Role of Vision and Mechanoreception in Bed Bug, Cimex lectularius L. Behavior

PubMed Central

Singh, Narinderpal; Wang, Changlu; Cooper, Richard

2015-01-01

The role of olfactory cues such as carbon dioxide, pheromones, and kairomones in bed bug, Cimex lectularius L. behavior has been demonstrated. However, the role of vision and mechanoreception in bed bug behavior is poorly understood. We investigated bed bug vision by determining their responses to different colors, vertical objects, and their ability to detect colors and vertical objects under low and complete dark conditions. Results show black and red paper harborages are preferred compared to yellow, green, blue, and white harborages. A bed bug trapping device with a black or red exterior surface was significantly more attractive to bed bugs than that with a white exterior surface. Bed bugs exhibited strong orientation behavior toward vertical objects. The height (15 vs. 30 cm tall) and color (brown vs. black) of the vertical object had no significant effect on orientation behavior of bed bugs. Bed bugs could differentiate color and detect vertical objects at very low background light conditions, but not in complete darkness. Bed bug preference to different substrate textures (mechanoreception) was also explored. Bed bugs preferred dyed tape compared to painted tape, textured painted plastic, and felt. These results revealed that substrate color, presence of vertical objects, and substrate texture affect host-seeking and harborage-searching behavior of bed bugs. Bed bugs may use a combination of vision, mechanoreception, and chemoreception to locate hosts and seek harborages. PMID:25748041

Role of vision and mechanoreception in bed bug, Cimex lectularius L. behavior.

PubMed

Singh, Narinderpal; Wang, Changlu; Cooper, Richard

2015-01-01

The role of olfactory cues such as carbon dioxide, pheromones, and kairomones in bed bug, Cimex lectularius L. behavior has been demonstrated. However, the role of vision and mechanoreception in bed bug behavior is poorly understood. We investigated bed bug vision by determining their responses to different colors, vertical objects, and their ability to detect colors and vertical objects under low and complete dark conditions. Results show black and red paper harborages are preferred compared to yellow, green, blue, and white harborages. A bed bug trapping device with a black or red exterior surface was significantly more attractive to bed bugs than that with a white exterior surface. Bed bugs exhibited strong orientation behavior toward vertical objects. The height (15 vs. 30 cm tall) and color (brown vs. black) of the vertical object had no significant effect on orientation behavior of bed bugs. Bed bugs could differentiate color and detect vertical objects at very low background light conditions, but not in complete darkness. Bed bug preference to different substrate textures (mechanoreception) was also explored. Bed bugs preferred dyed tape compared to painted tape, textured painted plastic, and felt. These results revealed that substrate color, presence of vertical objects, and substrate texture affect host-seeking and harborage-searching behavior of bed bugs. Bed bugs may use a combination of vision, mechanoreception, and chemoreception to locate hosts and seek harborages.

Stratigraphy and depositional environment of upper Cambrian Red Lion Formation, southwestern Montana

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

Hayden, L.L.; Bush, J.H.

1987-08-01

The Red Lion Formation was examined along a northwest-southeast transect from Missoula to Bozeman, Montana. Lateral equivalents are the Snowy Range Formation east of Bozeman and the upper Fishtrap Dolomite in northwest Montana. The basal Dry Creek Member (0-5 m) consists of shale interbedded with quartz siltstones and sandstones. The overlying Sage Member, up to 115 meters in thickness, is characterized by ribbon carbonate beds containing lime mudstone and quartzose calcisiltite couplets arranged in fining-upward sequences 1-5 cm thick. Couplets are interlayered in places with thin (1-5 cm) to medium bedded (6-70 cm) units of laminated and non-laminated calcareous siltstones,more » flat-pebble conglomerates, trilobite packstones, cryptalgal boundstones, bioturbated lime mudstones and shales. In places, the upper Sage contains columnar and domal algal features. The Red Lion Formation is considered to be one Grand Cycle with the Dry Creek representing a lower inner detrital half-cycle and the Sage an upper carbonate half-cycle. The Dry Creek formed as the result of a westward clastic pulse from the inner detrital belt across an intrashelf basin onto outer middle carbonate peritidal complexes of the underlying Pilgrim Formation. Lower Sage ribbon rocks were deposited in storm-crossed, below wave-base areas. During deposition of the upper Sage, shallowing formed discontinuous algal-peritidal complexes over much of western and central Montana. These complexes were less extensive than earlier Cambrian buildups owing to slower rates of basin subsidence and clastic input suppressing carbonate production.« less

Deccan volcanism and K-T boundary signatures

NASA Technical Reports Server (NTRS)

Murali, A. V.; Schuraytz, B. C.; Parekh, P. P.

1988-01-01

The Deccan Traps in the Indian subcontinent represent one of the most extensive flood basalt provinces in the world. These basalts occur mainly as flat-lying, subaerially erupted tholeiitic lava flows, some of which are traceable for distances of more than 100 km. Offshore drilling and geophysical surveys indicate that a part of the Deccan subsided or was downfaulted to the west beneath the Arabian Sea. The presence of 1 to 5 m thick intertrappean sediments deposited by lakes and rivers indicates periods of quiescence between eruptions. The occurrence of numerous red bole beds among the flows suggests intense weathering of flow tops between eruptive intervals. Although the causative relationship of the Cretaceous-Tertiary (K-T) biotic extinctions to Deccan volcanism is debatable, the fact that the main Deccan eruptions straddle the K-T event appears beyond doubt from the recent Ar-40/Ar-39 ages of various Deccan flows. This temporal relationship of the K-T event with Deccan volcanism makes the petrochemical signatures of the entire Deccan sequence (basalt flows, intercalated intertrappean sediments, infratrappean Lameta beds (with dinosaur fossils), and the bole beds) pertinent to studies of the K-T event. The results of ongoing study is presented.

Nugget-Navaho-Aztec sandstone: interaction of eolian sand sea with Andean-type volcanic arc

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

Marzolf, J.E.

1986-05-01

The Nugget-Navaho-Aztec sand sea was deposited east of an Andean-type volcanic arc. During the early stage of eolian deposition, fluvially transported sand was concentrated in the marine littoral zone and returned inland by onshore winds from the northwest. With progressive development of the arc, the sea withdrew. Wind direction changed from northwest to northeast. Previously deposited eolian sand was transported southwestward into the volcanic arc. Proximity of the arc can be detected with great difficulty by examining eolian and underlying red-bed facies. In southern Nevada, the volcanic arc is undetectable in eolian facies, but thin sandstone beds containing volcanic clastsmore » or weathered feldspar in the finer grained red-bed facies indicate arc volcanism; volcanic clasts are distinct in a basal conglomerate. Westward into California, the sub-Aztec Sandstone contains volcanic pebbles. The upper part of the Aztec Sandstone contains a 1 to 2-m thick volcaniclastic siltstone. Farther west, the Aztec Sandstone is interbedded with volcanic flows, ash flows, and flow breccias. These rocks might easily be mistaken for red beds in well cores or cuttings. Sand in sets of large-scale cross-beds remain virtually identical in composition and texture to sand in eolian facies of the Colorado Plateau. Where sets of eolian cross-beds lie on volcanics, the quartzose sandstone contains pebble to cobble-size volcanic clasts. Locally, cross-bed sets of yellowish-white, quartzose sandstone alternate with purplish-gray cross-bed sets containing numerous pebble to cobble-size volcanic clasts. The ability to recognize volcanic indicators within Nugget-Navaho-Aztec eolian facies is important in delineating the western margin of the back-arc eolian basin.« less

The 1.1-Ga Midcontinent Rift System, central North America: sedimentology of two deep boreholes, Lake Superior region

NASA Astrophysics Data System (ADS)

Ojakangas, Richard W.; Dickas, Albert B.

