer overlying the subaqueous evaporite sequence and composed of fenestral stromatolitic dolomite overlain by a nodular anhydrite layer. The nodular structure in the subaqueous as well as the sabkha sequences is formed diagenetically by transformation and recrystallization process. The dolomites in both sabkha sequences (a and b) are characterised by low Na + concentrations (143 to 755 ppm) and low values of δ 18O (- 1.85 to -8.7‰ PDB). This indicates that the dolomites were formed from saline water mixed with fresh water. These dolomites are also characterised by a low δ 13C (-12.95 to -27.1‰ PDB). This shows that the light carbon produced by the degradation of organic matter through the sulphate reduction process has played a significant role in the formation of these dolomites. Both microcrystalline and megacrystalline white dolomites are recognised in sabkha sequences. Relatively high concentrations of lead, zinc and copper are associated with the high percent of megacrystalline white dolomite.

Analysis of Facultative Lithotroph Distribution and Diversity on Volcanic Deposits by Use of the Large Subunit of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase†

PubMed Central

Nanba, K.; King, G. M.; Dunfield, K.

2004-01-01

A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass. PMID:15066819

Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase.

PubMed

Nanba, K; King, G M; Dunfield, K

2004-04-01

A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass.

Sedimentology and architecture of De Geer moraines in the western Scottish Highlands, and implications for grounding-line glacier dynamics

NASA Astrophysics Data System (ADS)

Golledge, Nicholas R.; Phillips, Emrys

2008-07-01

Sedimentary exposures in moraines in a Scottish Highland valley (Glen Chaorach), reveal stacked sequences of bedded and laminated silt, sand and gravel, interspersed or capped with diamicton units. In four examples, faults and folds indicate deformation by glaciotectonism and syndepositional loading. We propose that these sediments were laid down in an ice-dammed lake, close to the last ice margin to occupy this glen. Individual units within cross-valley De Geer moraine ridges are interpreted by comparison with examples from similar environments elsewhere: stratified diamictons containing laminated or bedded lenses are interpreted as subaqueous ice-marginal debris-flow deposits; massive fine-grained deposits as hyperconcentrated flow deposits, and massive gravel units as high-density debris-flow deposits. Using an allostratigraphic approach we argue that glaciotectonically deformed coarsening-upward sand and gravel sequences that culminate in deposition of subglacial diamicton represent glacier advances into the ice-marginal lake, whereas undisturbed cross-bedded sand and gravel reflects channel or fan deposits laid down during glacier retreat. A flat terrace of bedded sand and gravel at the northern end of Glen Chaorach is interpreted as subaerial glaciofluvial outwash. On the basis of these inferences we propose the following three stage deglacial event chronology for Glen Chaorach. During glacier recession, ice separation and intra-lobe ponding first led to subaquaeous deposition of sorted and unsorted facies. Subsequent glacier stabilisation and ice-marginal oscillation produced glaciotectonic structures in the ice-marginal sediment pile and formed De Geer moraines. Finally, drainage of the ice-dammed lake allowed a subaerial ice-marginal drainage system to become established. Throughout deglaciation, deposition within the lake was characterized by abrupt changes in grain size and in the architecture of individual sediment bodies, reflecting changing delivery paths and sediment supply, and by dynamic margin oscillations typical of water-terminating glaciers.

Tephrostratigraphy of the A.D. 79 pyroclastic deposits in perivolcanic areas of Mt. Vesuvio (Italy)

NASA Astrophysics Data System (ADS)

Lirer, Lucio; Munno, Rosalba; Petrosino, Paola; Vinci, Anna

1993-11-01

Correlations between pyroclastic deposits in perivolcanic areas are often complicated by lateral and vertical textural variations linked to very localized depositional effects. In this regard, a detailed sampling of A.D. 79 eruption products has been performed in the main archaeological sites of the perivolcanic area, with the aim of carrying out a grain-size, compositional and geochemical investigation so as to identify the marker layers from different stratigraphic successions and thus reconstruct the eruptive sequence. In order to process the large number of data available, a statistical approach was considered the most suitable. Statistical processing highlighted 14 marker layers among the fall, stratified surge and pyroclastic flow deposits. Furthermore statistical analysis made it possible to correlate pyroclastic flow and surge deposits interbedded with fall, interpreted as a lateral facies variation. Finally, the passage from magmatic to hydromagmatic activity is marked by the deposition of pyroclastic flow, surge and accretionary lapilli-bearing deposits. No transitional phase from magmatic to hydromagmatic activity has been recognized.

Stratigraphy of the layered terrain in Valles Marineris, Mars

NASA Technical Reports Server (NTRS)

Komatsu, G.; Strom, Roger G.

1991-01-01

The layered terrain in Valles Marineris provides information about its origin and the geologic history of this canyon system. Whether the terrain is sedimentary material deposited in a dry or lacustrine environment, or volcanic material related to the tectonics of the canyon is still controversial. However, recent studies of Gangis Layered Terrain suggests a cyclic sequence of deposition and erosion under episodic lacustrine conditions. The stratigraphic studies are extended to four other occurrences of layered terrains in Valles Marineris in an attempt to correlate and distinguish between depositional environments. The Juvantae Chasma, Hebes Chasma, Ophir and Candor Chasmata, Melas Chasma, and Gangis Layered Terrain were examined. Although there are broad similarities among the layered terrains, no two deposits are exactly alike. This suggests that there was no synchronized regional depositional processes to form all the layered deposits. However, the similar erosional style of the lower massive weakly bedded unit in Hebes, Gangis, and Ophir-Candor suggests it may have been deposited under similar circumstances.

Sequence stratigraphic and sedimentologic significance of biogenic structures from a late Paleozoic marginal- to open-marine reservoir, Morrow Sandstone, subsurface of southwest Kansas, USA

USGS Publications Warehouse

Buatois, L.A.; Mangano, M.G.; Alissa, A.; Carr, T.R.

2002-01-01

Integrated ichnologic, sedimentologic, and stratigraphic studies of cores and well logs from Lower Pennsylvanian oil and gas reservoirs (lower Morrow Sandstone, southwest Kansas) allow distinction between fluvio-estuarine and open marine deposits in the Gentzler and Arroyo fields. The fluvio-estuarine facies assemblage is composed of both interfluve and valley-fill deposits, encompassing a variety of depositional environments such as fluvial channel, interfluve paleosol, bay head delta, estuary bay, restricted tidal flat, intertidal channel, and estuary mouth. Deposition in a brackish-water estuarine valley is supported by the presence of a low diversity, opportunistic, impoverished marine ichnofaunal assemblage dominated by infaunal structures, representing an example of a mixed, depauperate Cruziana and Skolithos ichnofacies. Overall distribution of ichnofossils along the estuarine valley was mainly controlled by the salinity gradient, with other parameters, such as oxygenation, substrate and energy, acting at a more local scale. The lower Morrow estuarine system displays the classical tripartite division of wave-dominated estuaries (i.e. seaward-marine sand plug, fine-grained central bay, and sandy landward zone), but tidal action is also recorded. The estuarine valley displays a northwest-southeast trend, draining to the open sea in the southeast. Recognition of valley-fill sandstones in the lower Morrow has implications for reservoir characterization. While the open marine model predicts a "layer-cake" style of facies distribution as a consequence of strandline shoreline progradation, identification of valley-fill sequences points to more compartmentalized reservoirs, due to the heterogeneity created by valley incision and subsequent infill. The open-marine facies assemblage comprises upper, middle, and lower shoreface; offshore transition; offshore; and shelf deposits. In contrast to the estuarine assemblage, open marine ichnofaunas are characterized by a high diversity of biogenic structures representing the activity of a benthic fauna developed under normal salinity conditions. Trace fossil and facies analyses allow environmental subdivision of the shoreface-offshore successions and suggest deposition in a weakly storm-affected nearshore area. An onshore-offshore replacement of the Skolithos ichnofacies by the Cruziana ichnofacies is clearly displayed. The lower Morrow fluvio-estuarine valley was incised during a drop of sea level coincident with the Mississippian-Pennsylvanian transition, but was mostly filled during a subsequent transgression. The transgressive nature of the estuarine infill is further indicated by the upward replacement of depauperate brackish-water trace fossil assemblages by the open-marine Cruziana ichnofacies. Additional stratal surfaces of allostratigraphic significance identified within the estuary include the bayline surface, the tidal ravinement surface, the wave ravinement surface, and a basinwide flooding surface recording inundation of the valley interfluves. A younger sequence boundary within the lower Morrow is also recorded in the Gentzler field at the base of a forced regression shoreface, demarcated by the firmground Glossifungites ichnofacies, indicating a rapid basinward facies migration during a sea-level drop. Trace fossil models derived from the analysis of Mesozoic and Cenozoic reservoirs are generally applicable to the study of these late Paleozoic reservoirs. Pennsylvanian brackish-water facies differ ichnologically from their post-Paleozoic counterparts, however, in that they have: (1) lower trace fossil diversity, (2) lower degree of bioturbation, (3) scarcity of crustacean burrows, (4) absence of firmground suites, and (5) absence of ichnotaxa displaying specific architectures designed to protect the tracemaker from salinity fluctuations. Morrow open-marine ichnofaunas closely resemble their post-Paleozoic equivalents. ?? 2002 Elsevier Science B.V. All rights reserved.

Subsurface Structure in the Martian Polar Layered Deposits: The Deep Space 2 Impact Accelerometry Experiment

NASA Technical Reports Server (NTRS)

Moersch, J. E.; Lorenz, R. D.

1998-01-01

While primarily a technology demonstration mission, the New Millenium Mars Microprobes (also known as Deep Space 2, or simply DS2)will also provide the first in situ science measurements of the martian subsurface. The DS2 impact accelerometry experiment will provide both engineering data about the depth of probe emplacement and science data about the physical nature of the subsurface at the probes' landing sites. Little is known about the detailed physical properties or small-scale vertical structure of the subsurface at the DS2 landing site in the southern martian polar layered deposits. Imaging data from the Viking Orbiters and Mars Global Surveyor reveal alternating bands of light and dark material in this region with thicknesses at least as small as the limit of resolution, about 10 m. The overall composition of these layers is poorly constrained, but generally thought to be a mixture of dust and ice with the layers being caused by variations in the dust/ice ratio, or perhaps by dust deposits of different densities. Low thermal inertias in the region suggest that the top few centimeters of the surface are composed of a mantling of fine-grained dust. However, 3.5-cm radar returns indicate that the maximum depth of this dust is not greater than a few tens of centimeters. Thermal models generally agree that, while the layered deposits do provide a potential near-surface reservoir for ice, the uppermost few centimeters to meters in these regions are likely to be ice-free because of sublimation losses. Finally, while it is generally agreed that the layered deposits are the product of variations in the martian climate, no direct correlation has been made between band sequences and specific climate changes. Our intention is to shed light on some of these questions about the martian polar layered deposits by using the DS2 accelerometry experiment to determine the physical nature of the layered deposits, and to detect the presence of any subsurface layering of dust, ice, and/or rock. In the process, we will also determine the final resting depth of the two microprobes, an important parameter in the interpretation of other DS2 experiments.

Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition.

PubMed

Li, Baojun; Qiao, Liying; An, Lixia; Wang, Weiwei; Liu, Jianhua; Ren, Youshe; Pan, Yangyang; Jing, Jiongjie; Liu, Wenzhong

2018-05-08

The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5, and CD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene, and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that PPAR signaling pathway and ECM-receptor interaction were specifically enriched. Four genes, namely LOC101102230, PLTP, C1QTNF7, and OLR1 were up-regulated and two genes, SCD and UCP-1, were down-regulated in all the tested tissues of STH. Among the genes involved in ECM-receptor interaction, the genes encoding collagens, laminins, and integrins were quite different depending on the depots or the breeds. In STH, genes such as LAMB3, RELN, TNXB, and ITGA8, were identified to be up regulated and LAMB4 was observed to be down regulated. This study unravels the complex transcriptome profiles in sheep fat tissues, highlighting the candidate genes involved in fat deposition. Further studies are needed to investigate the roles of the candidate genes in fat deposition and in determining the meat quality of sheep.

Paleographic and sedimentologic significance of Mississippian sequence at Mt. Darby, Wyoming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dejarnett, J.

1985-05-01

Mississippian strata at Mt. Darby comprise the Madison Group and the overlying Humbug Formation. This sequence, although initially transgressive, exhibits an overall regressive character produced by progradation of platform carbonates in response to sea level fluctuations related to Antler orogenic events. The Paine Member of the Lodgepole Limestone, the basal formation of the Madison Group, consists of relatively deep-water carbonates including a possible Waulsortian-type carbonate bank that accumulated on a Kinderhookian foreslope. At least five shoaling-upward grainstone cycles are recognizable in the Woodhurst Member of the Lodgepole Limestone. These cycles record Osagean deposition in shallow agitated environments that developed highmore » on a clinoform ramp. Shelf-margin and platform carbonates dominate the Mission Canyon Limestone, the upper formation of the Madison Group. this unit consists of two asymmetric deposition cycles, each with a thick regressive phase, capped by an evaporite solution breccia and an overlying thin transgressive phase. The Humbug Formation, a sequence of fine-grained carbonates and sandstones, represents part of a deltaic complex that developed offshore from the Meramecian karst plain. Humbug sediments were transported northward to the Mt. Darby area from the area of the present Uinta Mountains, or another deltaic system formed there. Deposition in the study area was apparently continuous upward from the Madison carbonates into the Humbug. The middle Meramecian shoreline trended northwest between the present locations of Mt. Darby and Haystack Peak.« less

Trace fossils and sedimentology of a Late Cretaceous Progradational Barrier Island sequence: Bearpaw and Horseshoe Canyon Formations, Dorothy, Alberta

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saunders, T.D.; Pemberton, A.G.; Ranger, M.J.

A well-exposed example of a regressive barrier island succession crops out in the Alberta badlands along the Red Deer River Valley. In the most landward (northwestern) corner of the study area, only shallow-water and subaerial deposits are represented and are dominated by tidal inlet related facies. Seaward (southeast), water depth increases and the succession is typified by open-marine beach to offshore-related facies arranged in coarsening-upward progradational sequence. Detailed sedimentologic and ichnologic analyses of this sequence have allowed for its division into three distinct environmental zones (lower, middle, and upper). The lower zone comprises a laterally diverse assemblage of storm-influenced, lowermore » shoreface through offshore deposits. Outcrop in the northeast is dominated by thick beds of hummocky and/or swaley cross-stratified storm sand. In the southeast, storm events have only minor influence. This lower zone contains a wide diversity of well-preserved trace fossils whose distribution appears to have been influenced by gradients in wave energy, bottom stagnation, and the interplay of storm and fair-weather processes. The middle zone records deposition across an upper shoreface environment. Here, horizontal to low-angle bedding predominates, with interspersed sets of small- and large-scale cross-bedding increasing toward the top. A characteristic feature of the upper part of this zone is the lack of biogenic structures suggesting deposition in an exposed high-energy surf zone. The upper zone records intertidal to supratidal progradation of the shoreline complex. Planar-laminated sandstone forms a distinct foreshore interval above which rhizoliths and organic material become increasingly abundant, marking transition to the backshore. A significant feature of this zone is the occurrence of an intensely bioturbated interval toward the top of the foreshore.« less

"3D Depositional Model in a Complex Incised Valley Fill: An example from the late Messinian Abu Madi Formation, Nile Delta Basin, Egypt"

NASA Astrophysics Data System (ADS)

Nasr El-Deen Badawy, A. M. E. S.; Abu El-Ata, A. S. A.