2002-03-01

The Midcontinent Rift System (MRS) of central North America is a 1.1-Ga, 2500-km long structural feature that has been interpreted as a triple-junction rift developed over a mantle plume. As much as 20 km of subaerial lava flows, mainly flood basalts, are overlain by as much as 10 km of sedimentary rocks that are mostly continental fluvial red beds. This rock sequence, known as the Keweenawan Supergroup, has been penetrated by a few deep boreholes in the search for petroleum. In this paper, two deep boreholes in the Upper Peninsula of Michigan are described in detail for the first time. Both the Amoco Production #1-29R test, herein referred to as the St. Amour well, and the nearby Hickey Creek well drilled by Cleveland Cliffs Mining Services, were 100% cored. The former is 7238 ft (2410 m) deep and the latter is 5345 ft (1780 m) deep. The entirety of the stratigraphic succession of the Hickey Creek core correlates very well with the upper portion of the St. Amour core, as determined by core description and point-counting of 43 thin sections selected out of 100 studied thin sections. Two Lower Paleozoic units and two Keweenawan red bed units—the Jacobsville Sandstone and the underlying Freda Sandstone—are described. The Jacobsville is largely a feldspatholithic sandstone and the Freda is largely a lithofeldspathic sandstone. Below the Freda, the remaining footage of the St. Amour core consists of a thick quartzose sandstone unit that overlies a heterogenous unit of intercalated red bed units of conglomerate, sandstone, siltstone, and shale; black shale; individual basalt flows; and a basal ignimbritic rhyolite. This lower portion of the St. Amour core presents an enigma, as it correlates very poorly with other key boreholes located to the west and southwest. While a black shale sequence is similar to the petroleum-bearing Nonesuch Formation farther west, there is no conglomerate unit to correlate with the Copper Harbor Conglomerate. Other key boreholes are distributed over a 1300-km distance along the better known southwest arm of the triple-junction MRS, and can be correlated rather well with the units that are exposed in the Lake Superior region. However, a definitive explanation of the anomalous, deeper St. Amour stratigraphy is elusive and any explanation is tenuous. A possible explanation for this anomalous stratigraphy may be the geographic proximity of the St. Amour borehole to the Keweenawan Hot Spot (mantle plume), the suggested thermal force behind the development of the MRS. Similarly, a drastic change in structural architecture may be explained by this geographic relationship. Thus, within the locale of this rifting center, complexities of expansion tectonics may well be responsible for igneous and sedimentary sequences that differ considerably from those found farther west along the rift arm.

Tectonic rotations south of the Bohemian Massif from palaeomagnetic directions of Permian red beds in Hungary

USGS Publications Warehouse

Marton, E.; Elston, D.P.

1987-01-01

Palaeomagnetic studies were carried out in Permian red beds of the Balaton Highlands, the Mecsek Mountains and the Bu??kk Mountains of Hungary. Statistically well defined directions were obtained from six localities in the Balaton Highlands and two localities in the Mecsek Mountains. No meaningful results were obtained from the Bu??kk Mountains. Three magnetic components were identified from red beds of the Balaton Highlands: (1) in haematite with a very high unblocking temperature (700??C), interpreted as a Permian magnetization (Dc= 79??, Ic=-11??, k = 24, ??95 = 13.6 ??), in six samples from three beds in a single locality (2) a secondary but ancient component residing mainly inmaghemite (D = 314??, I = 49??, k = 48, ??95 = 10.0??), in 84 samples from six localities with a within-locality scatter increasing on unfolding; and (3) a direction parallel to the present field (D = 7??, I = 62??, k = 46, ??95 = 7.7 ??), in nine samples from a single locality. For the Balaton Highlands, the component 1 direction agrees with directions obtained from Permian red beds and volcanics in the eastern part of the Southern and Eastern Alps and the Inner West Carpathians. All show large, apparent rotations relative to stable Europe since the Permian. Component 2 is of post-folding (post-Aptian) age. Its direction agrees with known Late Cretaceous directions from the Transdanubian Central Mountains, which also show significant counterclockwise rotation relative to stable Europe. The characteristic magnetization for the Mecsek Mountains resides in haematite and may be primary. The directions indicate only a slight net counterclockwise rotation of the Mecsek Mountains with respect to stable Europe since the Permian. ?? 1987.

Production of red mold rice using a modified Nagata type koji maker.

PubMed

Chiu, Chiu-Hsia; Ni, Kuang-Huei; Guu, Yuan-Kuang; Pan, Tzu-Ming

2006-11-01

In this research, a commercial koji maker with a rotary perforated bed of 5-m diameter was modified for red mold rice production. Monascus purpureus BCRC 31499 was selected for its high production capacities of monacolin K and red pigment. The selected strain was first cultivated in a 120-l submerged type fermentor at 34 degrees C and 2 vvm aeration rate with 60 rpm agitation for 5 days using 20% liquefied rice porridge as carbon source. The high concentration red mold rice broth (>3.5 g/ml) was harvested for inocula and well mixed with cooked rice to an initial concentration of 2% v/w. The inoculated cooked rice then was directed into the modified koji maker, in which temperature and humidity profiles were kept at varied levels at different stages, respectively. Air was circulated to remove fermentation heat while the perforated bed rotated slowly for providing mild agitation. Lag phase of the Monascus sp. in the modified koji maker was determined to be 16 h by the time the koji temperature raised rapidly. Water was added into the koji bed by a water curtain at the 36th hour to keep the moisture content of the rice koji at 50% or above. At the final stage, temperature was adjusted to 34 degrees C to direct red pigment production. After 7 days, 1,200-kg high quality red mold rice was harvested per batch. Labor costs, space, and fermentation time were reduced tremendously compared with those made by traditional methods.

25. Typical valves used to control flow into and out ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

25. Typical valves used to control flow into and out of filtration bed. Left valve (painted red) drains the bed, and center valve (painted green) admits water into the bed. The right valve is a cross over valve which is used to admit water into a dry bed from the bottom. This bottom fill excludes entrapped air as the bed is filled. When the water reached to top of the bed, filling is continued from the top of the bed. - Lake Whitney Water Filtration Plant, Filtration Plant, South side of Armory Street between Edgehill Road & Whitney Avenue, Hamden, New Haven County, CT

Northern Cascadia Subduction Zone Earthquake Records from Onshore and Offshore Core Data

NASA Astrophysics Data System (ADS)

Hausmann, R. B.; Goldfinger, C.; Black, B.; Romsos, C. G.; Galer, S.; Collins, T.