2016-12-01

The study area lies in the Central Marine Delta, which is located in the Baltim offshore concession, about 25 kms from the shoreline and 40 kms North Abu Madi-El Qara fields. The current study is aiming to give a comprehensive combined and conjugated study between well data and seismic survey interpretations. The former includes well logging data, acquired results of actual drilling and biostratigraphic study, to give an integrated picture for the considered area in a true attempt to visualize the geological and geophysical data given from both wells and seismic reflection surveys, and hence introduce an updated sequence stratigraphic framework for the Messinian sequence at the offshore Nile Delta area. The 3D geological model, based on all the available well data (faunal contents, litho-facies, log signatures…...etc.) and the seismic expressions (facies and geometry), has been constructed for the study area. This model shows that, the study area was changed from shelf (considered as erosional), to delta channels and then directed to the north. It changed to delta front mouth bars on the shoreface and affected by the main Rosetta fault to collect deposits as sand bars in the southern part on the downthrown side of the fault. Most deposits on this face were highstand system tracts. This deduced from the sequence stratigraphy study. The area was then sloped to the north, as shelf slope with the deposition of slumps, which was formed during erosions and mass flows. Some mud diapers also formed upon this slope. After dropping the sea level with the activity of some syn-sedimentary faults, some channels with sediment supply started their activities to dig their ways to the north.

3D Depositional Model in a Complex Incised Valley Fill: An Example from the Late Messinian Abu Madi Formation, Nile Delta Basin, Egypt

NASA Astrophysics Data System (ADS)

Nasr El-Deen Badawy, A. M. E. S.

2015-12-01

The study area lies in the Central Marine Delta, which is located in the Baltim offshore concession, about 25 kms from the shoreline and 40 kms North Abu Madi-El Qara fields. The current study is aiming to give a comprehensive combined and conjugated study between well data and seismic survey interpretations. The former includes well logging data, acquired results of actual drilling and biostratigraphic study, to give an integrated picture for the considered area in a true attempt to visualize the geological and geophysical data given from both wells and seismic reflection surveys, and hence introduce an updated sequence stratigraphic framework for the Messinian sequence at the offshore Nile Delta area. The 3D geological model, based on all the available well data (faunal contents, litho-facies, log signatures…...etc.) and the seismic expressions (facies and geometry), has been constructed for the study area. This model shows that, the study area was changed from shelf (considered as erosional), to delta channels and then directed to the north. It changed to delta front mouth bars on the shoreface and affected by the main Rosetta fault to collect deposits as sand bars in the southern part on the downthrown side of the fault. Most deposits on this face were highstand system tracts. This deduced from the sequence stratigraphy study. The area was then sloped to the north, as shelf slope with the deposition of slumps, which was formed during erosions and mass flows. Some mud diapers also formed upon this slope. After dropping the sea level with the activity of some syn-sedimentary faults, some channels with sediment supply started their activities to dig their ways to the north.

3D Depositional Model in a Complex Incised Valley Fill: An Example from the Late Messinian Abu Madi Formation, Nile Delta Basin, Egypt

NASA Astrophysics Data System (ADS)

Nasr El-Deen Badawy, A. M. E. S.

2016-02-01

The study area lies in the Central Marine Delta, which is located in the Baltim offshore concession, about 25 kms from the shoreline and 40 kms North Abu Madi-El Qara fields. The current study is aiming to give a comprehensive combined and conjugated study between well data and seismic survey interpretations. The former includes well logging data, acquired results of actual drilling and biostratigraphic study, to give an integrated picture for the considered area in a true attempt to visualize the geological and geophysical data given from both wells and seismic reflection surveys, and hence introduce an updated sequence stratigraphic framework for the Messinian sequence at the offshore Nile Delta area. The 3D geological model, based on all the available well data (faunal contents, litho-facies, log signatures…...etc.) and the seismic expressions (facies and geometry), has been constructed for the study area. This model shows that, the study area was changed from shelf (considered as erosional), to delta channels and then directed to the north. It changed to delta front mouth bars on the shoreface and affected by the main Rosetta fault to collect deposits as sand bars in the southern part on the downthrown side of the fault. Most deposits on this face were highstand system tracts. This deduced from the sequence stratigraphy study. The area was then sloped to the north, as shelf slope with the deposition of slumps, which was formed during erosions and mass flows. Some mud diapers also formed upon this slope. After dropping the sea level with the activity of some syn-sedimentary faults, some channels with sediment supply started their activities to dig their ways to the north.

Depositional environments, sequence stratigraphy, and trapping mechanisms of Fall River Formation in Donkey Creek and Coyote Creek oil fields, Powder River basin, Wyoming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knox, P.R.

1989-09-01

Donkey Creek and Coyote Creek fields contain combined reserves of approximately 35 million bbl of oil and are within a trend of fields on the eastern flank of the Powder River basin that totals over 100 million bbl of reserves. The principal producing formation is the Lower Cretaceous Fall River Sandstone. A study of 45 cores and 248 logs from the three pools in the Donkey Creek and Coyote fields has shown that the Fall River is composed of three progradational deltaic units deposited during a period of rising relative sea level. These are locally eroded and are filled bymore » a fluvial point-bar complex deposited following a lowering of relative sea level. Four important depositional facies have been recognized: the delta-front and distributary-channel sandstone of the highstand deltaic sequence and the point-bar sandstone and channel-abandonment of the lowstand fluvial sequence. Stratigraphic traps in Coyote Creek and south Donkey Creek pools are the result of permeable (250 md) point-bar sandstone (250 bbl oil/day ip) bounded updip by impermeable (0.1 md) channel abandonment mudstone. Most of the oil in the central Donkey Creek pool is produced from permeable (76 md) distributary-channel sandstone (150 bbl oil/day ip), which is restricted to the western flank of a structural nose. Lesser production, on the crest and upper western flank of the structure, is obtained from the less permeable (2.8 md) delta-front sandstone (50 bbl oil/day ip). Production is possibly limited to the crest and western flank by hydrodynamic processes.« less

Aeolian dust supply from the Yellow River floodplain to the Pleistocene loess deposits of the Mangshan Plateau, central China: Evidence from zircon U-Pb age spectra

NASA Astrophysics Data System (ADS)

Shang, Yuan; Prins, Maarten A.; Beets, Christiaan J.; Kaakinen, Anu; Lahaye, Yann; Dijkstra, Noortje; Rits, Daniël S.; Wang, Bin; Zheng, Hongbo; van Balen, Ronald T.

2018-02-01

The thick loess-palaeosol sequences in the Mangshan Loess Plateau (MLP; central China) along the south bank of the lower reach of the Yellow River provide high-resolution records of Quaternary climate change. In addition, substantial increases in grain-size and accumulation rate have been inferred in the upper part of the loess sequence, above palaeosol layer S2. This study investigates the sources of the long-term dust supply to the MLP and explores the mechanism behind the sudden increase in sediment delivery and coarsening of the loess deposits since S2 (∼240 ka) by using end member modelling of the loess grain-size dataset and single-grain zircon U-Pb dating. Our results indicate that the lower Yellow River floodplain, directly north of the MLP, served as a major dust supply for the plateau at least since the deposition of loess unit L9 and indirectly suggest that the integration of the Yellow River and the disappearance of the Sanmen palaeolake took place before L9 (∼900 ka). The sudden change in sedimentology of the Mangshan sequence above palaeosol unit S2 may result from an increased fluvial sediment flux being transported to the lower reaches of the Yellow River because of tectonic movements (initiated) in the Weihe Basin around 240 ka. Furthermore, sediment coarsening can be explained by the gradual southward migration of the lower Yellow River floodplain towards the MLP since the deposition of palaeosol S2. The migration is evidenced by the formation of an impressive scarp, and is likely caused by tectonic tilting of the floodplain area.