2016-12-01

We are investigating the paleoseismic record at Bull Run Lake, at the latitude of Portland, Oregon, central Cascadia margin. Bull Run is a landslide dammed lake in a cirque basin on the western flanks of Mt. Hood, 65 km east of Portland, and is the City of Portland's primary water supply. We collected full coverage high-resolution multibeam and backscatter data, high resolution CHIRP sub-bottom profiles, and seven sediment cores which contain a correlative turbidite sequence of post Mazama beds. The continuity of the turbidite record shows little or no relationship to the minor stream inlets, suggesting the disturbance beds are not likely to be storm related. CT and physical property data were used to separate major visible beds and background sedimentation, which also contain thin laminae. The XRF element Compton scattering may show grading due to mineralogical variation and a change in wave profile, commonly found at bed boundaries. We have identified 27 post -Mazama event beds and 5 ashes in the lake, and constructed an OxCal age model anchored by radiocarbon ages, the Mazama ash, and the twin Timberline ash beds. The radiocarbon ages, age model results, as well as electron microprobe (EMP) data clearly identify the Mazama ash at the base of our cores. Two closely-spaced ash beds in our cores likely correlate to the Timberline eruptive period at 1.5ka. The number, timing and sequence of the event beds, and physical property log correlation, as well as key bed characteristics, closely matches offshore turbidite sequences off northern Oregon. For example, key regional bed T11, observed as a thick two-pulse bed in all offshore cores, also anchors the Bull Run sequence. One difference is that the twin Timberline ash occupies the stratigraphic position of regional offshore paleoseismic bed T4, which is also a two pulse event at this latitude. The cores also contain many faint laminae that may contain a storm record, however, the identification of small beds is complicated by the low sedimentation rate and low resolution of the Bull Run cores. The watershed and lake may also contain evidence of crustal faulting, though the event sequence appears to be primarily that of the Cascadia subduction zone earthquake sequence. See also Goldfinger et al. for investigation of slope stability and ground motions at Bull Run and other Cascadia lakes.

Integrated approaches to terminal Proterozoic stratigraphy: an example from the Olenek Uplift, northeastern Siberia

NASA Technical Reports Server (NTRS)

Knoll, A. H.; Grotzinger, J. P.; Kaufman, A. J.; Kolosov, P.

1995-01-01

In the Olenek Uplift of northeastern Siberia, the Khorbusuonka Group and overlying Kessyusa and Erkeket formations preserve a significant record of terminal Proterozoic and basal Cambrian Earth history. A composite section more than 350 m thick is reconstructed from numerous exposures along the Khorbusuonka River. The Khorbusuonka Group comprises three principal sedimentary sequences: peritidal dolomites of the Mastakh Formation, which are bounded above and below by red beds; the Khatyspyt and most of the overlying Turkut formations, which shallow upward from relatively deep-water carbonaceous micrites to cross-bedded dolomitic grainstones and stromatolites; and a thin upper Turkut sequence bounded by karst surfaces. The overlying Kessyusa Formation is bounded above and below by erosional surfaces and contains additional parasequence boundaries internally. Ediacaran metazoans, simple trace fossils, and vendotaenids occur in the Khatyspyt Formation; small shelly fossils, more complex trace fossils, and acritarchs all appear near the base of the Kessyusa Formation and diversify upward. The carbon-isotopic composition of carbonates varies stratigraphically in a pattern comparable to that determined for other terminal Proterozoic and basal Cambrian successions. In concert, litho-, bio-, and chemostratigraphic data indicate the importance of the Khorbusuonka Group in the global correlation of terminal Proterozoic sedimentary rocks. Stratigraphic data and a recently determined radiometric date on basal Kessyusa volcanic breccias further underscore the significance of the Olenek region in investigations of the Proterozoic-cambrian boundary.

Integrated approaches to terminal Proterozoic stratigraphy: an example from the Olenek Uplift, northeastern Siberia.

PubMed

Knoll, A H; Grotzinger, J P; Kaufman, A J; Kolosov, P

1995-01-01

In the Olenek Uplift of northeastern Siberia, the Khorbusuonka Group and overlying Kessyusa and Erkeket formations preserve a significant record of terminal Proterozoic and basal Cambrian Earth history. A composite section more than 350 m thick is reconstructed from numerous exposures along the Khorbusuonka River. The Khorbusuonka Group comprises three principal sedimentary sequences: peritidal dolomites of the Mastakh Formation, which are bounded above and below by red beds; the Khatyspyt and most of the overlying Turkut formations, which shallow upward from relatively deep-water carbonaceous micrites to cross-bedded dolomitic grainstones and stromatolites; and a thin upper Turkut sequence bounded by karst surfaces. The overlying Kessyusa Formation is bounded above and below by erosional surfaces and contains additional parasequence boundaries internally. Ediacaran metazoans, simple trace fossils, and vendotaenids occur in the Khatyspyt Formation; small shelly fossils, more complex trace fossils, and acritarchs all appear near the base of the Kessyusa Formation and diversify upward. The carbon-isotopic composition of carbonates varies stratigraphically in a pattern comparable to that determined for other terminal Proterozoic and basal Cambrian successions. In concert, litho-, bio-, and chemostratigraphic data indicate the importance of the Khorbusuonka Group in the global correlation of terminal Proterozoic sedimentary rocks. Stratigraphic data and a recently determined radiometric date on basal Kessyusa volcanic breccias further underscore the significance of the Olenek region in investigations of the Proterozoic-cambrian boundary.

Copper Deposits in Sedimentary and Volcanogenic Rocks

USGS Publications Warehouse

Tourtelot, Elizabeth B.; Vine, James David

1976-01-01

Copper deposits occur in sedimentary and volcanogenic rocks within a wide variety of geologic environments where there may be little or no evidence of hydrothermal alteration. Some deposits may be hypogene and have a deep-seated source for the ore fluids, but because of rapid cooling and dilution during syngenetic deposition on the ocean floor, the resulting deposits are not associated with hydrothermal alteration. Many of these deposits are formed at or near major tectonic features on the Earth's crust, including plate boundaries, rift valleys, and island arcs. The resulting ore bodies may be stratabound and either massive or disseminated. Other deposits form in rocks deposited in shallow-marine, deltaic, and nonmarine environments by the movement and reaction of interstratal brines whose metal content is derived from buried sedimentary and volcanic rocks. Some of the world's largest copper deposits were probably formed in this manner. This process we regard as diagenetic, but some would regard it as syngenetic, if the ore metals are derived from disseminated metal in the host-rock sequence, and others would regard the process as epigenetic, if there is demonstrable evidence of ore cutting across bedding. Because the oxidation associated with diagenetic red beds releases copper to ground-water solutions, red rocks and copper deposits are commonly associated. However, the ultimate size, shape, and mineral zoning of a deposit result from local conditions at the site of deposition - a logjam in fluvial channel sandstone may result in an irregular tabular body of limited size; a petroleum-water interface in an oil pool may result in a copper deposit limited by the size and shape of the petroleum reservoir; a persistent thin bed of black shale may result in a copper deposit the size and shape of that single bed. The process of supergene enrichment has been largely overlooked in descriptions of copper deposits in sedimentary rocks. However, supergene processes may be involved during erosion of any primary ore body and its ultimate displacement and redeposition as a secondary deposit. Bleached sandstone at the surface may indicate significant ore deposits near the water table.