Immunohistochemical localization of beta-amyloid precursor protein sequences in Alzheimer and normal brain tissue by light and electron microscopy.

PubMed

McGeer, P L; Akiyama, H; Kawamata, T; Yamada, T; Walker, D G; Ishii, T

1992-03-01

Immunohistochemical staining with antibodies directed against four segments of the amyloid precursor protein (APP) was studied by light and electron microscopy in normal and Alzheimer (AD) brain tissue. The segments according to the Kang et al. sequence were: 18-38 (T97); 527-540 (R36); 597-620 (1-24 of beta-amyloid protein [BAP], R17); and 681-695 (R37) (Kang et al. [1987]: Nature 325:733-736). The antibodies recognized full length APP in Western blots of extracts of APP transfected cells. They stained cytoplasmic granules in some pyramidal neurons in normal appearing tissue from control and AD cases. In AD affected tissue, the antibodies to amino terminal sections of APP stained tangled neurons and neuropil threads, and intensely stained dystrophic neurites in senile plaques. By electron microscopy, this staining was localized to abnormal filaments. The antibody to the carboxy terminal segment failed to stain neurofibrillary tangles or neuropil threads; it did stain some neurites with globular swellings. It also stained globular and elongated deposits in senile plaque areas. The antibody against the BAP intensely stained extracellular material in senile plaques and diffuse deposits. By electron microscopy, the antibodies all stained intramicroglial deposits. Some of the extracellular and intracellular BAP-positive deposits were fibrillary. Communication between intramicroglial and extracellular fibrils was detected in plaque areas. These data suggest the following sequence of events. APP is normally concentrated in intraneuronal granules. In AD, it accumulates in damaged neuronal fibers. The amino terminal portion binds to abnormal neurofilaments. Major fragments of APP are phagocytosed and processed by microglia with the BAP portion being preserved. The preserved BAP is then extruded and accumulates in extracellular tissue.

Dispersion model on PM₂.₅ fugitive dust and trace metals levels in Kuwait Governorates.

PubMed

Bu-Olayan, A H; Thomas, B V

2012-03-01

Frequent dust storms and recent environmental changes were found to affect the human health especially in residents of arid countries. Investigations on the PM(2.5) fugitive dust in six Kuwait Governorate areas using dispersion Gaussian plume modeling revealed significant relationship between low rate of pollutant emission, low wind velocity, and stable weather conditions' matrix causing high rate of dust deposition in summer than in winter. The rate of dust deposition and trace metals levels in PM(2.5) were in the sequence of G-VI > G-I > G-II > G-V > G-III > G-IV. Trace metals were observed in the sequence of Al > Fe > Zn > Ni > Pb > Cd irrespective of the Governorate areas and the two seasons. The high rate of dust deposition and trace metals in PM(2.5) was reflected by the vast open area, wind velocity, and rapid industrialization besides natural and anthropogenic sources. A combination of air dispersion modeling and nephalometric and gravimetric studies of this kind not only determines the seasonal qualitative and quantitative analyses on the PM(2.5) dust deposition besides trace metals apportionment in six Kuwait Governorate areas, but also characterizes air pollution factors that could be used by environmentalist to deduce preventive measures.

Stratigraphic framework and evolution of the Cretaceous continental sequences of the Bauru, Sanfranciscana, and Parecis basins, Brazil

NASA Astrophysics Data System (ADS)

Batezelli, Alessandro; Ladeira, Francisco Sergio Bernardes

2016-01-01

With the breakup of the supercontinent Gondwana, the South American Plate has undergone an intense process of tectonic restructuring that led to the genesis of the interior basins that encompassed continental sedimentary sequences. The Brazilian Bauru, Sanfranciscana and Parecis basins during Late Cretaceous have had their evolution linked to this process of structuring and therefore have very similar sedimentary characteristics. The purpose of this study is to establish a detailed understanding of alluvial sedimentary processes and architecture within a stratigraphic sequence framework using the concept of the stratigraphic base level or the ratio between the accommodation space and sediment supply. The integration of the stratigraphic and facies data contributed to defining the stratigraphic architecture of the Bauru, Sanfranciscana and Parecis Basins, supporting a model for continental sequences that depicts qualitative changes in the sedimentation rate (S) and accommodation space (A) that occurred during the Cretaceous. This study discusses the origin of the unconformity surfaces (K-0, K-1 and K-1A) that separate Sequences 1, 2A and 2B and the sedimentary characteristics of the Bauru, Sanfranciscana and Parecis Basins from the Aptian to the Maastrichtian, comparing the results with other Cretaceous Brazilian basins. The lower Cretaceous Sequence 1 (Caiuá and Areado groups) is interpreted as a low-accommodation systems tract compound by fluvial and aeolian systems. The upper Cretaceous lacustrine, braided river-dominated alluvial fan and aeolian systems display characteristics of the evolution from high-to low-accommodation systems tracts (Sequences 2A and 2B). Unconformity K-0 is related to the origin of the Bauru Basin itself in the Early Cretaceous. In Sanfranciscana and Parecis basins, the unconformity K-0 marks the contact between aeolian deposits from Lower Cretaceous and Upper Cretaceous alluvial systems (Sequences 1 and 2). Unconformity K-1, which was generated in the Late Cretaceous, is related to an increase of the A/S ratio, whereas Unconformity K-1A is the result of the decrease in the A/S ratio. Unconformity K-1A bound Sequence 2A (lacustrine and fluvial systems) and Sequence 2B (alluvial deposits) in Bauru Basin whereas in the Sanfranciscana and Parecis basins this unconformity marks the transition from alluvial system to aeolian system (Sequences 2A and 2B). Changes in depositional style in both basins correspond to two distinct tectonic moments occurring within the South American plate. The first associated with post-volcanic thermal subsidence of the Early Cretaceous (Serra Geral and Tapirapuã volcanismos), and the second moment associated with the uplift occurred in the Late Cretaceous (Alto Paranaíba, Vilhena and Serra Formosa Arcs).

Effects of specific surface area of metallic nickel particles on carbon deposition kinetics

NASA Astrophysics Data System (ADS)

Chen, Zhi-yuan; Bian, Liu-zhen; Yu, Zi-you; Wang, Li-jun; Li, Fu-shen; Chou, Kuo-Chih

2018-02-01

Carbon deposition on nickel powders in methane involves three stages in different reaction temperature ranges. Temperature programing oxidation test and Raman spectrum results indicated the formation of complex and ordered carbon structures at high deposition temperatures. The values of I(D)/ I(G) of the deposited carbon reached 1.86, 1.30, and 1.22 in the first, second, and third stages, respectively. The structure of carbon in the second stage was similar to that in the third stage. Carbon deposited in the first stage rarely contained homogeneous pyrolytic deposit layers. A kinetic model was developed to analyze the carbon deposition behavior in the first stage. The rate-determining step of the first stage is supposed to be interfacial reaction. Based on the investigation of carbon deposition kinetics on nickel powders from different resources, carbon deposition rate is suggested to have a linear relation with the square of specific surface area of nickel particles.

Landscapes, depositional environments and human occupation at Middle Paleolithic open-air sites in the southern Levant, with new insights from Nesher Ramla, Israel

NASA Astrophysics Data System (ADS)

Zaidner, Yossi; Frumkin, Amos; Friesem, David; Tsatskin, Alexander; Shahack-Gross, Ruth

2016-04-01

Middle Paleolithic human occupation in the Levant (250-50 ka ago) has been recorded in roofed (cave and rockshelter) and open-air sites. Research at these different types of sites yielded different perspectives on the Middle Paleolithic human behavior and evolution. Until recently, open-air Middle Paleolithic sites in the Levant were found in three major sedimentary environments: fluvial, lake-margin and spring. Here we describe a unique depositional environment and formation processes at the recently discovered open-air site of Nesher Ramla (Israel) and discuss their contribution to understanding site formation processes in open-air sites in the Levant. The site is 8-m-thick Middle Paleolithic sequence (OSL dated to 170-80 ka) that is located in a karst sinkhole formed by gravitational deformation and sagging into underground voids. The sedimentary sequence was shaped by gravitational collapse, cyclic colluviation of soil and gravel into the depression, waterlogging, in situ pedogenesis and human occupation. Original bedding and combustion features are well-preserved in the Lower archaeological sequence, a rare occurrence in comparison to other open-air archaeological sites. This phenomenon coincides with episodes of fast sedimentation/burial, which also allowed better preservation of microscopic remains such as ash. The Upper archaeological sequence does not exhibit bedding or preservation of ash, despite presence of heat-affected lithic artifacts, which makes it similar to other open-air sites in the Levant. We suggest that rate of burial is the major factor that caused the difference between the Upper and Lower sequences. The differences in the burial rate may be connected to environmental and vegetation changes at the end of MIS 6. We also identified an interplay between sediment in-wash and density of human activity remains, i.e. during episodes of low natural sediment input the density of artifacts is higher relative to episodes with high rate of sediment in-wash. The detailed analysis of natural and anthropogenic processes at Nesher Ramla suggests a much wider spectrum of processes than previously reported for southern Levantine Paleolithic sites. Nesher Ramla shares certain depositional and post-depositional characteristics with both cave and open-air sites and provides a better insight into processes which control both types of sites.

Comparison of chemical and heating methods to enhance latent fingerprint deposits on thermal paper.

PubMed

Bond, John W

2014-03-01

A comparison is made of proprietary methods to develop latent fingerprint deposits on the inked side of thermal paper using either chemical treatment (Thermanin) or the application of heat to the paper (Hot Print System). Results with a trial of five donors show that the application of heat produces statistically significantly more fingerprint ridge detail than the chemical treatment for both fingerprint deposits aged up to 4 weeks and for a nine sequence depletion series. Subjecting the thermal paper to heat treatment with the Hot Print System did not inhibit subsequent ninhydrin chemical development of fingerprint deposits on the noninked side of the paper. A further benefit of the application of heat is the rapid development of fingerprint deposits (less than a minute) compared with up to 12 h for the Thermanin chemical treatment.

Stratigraphy, climate and downhole logging data - an example from the ICDP Dead Sea deep drilling project

NASA Astrophysics Data System (ADS)

Coianiz, Lisa; Ben-Avraham, Zvi; Lazar, Michael

2017-04-01

During the late Quaternary a series of lakes occupied the Dead Sea tectonic basin. The sediments that accumulated within these lakes preserved the environmental history (tectonic and climatic) of the basin and its vicinity. Most of the information on these lakes was deduced from exposures along the marginal terraces of the modern Dead Sea, e.g. the exposures of the last glacial Lake Lisan and Holocene Dead Sea. The International Continental Drilling Program (ICDP) project conducted in the Dead Sea during 2010-2011 recovered several cores that were drilled in the deep depocenter of the lake (water depth of 300 m) and at the margin (depth of 3 m offshore Ein Gedi spa). New high resolution logging data combined with a detailed lithological description and published age models for the deep 5017-1-A borehole were used to establish a sequence stratigraphic framework for the Lakes Amora, Samra, Lisan and Zeelim strata. This study presents a stratigraphic timescale for reconstructing the last ca 225 ka. It provides a context within which the timing of key sequence surfaces identified in the distal part of the basin can be mapped on a regional and stratigraphic time frame. In addition, it permitted the examination of depositional system tracts and related driving mechanisms controlling their formation. The sequence stratigraphic model developed for the Northern Dead Sea Basin is based on the identification of sequence bounding surfaces including: sequence boundary (SB), transgressive surface (TS) and maximum flooding surface (MFS). They enabled the division of depositional sequences into a Lowstand systems tracts (LST), Transgressive systems tracts (TST) and Highstand systems tracts (HST), which can be interpreted in terms of relative lake level changes. The analysis presented here show that system tract stacking patterns defined for the distal 5017-1-A borehole can be correlated to the proximal part of the basin, and widely support the claim that changes in relative lake levels were synchronous across the northern Dead Sea, although differences do exist. These discrepancies can possibly be explained in part by the tectonic nature of the basin. Within the 5017-1-A section, the interpreted changes in depositional environments derived primarily from the gamma ray log patterns show a good correlation in time with sequence-chronostratigraphic framework, extracted lake level curves and paleohydrological records of other areas worldwide. Sequence stratigraphic analysis presented here allows for a detailed, high resolution examination of the sedimentary sequences in the Northern Dead Sea Basin together with an independent proxy that is an indirect indicator of changes in relative lake level.

Stratigraphy, sedimentology and eruptive mechanism of the El Golfo phreatomagmatic edifice (Lanzarote, Canary Islands)

NASA Astrophysics Data System (ADS)

Pedrazzi, D.; Marti, J.; Geyer, A.

2012-04-01

The El Golfo tuff cone is an example of phreatomagmatic edifice, developed in the western coast of Lanzarote (Canary Islands). El Golfo, together with other edifices of the same age, is aligned along a fracture oriented NEE-SWW coinciding with the main lineation of the historic volcanism in this part of the island. In this contribution we present a detailed stratigraphic study of the succession of deposits and we interpret them in terms of depositional processes and eruptive dynamics. The eruptive sequence is exclusively represented by a succession of pyroclastic deposits, and we infer it according to variations in flow regime and the magma-water interaction. Several pyroclastic units were identified according to facies variations based on sedimentary discontinuities, grain size, components, variations in primary laminations and bedforms following the facies model proposed by Chough and Sohn (1990). The growth of the El Golfo tuff cone involved several stages based on variations in depositional processes. The edifice was constructed very rapidly around the vent controlling the amount of water that got access to the eruption conduit. Although the invariable phreatomagmatic character of most of the pyroclastic sequence, it is possible to deduce variations in the explosive energy, with a general increment upwards, according to the increase in the degree of fragmentation of pyroclasts, The absence of hyaloclastites, the nature of the palagonite alteration and the observed sedimentary structures, demonstrate the subaereal character of most of the deposits

Estimation of submarine mass failure probability from a sequence of deposits with age dates

USGS Publications Warehouse

Geist, Eric L.; Chaytor, Jason D.; Parsons, Thomas E.; ten Brink, Uri S.