USE OF CORTICAL BONE FENESTRATION, AUTOGENOUS FREE SKIN GRAFT, AND THERMOGRAPHY FOR WOUND TREATMENT AND MONITORING IN A RED WOLF (CANIS RUFUS GREGORYI).

PubMed

Hurley-Sanders, Jennifer L; Sladky, Kurt K; Nolan, Elizabeth C; Loomis, Michael R

2015-09-01

A 2-yr-old female red wolf (Canis rufus gregoryi) sustained a degloving injury to the left thoracic limb while in a display habitat. Initial attempts to resolve the extensive wound by using conservative measures were unsuccessful. Subsequent treatment using a free skin graft consisted first of establishment of an adequate granulation bed via cortical bone fenestration. After establishment of a healthy granulation bed was achieved, free skin graft was harvested and transposed over the bed. To monitor viability and incorporation of the graft, serial thermographic imaging was performed. Thermography noninvasively detects radiant heat patterns and can be used to assess vascularization of tissue, potentially allowing early detection of graft failure. In this case, thermography documented successful graft attachment.

The Nature of Red-Sequence Cluster Spiral Galaxies

NASA Astrophysics Data System (ADS)

Kashur, Lane; Barkhouse, Wayne; Sultanova, Madina; Kalawila Vithanage, Sandanuwa; Archer, Haylee; Foote, Gregory; Mathew, Elijah; Rude, Cody; Lopez-Cruz, Omar

2017-01-01

Preliminary analysis of the red-sequence galaxy population from a sample of 57 low-redshift galaxy clusters observed using the KPNO 0.9m telescope and 74 clusters from the WINGS dataset, indicates that a small fraction of red-sequence galaxies have a morphology consistent with spiral systems. For spiral galaxies to acquire the color of elliptical/S0s at a similar luminosity, they must either have been stripped of their star-forming gas at an earlier epoch, or contain a larger than normal fraction of dust. To test these ideas we have compiled a sample of red-sequence spiral galaxies and examined their infrared properties as measured by 2MASS, WISE, Spitzer, and Herschel. These IR data allows us to estimate the amount of dust in each of our red-sequence spiral galaxies. We compare the estimated dust mass in each of these red-sequence late-type galaxies with spiral galaxies located in the same cluster field but having colors inconsistent with the red-sequence. We thus provide a statistical measure to discriminate between purely passive spiral galaxy evolution and dusty spirals to explain the presence of these late-type systems in cluster red-sequences.

Mesoarchean black shale -iron sedimentary sequences in Cleaverville Formation, Pilbara Australia: drilling preliminary result of DXCL2

NASA Astrophysics Data System (ADS)

Kiyokawa, S.; Ito, T.; Ikehara, M.; Yamaguchi, K. E.; Onoue, T.; Horie, K.; Sakamoto, R.; Teraji, S.; Aihara, Y.

2012-12-01

The 3.2-3.1 Ga Dixon island-Cleaverville formations are well-preserved hydrothermal oceanic sequence at oceanic island arc setting (Kiyokawa et al., 2002, 2006, 2012). The Dixon Island (3195+15 Ma) - Cleaverville (3108+13 Ma) formations formed volcano-sedimentary sequences with hydrothermal chert, black shale and banded iron formation to the top. Based on the scientific drilling as DXCL1 at 2007 and DXCL2 at 2011, lithology was clearly understood. Four drilling holes had been done at coastal sites; the Dixon Island Formation is DX site (100m) and the Cleaverville Formation is CL2 (40m), CL1 (60m) and CL3 (200m) sites and from stratigraphic bottom to top. These sequences formed coarsening and thickening upward black shale-BIF sequences. The Dixon Island Formation consists komatiite-rhyolite sequences with many hydrothermal veins and very fine laminated cherty rocks above them. The Cleaverville Formation contains black shale, fragments-bearing pyroclastic beds, white chert, greenish shale and BIF. Especially, CL3 core, which drilled through the Iron formation, shows siderite-chert beds above black shale identified before magnetite lamination bed. The magnetite bed formed very thin laminated bed with siderite lamination. This magnetite bed was covered by black shale beds again. New U-Pb SHRIMP data of the pyroclastic in black shale is 3109Ma. Estimated 2-8 cm/1000year sedimentation rate are identified in these sequences. Our preliminary result show that siderite and chert layers formed before magnetite iron sedimentation. The lower-upper sequence of organic carbon rich black shales are similar amount of organic content and 13C isotope (around -30per mill). So we investigate that the Archean iron formation, especially Cleaverville iron formation, was highly related by hydrothermal input and started pre-syn iron sedimentation at anoxic oceanic condition.

Three-dimensional mapping of red stingray ( Dasyatis akajei) movement with reference to bottom topography

NASA Astrophysics Data System (ADS)

Otaki, Takayoshi; Hamana, Masahiro; Tanoe, Hideaki; Miyazaki, Nobuyuki; Shibuno, Takuro; Komatsu, Teruhisa

2015-06-01

Most demersal fishes maintain strong relations with bottom substrates and bottom depths and/or topography during their lives. It is important to know these relations to for understand their lives. In Tokyo Bay, red stingray, Dasyatis akajei, classified as near-threatened species by IUCN, has increased since the 1980s. It is a top predator and engages in ecosystem engineer by mixing the sand bed surface through burring behavior, and greatly influences a coastal ecosystem. It is reported that this species invades in plage and tidal flats and has sometimes injured beachgoers and people gathering clams in Tokyo bay. Thus, it is necessary to know its behavior and habitat use to avoid accidents and to better conserve the biodiversity of ecosystems. However, previous studies have not examined its relationship with the bottom environment. This study aims to describe its behavior in relation to the bottom environment. We sounded three dimensional bottom topography of their habitat off Kaneda Cove in Tokyo Bay with interferometric sidescan sonar system and traced the movement of red stingrays by attaching a data logger system to survey their migration. The results revealed that red stingray repeated vertical movement between the surface and bottom, and used not only sand beds but also rocky beds.

Pediatric intensive care unit admission tool: a colorful approach.

PubMed

Biddle, Amy

2007-12-01

This article discusses the development, implementation, and utilization of our institution's Pediatric Intensive Care Unit (PICU) Color-Coded Admission Status Tool. Rather than the historical method of identifying a maximum number of staffed beds, a tool was developed to color code the PICU's admission status. Previous methods had been ineffective and led to confusion between the PICU leadership team and the administration. The tool includes the previously missing components of staffing and acuity, which are essential in determining admission capability. The PICU tool has three colored levels: green indicates open for admissions; yellow, admission alert resulting from available beds or because staffing is not equal to the projected patient numbers or required acuity; and red, admissions on hold because only one trauma or arrest bed is available or staffing is not equal to the projected acuity. Yellow and red designations require specific actions and the medical director's approval. The tool has been highly successful and significantly impacted nursing with the inclusion of the essential component of nurse staffing necessary in determining bed availability.