2013-01-01

The empirical probability of submarine mass failure is quantified from a sequence of dated mass-transport deposits. Several different techniques are described to estimate the parameters for a suite of candidate probability models. The techniques, previously developed for analyzing paleoseismic data, include maximum likelihood and Type II (Bayesian) maximum likelihood methods derived from renewal process theory and Monte Carlo methods. The estimated mean return time from these methods, unlike estimates from a simple arithmetic mean of the center age dates and standard likelihood methods, includes the effects of age-dating uncertainty and of open time intervals before the first and after the last event. The likelihood techniques are evaluated using Akaike’s Information Criterion (AIC) and Akaike’s Bayesian Information Criterion (ABIC) to select the optimal model. The techniques are applied to mass transport deposits recorded in two Integrated Ocean Drilling Program (IODP) drill sites located in the Ursa Basin, northern Gulf of Mexico. Dates of the deposits were constrained by regional bio- and magnetostratigraphy from a previous study. Results of the analysis indicate that submarine mass failures in this location occur primarily according to a Poisson process in which failures are independent and return times follow an exponential distribution. However, some of the model results suggest that submarine mass failures may occur quasiperiodically at one of the sites (U1324). The suite of techniques described in this study provides quantitative probability estimates of submarine mass failure occurrence, for any number of deposits and age uncertainty distributions.

Distribution and phylogeny of Wolbachia strains in wild mosquito populations in Sri Lanka.

PubMed

Nugapola, N W Nalaka P; De Silva, W A Priyanka P; Karunaratne, S H P Parakrama

2017-05-10

Wolbachia are a group of maternally inherited intracellular bacteria known to be widespread among arthropods. Infections with Wolbachia cause declines of host populations, and also induce host resistance to a wide range of pathogens. Over the past few decades, researchers were curious to use Wolbachia as a biological tool to control mosquito vectors. During the present study, assessment of the prevalence of Wolbachia infections among wild mosquito populations in Sri Lanka where mosquito-borne diseases are a major health concern, was carried out for the first time. DNA was extracted from the abdomens of mosquitoes, collected from seven provinces, and screened for the presence of Wolbachia by PCR using wsp and groE primers. Group-specific and strain-specific primers were used to classify Wolbachia into the supergroups A and B, and into the strains Mel, AlbA and Pip. A total of 330 individual mosquitoes belonging to 22 species and 7 genera were screened. Eighty-seven mosquitoes (26.36%) belonging to four species (i.e. Aedes albopictus, Culex quinquefasciatus, Armigeres subalbatus and Mansonia uniformis) were positive for Wolbachia infections. Primary vector of the dengue fever, Ae. aegypti was negative for Wolbachia infections while the secondary vector, Ae. albopictus, showed a very high infection rate. The filarial vector C. quinquefasciatus had a relatively high rate of infection. Japanese encephalitis vectors C. gelidus and C. triteaneorynchus, and the Anopheles vectors of malaria were negative for Wolbachia infections. Nine sequences of Wolbachia-positive PCR products were deposited in the GenBank and compared with other available data. Aedes albopictus was infected with both Wolbachia strains A (AlbA) and B (Pip) supergroups. Phylogenetic analysis of the wsp sequences showed two major branches confirming identities obtained from the PCR screening with strain-specific primers. Wolbachia infections were found only among four mosquito species in Sri Lanka: Aedes albopictus, Culex quinquefasciatus, Armigeres subalbatus and Mansonia uniformis. Sequence data showed high haplotype diversity among the Wolbachia strains.

Raw Sewage Harbors Diverse Viral Populations

PubMed Central

Cantalupo, Paul G.; Calgua, Byron; Zhao, Guoyan; Hundesa, Ayalkibet; Wier, Adam D.; Katz, Josh P.; Grabe, Michael; Hendrix, Roger W.; Girones, Rosina; Wang, David; Pipas, James M.

2011-01-01

ABSTRACT At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity. Importance At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected. PMID:21972239

Architecture and reservoir quality of low-permeable Eocene lacustrine turbidite sandstone from the Dongying Depression, East China

NASA Astrophysics Data System (ADS)

Munawar, Muhammad Jawad; Lin, Chengyan; Chunmei, Dong; Zhang, Xianguo; Zhao, Haiyan; Xiao, Shuming; Azeem, Tahir; Zahid, Muhammad Aleem; Ma, Cunfei

2018-05-01

The architecture and quality of lacustrine turbidites that act as petroleum reservoirs are less well documented. Reservoir architecture and multiscale heterogeneity in turbidites represent serious challenges to production performance. Additionally, establishing a hierarchy profile to delineate heterogeneity is a challenging task in lacustrine turbidite deposits. Here, we report on the turbidites in the middle third member of the Eocene Shahejie Formation (Es3), which was deposited during extensive Middle to Late Eocene rifting in the Dongying Depression. Seismic records, wireline log responses, and core observations were integrated to describe the reservoir heterogeneity by delineating the architectural elements, sequence stratigraphic framework and lithofacies assemblage. A petrographic approach was adopted to constrain microscopic heterogeneity using an optical microscope, routine core analyses and X-ray diffraction (XRD) analyses. The Es3m member is interpreted as a sequence set composed of four composite sequences: CS1, CS2, CS3 and CS4. A total of forty-five sequences were identified within these four composite sequences. Sand bodies were mainly deposited as channels, levees, overbank splays, lobes and lobe fringes. The combination of fining-upward and coarsening-upward lithofacies patterns in the architectural elements produces highly complex composite flow units. Microscopic heterogeneity is produced by diagenetic alteration processes (i.e., feldspar dissolution, authigenic clay formation and quartz cementation). The widespread kaolinization of feldspar and mobilization of materials enhanced the quality of the reservoir by producing secondary enlarged pores. In contrast, the formation of pore-filling authigenic illite and illite/smectite clays reduced its permeability. Recovery rates are higher in the axial areas and smaller in the marginal areas of architectural elements. This study represents a significant insight into the reservoir architecture and heterogeneity of lacustrine turbidites, and the understanding of compartmentalization and distribution of high-quality sand reservoirs can be applied to improve primary and secondary production in these fields.

Oligo-Miocene reservoir sequence characterization and structuring in the Sisseb El Alem-Kalaa Kebira regions (Northeastern Tunisia)

NASA Astrophysics Data System (ADS)

Houatmia, Faten; Khomsi, Sami; Bédir, Mourad

2015-11-01

The Sisseb El Alem-Enfidha basin is located in the northeastern Tunisia, It is borded by Nadhour - Saouaf syncline to the north, Kairouan plain to the south, the Mediterranean Sea to the east and Tunisian Atlassic "dorsale" to the west. Oligocene and Miocene deltaic deposits present the main potential deep aquifers in this basin with high porosity (25%-30%). The interpretation of twenty seismic reflection profiles, calibrated by wire line logging data of twelve oil wells, hydraulic wells and geologic field sections highlighted the impact of tectonics on the structuring geometry of Oligo-Miocene sandstones reservoirs and their distribution in raised structures and subsurface depressions. Miocene seismostratigraphy analysis from Ain Ghrab Formation (Langhian) to the Segui Formation (Quaternary) showed five third-order seismic sequence deposits and nine extended lenticular sandy bodies reservoirs limited by toplap and downlap surfaces unconformities, Oligocene deposits presented also five third- order seismic sequences with five extended lenticular sandy bodies reservoirs. The Depth and the thickness maps of these sequence reservoir packages exhibited the structuring of this basin in sub-basins characterized by important lateral and vertical geometric and thichness variations. Petroleum wells wire line logging correlation with clay volume calculation showed an heterogeneous multilayer reservoirs of Oligocene and Miocene formed by the arrangement of fourteen sandstone bodies being able to be good reservoirs, separated by impermeable clay packages and affected by faults. Reservoirs levels correspond mainly to the lower system tract (LST) of sequences. Intensive fracturing by deep seated faults bounding the different sub-basins play a great role for water surface recharge and inter-layer circulations between affected reservoirs. The total pore volume of the Oligo-Miocene reservoir sandy bodies in the study area, is estimated to about 4 × 1012 m3 and equivalent to 4 × 109 m3 of deep water reserves.

Cover sequences at the northern margin of the Antongil Craton, NE Madagascar

USGS Publications Warehouse

Bauer, W.; Walsh, G.J.; De Waele, B.; Thomas, Ronald J.; Horstwood, M.S.A.; Bracciali, L.; Schofield, D.I.; Wollenberg, U.; Lidke, D.J.; Rasaona, I.T.; Rabarimanana, M.H.

2011-01-01

The island of Madagascar is a collage of Precambrian, generally high-grade metamorphic basement domains, that are locally overlain by unmetamorphosed sedimentary rocks and poorly understood low-grade metasediments. In the Antalaha area of NE Madagascar, two distinct cover sequences rest on high-grade metamorphic and igneous basement rocks of the Archaean Antongil craton and the Neoproterozoic Bemarivo belt. The older of these two cover sequences, the Andrarona Group, consists of low-grade metasedimentary rocks. The younger sequence, the newly defined Ampohafana Formation, consists of unmetamorphosed sedimentary rocks. The Andrarona Group rests on Neoarchaean granites and monzogranites of the Antongil craton and consists of a basal metagreywacke, thick quartzites and an upper sequence of sericite-chlorite meta-mudstones, meta-sandstones and a volcaniclastic meta-sandstone. The depositional age of the volcaniclastic meta-sandstone is constrained in age by U–Pb laser-ablation ICP-MS analyses of euhedral zircons to 1875 ± 8 Ma (2σ). Detrital zircons of Archaean and Palaeoproterozoic age represent an input from the Antongil craton and a newly defined Palaeoproterozoic igneous unit, the Masindray tonalite, which underlies the Andrarona Group, and yielded a U–Pb zircon age of 2355 ± 11 Ma (2σ), thus constraining the maximum age of deposition of the basal part of the Andrarona Group. The Andrarona Group shows a low-grade metamorphic overprint in the area near Antalaha; illite crystallinity values scatter around 0.17°Δ2Θ CuKα, which is within the epizone. The Ampohafana Formation consists of undeformed, polymict conglomerate, cross-bedded sandstone, and red mudstone. An illite crystallinity value of >0.25°Δ2Θ CuKα obtained from the rocks is typical of the diagenetic zone. Occurrences of rhyodacite pebbles in the Ampohafana Formation and the intrusion of a basaltic dyke suggest a deposition in a WSW-ENE-trending graben system during the opening of the Indian Ocean in the Upper Cretaceous, that was characterized by extensive rhyolitic to basaltic magmatism along Madagascar's eastern coast.

Enhanced pulmonary absorption of a macromolecule through coupling to a sequence-specific phage display-derived peptide.

PubMed

Morris, Christopher J; Smith, Mathew W; Griffiths, Peter C; McKeown, Neil B; Gumbleton, Mark

2011-04-10

With the aim of identifying a peptide sequence that promotes pulmonary epithelial transport of macromolecule cargo we used a stringent peptide-phage display library screening protocol against rat lung alveolar epithelial primary cell cultures. We identified a peptide-phage clone (LTP-1) displaying the disulphide-constrained 7-mer peptide sequence, C-TSGTHPR-C, that showed significant pulmonary epithelial translocation across highly restrictive polarised cell monolayers. Cell biological data supported a differential alveolar epithelial cell interaction of the LTP-1 peptide-phage clone and the corresponding free synthetic LTP-1 peptide. Delivering select phage-clones to the intact pulmonary barrier of an isolated perfused rat lung (IPRL) resulted in 8.7% of lung deposited LTP-1 peptide-phage clone transported from the IPRL airways to the vasculature compared (p<0.05) to the cumulative transport of less than 0.004% for control phage-clone groups. To characterise phage-independent activity of LTP-1 peptide, the LTP-1 peptide was conjugated to a 53kDa anionic PAMAM dendrimer. Compared to respective peptide-dendrimer control conjugates, the LTP-1-PAMAM conjugate displayed a two-fold (bioavailability up to 31%) greater extent of absorption in the IPRL. The LTP-1 peptide-mediated enhancement of transport, when LTP-1 was either attached to the phage clone or conjugated to dendrimer, was sequence-dependent and could be competitively inhibited by co-instillation of excess synthetic free LTP-1 peptide. The specific nature of the target receptor or mechanism involved in LTP-1 lung transport remains unclear although the enhanced transport is enabled through a mechanism that is non-disruptive with respect to the pulmonary transport of hydrophilic permeability probes. This study shows proof-of principle that array technologies can be effectively exploited to identify peptides mediating enhanced transmucosal delivery of macromolecule therapeutics across an intact organ. Copyright © 2010 Elsevier B.V. All rights reserved.

The loess/paleosol record and the nature of the younger dryas climate in central China

USGS Publications Warehouse

Madsen, D.B.; Jingzen, L.; Elston, R.G.; Cheng, X.; Bettinger, R.L.; Kan, G.; Jeff, Brantingham P.; Kan, Z.

1998-01-01

The use of latest Pleistocene-Holocene paleosols in defining Chinese climatic sequences is plagued by poor chronological controls caused primarily by the use of radiocarbon dates derived from bulk soil carbon. Dating of a post-glacial aeolian/paleosol sequence in the Pigeon Mountain basin of north-central China, using culturally deposited charcoal, support a wide array of other data suggesting the Younger Dryas was a period of cooler dryer conditions marked by wide-spread aeolian deposition. Periods of soil formation and higher lake levels bracket this climatic event. Climatic variability immediately before, during and immediately after the Younger Dryas interval is associated with rapid technological elaboration and innovation in the production and use of chipped stone tools, and perhaps, ground stone. ?? 1998 John Wiley & Sons, Inc.

Short genome report of cellulose-producing commensal Escherichia coli 1094.

PubMed

Bernal-Bayard, Joaquin; Gomez-Valero, Laura; Wessel, Aimee; Khanna, Varun; Bouchier, Christiane; Ghigo, Jean-Marc

2018-01-01

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E. coli strains. Data deposition: The annotated genome sequence has been deposited at the European Nucleotide Archive under the accession number PRJEB21000.

Paleogeography and sedimentology of Upper Cretaceous turbidites, San Diego, California.

USGS Publications Warehouse

Nilsen, T.H.; Abbott, P.L.

1981-01-01

Upper Cretaceous (Campanian and Maestrichtian) marine strata of the Rosario Group in the San Diego area include the Point Loma Formation and overlying Cabrillo Formation. Thes units contain 6 facies associations which define a deep-sea fan deposited by westward-flowing sediment gravity flows that transported sediments derived chiefly from batholithic and pre-batholithic metamorphic rocks of the Peninsular Ranges. The sedimentary basin initially deepened abruptly. The fan then prograded westward into the basin, with a retrogradational phase recorded in the uppermost part of the sequence. The fan was deposited along the eastern edge of a forearc basin similar to that of the Great Valley sequence in northern California. The western part of the fan appears to have been truncated by late Cenozoic strike-slip faulting.-from Authors

Femtosecond laser-induced periodic surface structures on silicon upon polarization controlled two-color double-pulse irradiation.

PubMed

Höhm, Sandra; Herzlieb, Marcel; Rosenfeld, Arkadi; Krüger, Jörg; Bonse, Jörn

2015-01-12

Two-color double-fs-pulse experiments were performed on silicon wafers to study the temporally distributed energy deposition in the formation of laser-induced periodic surface structures (LIPSS). A Mach-Zehnder interferometer generated parallel or cross-polarized double-pulse sequences at 400 and 800 nm wavelength, with inter-pulse delays up to a few picoseconds between the sub-ablation 50-fs-pulses. Multiple two-color double-pulse sequences were collinearly focused by a spherical mirror to the sample. The resulting LIPSS characteristics (periods, areas) were analyzed by scanning electron microscopy. A wavelength-dependent plasmonic mechanism is proposed to explain the delay-dependence of the LIPSS. These two-color experiments extend previous single-color studies and prove the importance of the ultrafast energy deposition for LIPSS formation.