Experiments on Pool-riffle Sequences with Multi-fractional Sediment Bed During Floods

NASA Astrophysics Data System (ADS)

Rodriguez, J. F.; Vahidi, E.; Bayat, E.; de Almeida, G. A. M.; Saco, P. M.

2017-12-01

The morphodynamics of pools and riffles has been the subject of research for over a century and has more recently attracted intense attention for their central role in providing habitat diversity conditions, both in terms of flow and substrate. Initial efforts to explain the long-term stability of the pool-riffle (PR) sequences (often referred to as self-maintenance) focused almost exclusively on cross sectional flow characteristics (either average or near bed velocity or shear stress), using episodic shifts in higher shear stress or velocities from riffles to pools during floods (i.e. reversal conditions) as an indication of the long-term self-maintenance of the structures.. However, less attention has been paid to the interactions of flow unsteadiness, sediment supply and sedimentological contrasts as the drivers for maintaining PR sequences. Here we investigate these effects through laboratory experiments on a scaled-down PR sequence of an existing gravel bed river. Froude similitude and equality of Shields' number were applied to scale one- to four-year recurrence flood events and sediment size distributions, respectively. We conducted experiments with different hydrographs and different sedimentological conditions. In each experiment we continuously measured velocities and shear stresses (using acoustic velocity profilers) bed levels (using a bed profiler) and bed grain size distribution (using an automatic digital technique on the painted bed sediments) during the hydrographs. Our results show that the most important factors for self-maintenance were the sediment bed composition, the level of infilling of the pool and the sediment supply grainsize distribution. These results highlight the need to consider the time varying sedimentological characteristics of a PR sequence to assess its capacity for self-maintenance.

Bed II Sequence Stratigraphic context of EF-HR and HWK EE archaeological sites, and the Oldowan/Acheulean succession at Olduvai Gorge, Tanzania.

PubMed

Stanistreet, Ian G; McHenry, Lindsay J; Stollhofen, Harald; de la Torre, Ignacio

2018-04-20

Archaeological excavations at EF-HR and HWK EE allow reassessment of Bed II stratigraphy within the Junction Area and eastern Olduvai Gorge. Application of Sequence Stratigraphic methods provides a time-stratigraphic framework enabling correlation of sedimentary units across facies boundaries, applicable even in those areas where conventional timelines, such as tephrostratigraphic markers, are absent, eroded, or reworked. Sequence Stratigraphically, Bed II subdivides into five major Sequences 1 to 5, all floored by major disconformities that incise deeply into the underlying succession, proving that simple "layer cake" stratigraphy is inappropriate. Previous establishment of the Lemuta Member has invalidated the use of Tuff IIA as the boundary between Lower and Middle Bed II, now redefined at the disconformity between Sequences 2 and 3, a lithostratigraphic contact underlying the succession containing the Lower, Middle, and Upper Augitic Sandstones. HWK EE site records Oldowan technology in the Lower Augitic Sandstone at the base of Sequence 3, within Middle Bed II. We suggest placement of recently reported Acheulean levels at FLK W within the Middle Augitic Sandstone, thus emphasizing that handaxes are yet to be found in earlier stratigraphic units of the Olduvai sequence. This would place a boundary between the Oldowan and Acheulean technologies at Olduvai in the Tuff IIB zone or earliest Middle Augitic Sandstone. A major disconformity between Sequences 3 and 4 at and near EF-HR cuts through the level of Tuff IIC, placing the main Acheulean EF-HR assemblage at the base of Sequence 4, within Upper rather than Middle Bed II. Sequence stratigraphic methods also yield a more highly resolved Bed II stratigraphic framework. Backwall and sidewall surveying of archaeological trenches at EF-HR and HWK EE permits definition of "Lake-parasequences" nested within the major Sequences that record downcutting of disconformities associated with lake regression, then sedimentation associated with lake transgression, capped finally by another erosional disconformity or hiatal paraconformity caused by the next lake withdrawal. On a relative time-scale rather than a vertical metre scale, the resulting Wheeler diagram framework provides a basis for recognizing time-equivalent depositional episodes and the position of time gaps at various scales. Relative timing of archaeological assemblage levels can then be differentiated at a millennial scale within this framework. Copyright © 2018 Elsevier Ltd. All rights reserved.

Facies architecture of basin-margin units in time and space: Lower to Middle Miocene Sivas Basin, Turkey

NASA Astrophysics Data System (ADS)

Çiner, A.; Kosun, E.

2003-04-01

The Miocene Sivas Basin is located within a collision zone, forming one of the largest basins in Central Turkey that developed unconformably on a foundered Paleozoic-Mesozoic basement and Eocene-Oligocene deposits. The time and space relationships of sedimentary environments and depositional evolution of Lower to Middle Miocene rocks exposed between Zara and Hafik towns is studied. A 4 km thick continuous section is subdivided into the Agilkaya and Egribucak Formations. Each formation shows an overall fining upward trend and contains three members. Although a complete section is present at the western part (near Hafik) of the basin, to the east the uppermost two members (near Zara) are absent. The lower members of both formations are composed of fluvial sheet-sandstone and red mudstone that migrate laterally on a flood basin within a semi-arid fan system. In the Agilkaya Formation that crops out near Zara, alluvial fans composed of red-pink volcanic pebbles are also present. The middle members are composed of bedded to massive gypsum and red-green mudstone of a coastal and/or continental sabkha environment. While the massive gypsum beds reach several 10’s of m in Hafik area, near Zara, they are only few m thick and alternate with green mudstones. In Hafik, bedded gypsums are intercalated with lagoonal dolomitic limestone and bituminous shale in the Agilkaya Formation and with fluvial red-pink sandstone-red mudstone in the Egribucak Formation. The upper members are made up of fossiliferous mudstone and discontinuous sandy limestone beds with gutter casts, HCS, and 3-D ripples. They indicate storm-induced sedimentation in a shallow marine setting. The disorganized accumulations of ostreid and cerithiid shells, interpreted as coquina bars, are the products of storm generated reworking processes in brackish environments. Rapid vertical and horizontal facies changes and the facies associations in both formations reflect the locally subsiding nature of this molassic basin.

The accelerated build-up of the red sequence in high-redshift galaxy clusters

NASA Astrophysics Data System (ADS)

Cerulo, P.; Couch, W. J.; Lidman, C.; Demarco, R.; Huertas-Company, M.; Mei, S.; Sánchez-Janssen, R.; Barrientos, L. F.; Muñoz, R. P.

2016-04-01

We analyse the evolution of the red sequence in a sample of galaxy clusters at redshifts 0.8 < z < 1.5 taken from the HAWK-I Cluster Survey (HCS). The comparison with the low-redshift (0.04 < z < 0.08) sample of the WIde-field Nearby Galaxy-cluster Survey (WINGS) and other literature results shows that the slope and intrinsic scatter of the cluster red sequence have undergone little evolution since z = 1.5. We find that the luminous-to-faint ratio and the slope of the faint end of the luminosity distribution of the HCS red sequence are consistent with those measured in WINGS, implying that there is no deficit of red galaxies at magnitudes fainter than M_V^{ast } at high redshifts. We find that the most massive HCS clusters host a population of bright red sequence galaxies at MV < -22.0 mag, which are not observed in low-mass clusters. Interestingly, we also note the presence of a population of very bright (MV < -23.0 mag) and massive (log (M*/M⊙) > 11.5) red sequence galaxies in the WINGS clusters, which do not include only the brightest cluster galaxies and which are not present in the HCS clusters, suggesting that they formed at epochs later than z = 0.8. The comparison with the luminosity distribution of a sample of passive red sequence galaxies drawn from the COSMOS/UltraVISTA field in the photometric redshift range 0.8 < zphot < 1.5 shows that the red sequence in clusters is more developed at the faint end, suggesting that halo mass plays an important role in setting the time-scales for the build-up of the red sequence.

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

PubMed

Benoit, Joshua B; Adelman, Zach N; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C; Szuter, Elise M; Hagan, Richard W; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M; Nelson, David R; Rosendale, Andrew J; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R; Ioannidis, Panagiotis; Waterhouse, Robert M; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J Spencer; Gondhalekar, Ameya D; Scharf, Michael E; Peterson, Brittany F; Raje, Kapil R; Hottel, Benjamin A; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S T; Duncan, Elizabeth J; Murali, Shwetha C; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C; Muzny, Donna M; Wheeler, David; Panfilio, Kristen A; Vargas Jentzsch, Iris M; Vargo, Edward L; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T; Anderson, Michelle A E; Jones, Jeffery W; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D; Attardo, Geoffrey M; Robertson, Hugh M; Zdobnov, Evgeny M; Ribeiro, Jose M C; Gibbs, Richard A; Werren, John H; Palli, Subba R; Schal, Coby; Richards, Stephen

2016-02-02

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

PubMed Central

Benoit, Joshua B.; Adelman, Zach N.; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C.; Szuter, Elise M.; Hagan, Richard W.; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M.; Nelson, David R.; Rosendale, Andrew J.; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M.; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R.; Ioannidis, Panagiotis; Waterhouse, Robert M.; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J. Spencer; Gondhalekar, Ameya D.; Scharf, Michael E.; Peterson, Brittany F.; Raje, Kapil R.; Hottel, Benjamin A.; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S. T.; Duncan, Elizabeth J.; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Wheeler, David; Panfilio, Kristen A.; Vargas Jentzsch, Iris M.; Vargo, Edward L.; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T.; Anderson, Michelle A. E.; Jones, Jeffery W.; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D.; Attardo, Geoffrey M.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Ribeiro, Jose M. C.; Gibbs, Richard A.; Werren, John H.; Palli, Subba R.; Schal, Coby; Richards, Stephen

2016-01-01

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

Remagnetization mechanisms in Triassic red beds from South China

NASA Astrophysics Data System (ADS)

Jiang, Zhaoxia; Liu, Qingsong; Dekkers, Mark J.; Zhao, Xiang; Roberts, Andrew P.; Yang, Zhenyu; Jin, Chunsheng; Liu, Jianxing

2017-12-01

Paleogeographic reconstructions based on paleomagnetic data rely on the reliability of the natural remanent magnetization (NRM) as a primary geomagnetic signal. Remagnetizations, however, can be common in many rock types, including late Paleozoic and Mesozoic red beds, and they complicate paleogeographic interpretations. Extracting the primary NRM from partially remagnetized rocks, and understanding the remagnetization mechanism are important in these contexts. We carried out a systematic paleomagnetic study of red bed samples from the Triassic Huangmaqing Formation, Nanjing (32.0°N, 118.9°E), South China. Two NRM components carried by secondary and primary hematite are isolated in 47 of the 94 samples studied, where the latter component has a direction in stratigraphic coordinates of D = 29.2 °, I = 34.6 ° (α95 = 10.9 °, 47 samples from 6 sites) that yields a paleopole of λ = 60.8°N, ϕ = 228.1°E, dp / dm = 12.5 / 7.2, which is consistent with Triassic pole positions for the South China Block. A secondary chemical remanent magnetization (CRM) (D = 227.1 °, I = 80.8 °, α95 = 7.3 °) is documented in all 94 samples from 10 sites and is carried by pigmentary hematite that is inferred to have been generated by magnetite oxidation during orogenic activity. This secondary component has steep inclinations and is interpreted to have been influenced by a combination of the remanence carried by original parent magnetite, the orogenic stress field, and the prevailing geomagnetic field direction during deformation. This CRM direction is recorded commonly by red beds from the South China Block, and is significant for regional tectonic studies in the area.

Acquisition of chemical remanent magnetization during experimental ferrihydrite-hematite conversion in Earth-like magnetic field-implications for paleomagnetic studies of red beds

NASA Astrophysics Data System (ADS)

Jiang, Zhaoxia; Liu, Qingsong; Dekkers, Mark J.; Tauxe, Lisa; Qin, Huafeng; Barrón, Vidal; Torrent, José

2015-10-01

Hematite-bearing red beds are renowned for their chemical remanent magnetization (CRM). If the CRM was acquired substantially later than the sediment was formed, this severely compromises paleomagnetic records. To improve our interpretation of the natural remanent magnetization, the intricacies of the CRM acquisition process must be understood. Here, we contribute to this issue by synthesizing hematite under controlled 'Earth-like' field conditions (≲ 100 μ T). CRM was imparted in 90 oriented samples with varying inclinations. The final synthesis product appeared to be dominated by hematite with traces of ferrimagnetic iron oxides. When the magnetic field intensity is ≳ 40 μ T, the CRM records the field direction faithfully. However, for field intensities ≲ 40 μ T, the CRM direction may deviate considerably from that of the applied field during synthesis. The CRM intensity normalized by the isothermal remanent magnetization (CRM/IRM@2.5 T) increases linearly with the intensity of growth field, implying that CRM could potentially be useful for relative paleointensity studies if hematite particles of chemical origins have consistent properties. CRM in hematite has a distributed unblocking temperature spectrum from ∼200 to ∼650 °C, while hematite with a depositional remanent magnetization (DRM) has a more confined spectrum from ∼ 600to 680 °C because it is usually coarser-grained and more stoichiometric. Therefore, the thermal decay curves of CRM with their concave shape are notably different from their DRM counterparts which are convex. These differences together are suggested to be a potential discriminator of CRM from DRM carried by hematite in natural red beds, and of significance for the interpretation of paleomagnetic studies on red beds.