Meta-evaporite in the Carajás mineral province, northern Brazil

NASA Astrophysics Data System (ADS)

Riehl, Walter; Cabral, Alexandre Raphael

2018-05-01

Evidence for connecting evaporite-sourced high-salinity fluids with iron-oxide-copper-gold (IOCG) deposits in the Carajás mineral province has solely been based on boron-isotope compositions of tourmaline. Presence of meta-evaporitic rocks remains unrecognised. Here, we report laminated albitite, tourmalinite and banded albite-phlogopite rock, intercepted by exploratory drilling in a clastic metasedimentary sequence. These rocks represent evaporite precursors. Their location in the copper-gold prospects Açaí and Angélica, in the westernmost part of the Carajás mineral province, indicates that (i) evaporite-sourced fluids were regional and (ii) evaporite-bearing metasedimentary sequences may have been an important source of high-salinity fluids and/or sulfur for the IOCG deposits of the Carajás mineral province.

Archaea were widespread in sediments of the Messinian Salinity Crisis

NASA Astrophysics Data System (ADS)

Birgel, Daniel; Peckmann, Jörn

2015-04-01

The Messinian salinity crisis (MSC) was among the most extreme and short-lived paleooceanographic events in Earth history and dramatically impacted the depositional environments of the Mediterranean. Many of the Messinian sedimentary sequences reflect environmental variability on extremely short time scales, typified by phenomena like evaporation and high salinities, anoxia, and desiccation. Only few organisms tolerate such severe conditions. Among those are archaea, many of which are especially well adapted to extreme conditions. We studied various MSC locations and deposits to shed light onto the role of archaea in the MSC, focusing on lipid biomarkers. These are (1) primary gypsum with abundant, yet problematic filamentous microfossils from various locations in the Mediterranean, (2) Calcare di Base, limestones from Sicily and Calabria, and (3) Calcare Solfifero, authigenic carbonates associated with native sulfur from Sicily. (1) Primary gypsum beds with abundant filamentous fossils are widespread in the Mediterranean. Archaea were found as important contributor of organic matter in these evaporites. The filaments, however, have previously been interpreted to represent cyanobacteria based on the extraction and amplification of cyanobacterial DNA. Cyanobacteria produce specific and long-lasting biomarkers, but no such compounds were found in the studied deposits, thus, the assignment of the filaments to cyanobacteria necessitates further verification. (2) The Calcare di Base are widespread, genetically heterogeneous Messinian limestones, which are particularly common in Sicily and Calabria. The environmental conditions during their deposition, as well as mechanisms and timing of formation are a matter of debate. The studied Calcare di Base samples were found to contain specific halophilic archaeal signatures and numerous pseudomorphs after halite. (3) The Calcare Solfifero, authigenic carbonates accompanied by elemental sulfur formed in the course of microbial sulfate reduction. One of the important processes fuelling authigenesis was microbial oxidation of methane. Lipid biomarker patterns reveal that a consortium of methanotrophic archaea and sulfate-reducing bacteria consumed methane in anoxic and hypersaline environments. Halophilic archaea other than those archaea involved in methane oxidation have been present in the depositional environment as well. This as to yet still somewhat random selection of examples provides evidence for the great diversity of environmental settings created during the MSC and the abundance of archaea in these environments, calling for more work on the geomicrobiology of the unrivaled archive of dramatic paleooceanographic change during the MSC.

Conservation of the sequence of the Alzheimer's disease amyloid peptide in dog, polar bear and five other mammals by cross-species polymerase chain reaction analysis.

PubMed

Johnstone, E M; Chaney, M O; Norris, F H; Pascual, R; Little, S P

1991-07-01

Neuritic plaque and cerebrovascular amyloid deposits have been detected in the aged monkey, dog, and polar bear and have rarely been found in aged rodents (Biochem. Biophy. Res. Commun., 12 (1984) 885-890; Proc. Natl. Acad. Sci. U.S.A., 82 (1985) 4245-4249). To determine if the primary structure of the 42-43 residue amyloid peptide is conserved in species that accumulate plaques, the region of the amyloid precursor protein (APP) cDNA that encodes the peptide region was amplified by the polymerase chain reaction and sequenced. The deduced amino acid sequence was compared to those species where amyloid accumulation has not been detected. The DNA sequences of dog, polar bear, rabbit, cow, sheep, pig and guinea pig were compared and a phylogenetic tree was generated. We conclude that the amino acid sequence of dog and polar bear and other mammals which may form amyloid plaques is conserved and the species where amyloid has not been detected (mouse, rat) may be evolutionarily a distinct group. In addition, the predicted secondary structure of mouse and rat amyloid that differs from that of amyloid bearing species is its lack of propensity to form a beta sheeted structure. Thus, a cross-species examination of the amyloid peptide may suggest what is essential for amyloid deposition.

Identification of a Unique Amyloid Sequence in AA Amyloidosis of a Pig Associated With Streptococcus Suis Infection.

PubMed

Kamiie, J; Sugahara, G; Yoshimoto, S; Aihara, N; Mineshige, T; Uetsuka, K; Shirota, K

2017-01-01

Here we report a pig with amyloid A (AA) amyloidosis associated with Streptococcus suis infection and identification of a unique amyloid sequence in the amyloid deposits in the tissue. Tissues from the 180-day-old underdeveloped pig contained foci of necrosis and suppurative inflammation associated with S. suis infection. Congo red stain, immunohistochemistry, and electron microscopy revealed intense AA deposition in the spleen and renal glomeruli. Mass spectrometric analysis of amyloid material extracted from the spleen showed serum AA 2 (SAA2) peptide as well as a unique peptide sequence previously reported in a pig with AA amyloidosis. The common detection of the unique amyloid sequence in the current and past cases of AA amyloidosis in pigs suggests that this amyloid sequence might play a key role in the development of porcine AA amyloidosis. An in vitro fibrillation assay demonstrated that the unique AA peptide formed typically rigid, long amyloid fibrils (10 nm wide) and the N-terminus peptide of SAA2 formed zigzagged, short fibers (7 nm wide). Moreover, the SAA2 peptide formed long, rigid amyloid fibrils in the presence of sonicated amyloid fibrils formed by the unique AA peptide. These findings indicate that the N-terminus of SAA2 as well as the AA peptide mediate the development of AA amyloidosis in pigs via cross-seeding polymerization.

Sputter deposition of indium tin oxide onto zinc pthalocyanine: Chemical and electronic properties of the interface studied by photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Gassmann, Jürgen; Brötz, Joachim; Klein, Andreas

2012-02-01

The interface chemistry and the energy band alignment at the interface formed during sputter deposition of transparent conducting indium tin oxide (ITO) onto the organic semiconductor zinc phtalocyanine (ZnPc), which is important for inverted, transparent, and stacked organic light emitting diodes, is studied by in situ photoelectron spectroscopy (XPS and UPS). ITO was sputtered at room temperature and a low power density with a face to face arrangement of the target and substrate. With these deposition conditions, no chemical reaction and a low barrier height for charge injection at this interface are observed. The barrier height is comparable to those observed for the reverse deposition sequence, which also confirms the absence of sputter damage.

Sequencing intractable DNA to close microbial genomes.

PubMed

Hurt, Richard A; Brown, Steven D; Podar, Mircea; Palumbo, Anthony V; Elias, Dwayne A

2012-01-01

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.