Paleozoic sedimentary rocks in the Red Dog Zn-Pb-Ag district and vicinity, western Brooks Range, Alaska: provenance, deposition, and metallogenic significance

USGS Publications Warehouse

Slack, John F.; Dumoulin, Julie A.; Schmidt, J.M.; Young, L.E.; Rombach, Cameron

2004-01-01

The distribution and composition of Paleozoic strata in the western Brooks Range may have played a fundamental role in Zn-Pb mineralization of the Red Dog district. In our model, deposition and early lithification of biogenic chert and bedded siliceous rocks in the upper part of the Kuna Formation served as a regional hydrologic seal, acting as a cap rock to heat and hydrothermal fluids during Late Mississippian base-metal mineralization. Equally important was the iron-poor composition of black shales of the Kuna Formation (i.e., low Fe/Ti ratios), which limited synsedimentary pyrite formation in precursor sediments, resulting in significant H2S production in pore waters through the interaction of aqueous sulfate with abundant organic matter. This H2S may have been critical to the subsurface deposition of the huge quantities of Zn and Pb in the district. On the basis of this model, we propose that low Fe/Ti and S/C ratios in black shale sequences are potential basin-scale exploration guides for giant sediment-hosted, stratiform Zn-Pb-Ag deposits.

Supply-Limited Bedforms in a Gravel-Sand Transition

NASA Astrophysics Data System (ADS)

Venditti, J. G.; Nittrouer, J. A.; Humphries, R. P.; Allison, M. A.

2009-12-01

Rivers often exhibit an abrupt transition from gravel to sand-bedded conditions as river channel slopes decrease. A distinct suite of bedforms has been observed through these reaches where sand supply to the bed is limited. The suite of bedforms includes a sequence of sand ribbons, barchans, and channel spanning dunes as sediment supply increases in the downstream direction. While these bedforms have been extensively documented in laboratory channels, there are relatively few observations of this sequence of supply-limited bedforms from large natural channels. Here we examine the sequence through the gravel-sand transition of the Fraser River in Southwestern British Columbia. We mapped the bed using multi-beam swath-bathymetry (Reson 8101 Seabat) at high flow (~9,000 m3s-1) immediately following a high peak flow of 11,800 m3s-1 in June 2007 The bed material grades from >70% gravel to entirely sand through the reach. The bedforms follow the expected sequence where sand ribbons and barchanoid forms cover the bed where it is primarily gravel. Channel spanning dunes form as the sand bed coverage increases. Bedform dimensions (height and length) increase moving downstream as the sand moving on the bed increases. Supply-unlimited bedforms typically scale with the flow depth where the height is 1/5 the flow depth. The bedforms developed over the gravel are undersized by this criterion. Downstream, where the bed is dominantly sand, bedforms do scale with flow depth. These data highlight the dominant role sediment supply can play in bedform morphology and scaling, confirming patterns observed in laboratory data.

Effect of leg exercise training on vascular volumes during 30 days of 6 deg head-down bed rest

NASA Technical Reports Server (NTRS)

Greenleaf, J. E.; Vernikos, J.; Wade, C. E.; Barnes, P. R.

1992-01-01

In order to investigate the effects of leg exercise training on vascular volumes during 30 d of 6-deg head-down bed rest, plasma and red cell volumes, body density, and water balance were measured in 19 men confined to bed rest (BR). One group had no exercise training (NOE), another near-maximal variable-intensity isotonic exercise (ITE) for 60 min/d, and the third near-maximal intermittent isokinetic exercise (IKE) for 60 min/d. Mean energy costs for the NOE, IKE, and ITE regimens were determined. Body densities within groups and mean urine volumes between groups were unchanged during BR. Changes in red cell volume followed changes in plasma volume. There was close coupling between resting plasma volume and plasma protein and osmotic content. It is argued that the ITE training protocol is better than the IKE protocol for maintaining plasma volume during prolonged exposure to BR.

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.

Deposition and deformation of fluvial-lacustrine sediments of the Upper Triassic-Lower Jurassic Whitmore Point Member, Moenave Formation, northern Arizona

NASA Astrophysics Data System (ADS)

Tanner, Lawrence H.; Lucas, Spencer G.

2010-01-01

The stratigraphic section of the Upper Triassic-Lower Jurassic Whitmore Point Member of the Moenave Formation at Potter Canyon, Arizona, comprises c. 26 m of gray to black shales and red mudstones interbedded with mainly sheet-like siltstones and sandstones. These strata represent deposition from suspension and sheetflow processes in shallow, perennial meromictic to ephemeral lakes, and on dry mudflats of the terminal floodout of the northward-flowing Moenave stream system. The lakes were small, as indicated by the lack of shoreline features and limited evidence for deltas. Changes in base level, likely forced by climate change, drove the variations between mudflat and perennial lacustrine conditions. Lenticular sandstones that occur across the outcrop face in the same stratigraphic interval in the lower part of the sequence represent the bedload fill of channels incised into a coarsening-upward lacustrine sequence following a fall in base level. These sandstones are distinctive for the common presence of over-steepened bedding, dewatering structures, and less commonly, folding. Deformation of these sandstones is interpreted as aseismic due to the lack of features typically associated with seismicity, such as fault-graded bedding, diapirs, brecciated fabrics and clastic dikes. Rapid deposition of the sands on a fluid-rich substrate produced a reverse density gradient that destabilized, and potentially fluidized the underlying, finer-grained sediments. This destabilization allowed synsedimentary subsidence of most of the channel sands, accompanied by longitudinal rotation and/or ductile deformation of the sand bodies.

Distinct Element Method modelling of fold-related fractures in a multilayer sequence

NASA Astrophysics Data System (ADS)

Kaserer, Klemens; Schöpfer, Martin P. J.; Grasemann, Bernhard

2017-04-01

Natural fractures have a significant impact on the performance of hydrocarbon systems/reservoirs. In a multilayer sequence, both the fracture density within the individual layers and the type of fracture intersection with bedding contacts are key parameters controlling fluid pathways. In the present study the influence of layer stacking and interlayer friction on fracture density and connectivity within a folded sequence is systematically investigated using 2D Distinct Element Method modelling. Our numerical approach permits forward modelling of both fracture nucleation/propagation/arrest and (contemporaneous) frictional slip along bedding planes in a robust and mechanically sound manner. Folding of the multilayer sequence is achieved by enforcing constant curvature folding by means of a velocity boundary condition at the model base, while a constant overburden pressure is maintained at the model top. The modelling reveals that with high bedding plane friction the multilayer stack behaves mechanically as a single layer so that the neutral surface develops in centre of the sequence and fracture spacing is controlled by the total thickness of the folded sequence. In contrast, low bedding plane friction leads to decoupling of the individual layers (flexural slip folding) so that a neutral surface develops in the centre of each layer and fracture spacing is controlled by the thickness of the individual layers. The low interfacial friction models illustrate that stepping of fractures across bedding planes is a common process, which can however have two contrasting origins: The mechanical properties of the interface cause fracture stepping during fracture propagation. Originally through-going fractures are later offset by interfacial slip during folding. A combination of these two different origins may lead to (apparently) inconsistent fracture offsets across bedding planes within a flexural slip fold.

Effect of acorn moisture content at sowing on germination and seedling growth of white oak and northern red oak

Treesearch

Shi-Jean Susana Sung; Paul P. Kormanik; Catharine D. Cook; Stanley J. Zarnoch; Taryn L. Kormanik

2006-01-01

White oak (Quercus alba L.) and northern red oak (Q. rubra L.) acorns were collected locally or from seed orchards in October 2002. Mean acorn moisture content (MC) was 48 percent for white oak and 39 percent for northern red oak. These acorns were air dried to different MCs before being sown into nursery beds in early December...

The Transfiguration continental red-bed Cu-Pb-Zn-Ag deposit, Quebec Appalachians, Canada

NASA Astrophysics Data System (ADS)

Cabral, Alexandre Raphael; Beaudoin, Georges; Taylor, Bruce E.

2009-04-01

The Transfiguration Cu-Pb-Zn-Ag deposit, enclosed within reduced grey sandstone, is associated with continental red beds of the Lower Silurian Robitaille Formation in the Quebec Appalachians, Canada. The Robitaille Formation rests unconformably on foliated Cambro-Ordovician rocks. The unconformity is locally cut by barite veins. The basal unit of the Robitaille Formation comprises green wacke and pebble conglomerate, which locally contain calcite nodules. The latter have microstructures characteristic of alpha-type calcretes, such as “floating” fabrics, calcite-filled fractures (crystallaria) and circumgranular cracks. Massive, grey sandstone overlies the basal green wacke and pebble conglomerate unit, which is overlain, in turn, by red, fine-grained sandstone. Mineralisation occurred underneath the red sandstone unit, chiefly in the grey sandstone unit, as disseminated and veinlet sulphides. Chalcopyrite, the most abundant Cu sulphide, replaced early pyrite. Calcrete, disseminated carbonate and vein carbonate have stable isotope ratios varying from -7.5‰ to -1.1‰ δ13C and from 14.7‰ to 21.3‰ δ18O. The negative δ13C values indicate the oxidation of organic matter in a continental environment. Sulphur isotope ratios for pyrite, chalcopyrite and galena vary from -19‰ to 25‰ δ34S, as measured on mineral concentrates by a conventional SO2 technique. Laser-assisted microanalyses (by fluorination) of S isotopes in pyrite show an analogous range in δ34S values, from -21‰ to 25‰. Negative and positive δ34S values are compatible with bacterial sulphate reduction (BSR) in systems open and closed with respect to sulphate. We interpret similarly high δ34S values for sulphide concentrates (25.1‰) and for vein barite (26.2‰) to result from rapid and complete thermochemical reduction of pore-water sulphate. Two early to late diagenetic stages of mineralisation best explain the origin of the Transfiguration deposit. The first stage was characterised by the ponding of groundwater over the Taconian unconformity, recorded by calcrete and early pyrite formation via BSR in grey sandstone. Early pyrite contains up to 2 wt.% Pb, which is consistent with Pb fixation by sulphate-reducing bacteria. The second stage (II) is defined by the replacement of early pyrite by chalcopyrite, as well as by sulphide precipitation via either BSR or thermochemical sulphate reduction (TSR) in grey sandstone. This event resulted from the synsedimentary fault-controlled percolation and mixing of (1) an oxidising, sulphate-bearing cupriferous fluid migrating per descensum from the red-bed sequence and (2) a hydrocarbon-bearing fluid migrating per ascensum from the Cambro-Ordovician basement. Mixing between the two fluids led to sulphate reduction, causing Cu sulphide precipitation. The positive correlation between Cu and Fe3+/Fe2+ bulk rock values suggests that Fe acted as a redox agent during sulphate reduction. Stage II diagenetic fluid migration is tentatively attributed to the Late Silurian Salinic extensional event.

A TALE OF DWARFS AND GIANTS: USING A z = 1.62 CLUSTER TO UNDERSTAND HOW THE RED SEQUENCE GREW OVER THE LAST 9.5 BILLION YEARS

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

Rudnick, Gregory H.; Tran, Kim-Vy; Papovich, Casey

2012-08-10

We study the red sequence in a cluster of galaxies at z = 1.62 and follow its evolution over the intervening 9.5 Gyr to the present day. Using deep YJK{sub s} imaging with the HAWK-I instrument on the Very Large Telescope, we identify a tight red sequence and construct its rest-frame i-band luminosity function (LF). There is a marked deficit of faint red galaxies in the cluster that causes a turnover in the LF. We compare the red-sequence LF to that for clusters at z < 0.8, correcting the luminosities for passive evolution. The shape of the cluster red-sequence LFmore » does not evolve between z = 1.62 and z = 0.6 but at z < 0.6 the faint population builds up significantly. Meanwhile, between z = 1.62 and 0.6 the inferred total light on the red sequence grows by a factor of {approx}2 and the bright end of the LF becomes more populated. We construct a simple model for red-sequence evolution that grows the red sequence in total luminosity and matches the constant LF shape at z > 0.6. In this model the cluster accretes blue galaxies from the field whose star formation is quenched and who are subsequently allowed to merge. We find that three to four mergers among cluster galaxies during the 4 Gyr between z = 1.62 and z = 0.6 match the observed LF evolution between the two redshifts. The inferred merger rate is consistent with other studies of this cluster. Our result supports the picture that galaxy merging during the major growth phase of massive clusters is an important process in shaping the red-sequence population at all luminosities.« less

Effects of cylinder Reynolds number on the turbulent horseshoe vortex system and near wake of a surface-mounted circular cylinder

NASA Astrophysics Data System (ADS)

Kirkil, Gokhan; Constantinescu, George

2015-07-01

The turbulent horseshoe vortex (HV) system and the near-wake flow past a circular cylinder mounted on a flat bed in an open channel are investigated based on the results of eddy-resolving simulations and supporting flow visualizations. Of particular interest are the changes in the mean flow and turbulence statistics within the HV region as the necklace vortices wrap around the cylinder's base and the variation of the mean flow and turbulence statistics in the near wake, in between the channel bed and the free surface. While it is well known that the drag crisis induces important changes in the flow past infinitely long circular cylinders, the changes are less understood and more complex for the case of flow past a surface-mounted cylinder. This is because even at very high cylinder Reynolds numbers, ReD, the flow regime remains subcritical in the vicinity of the bed surface due to the reduction of the incoming flow velocity within the bottom boundary layer. The paper provides a detailed discussion of the changes in the flow physics between cylinder Reynolds numbers at which the flow in the upstream part of the separated shear layers (SSLs) is laminar (ReD = 16 000, subcritical flow regime) and Reynolds numbers at which the transition occurs inside the attached boundary layers away from the bed and the flow within the SSLs is turbulent (ReD = 5 ∗ 105, supercritical flow regime). The changes between the two regimes in the dynamics and level of coherence of the large-scale coherent structures (necklace vortices, vortex tubes shed in the SSLs and roller vortices shed in the wake) and their capacity to induce high-magnitude bed friction velocities in the mean and instantaneous flow fields and to amplify the near-bed turbulence are analyzed. Being able to quantitatively and qualitatively describe these changes is critical to understand Reynolds-number-induced scale effects on sediment erosion mechanisms around cylinders mounted on a loose bed, which is a problem of great practical relevance (e.g., for pier scour studies).

Bioremoval of heavy metals from industrial effluent by fixed-bed column of red macroalgae.

PubMed

Ibrahim, Wael M; Mutawie, Hawazin H

2013-02-01

Three different species of nonliving red algal biomass Laurancia obtusa, Geldiella acerosa and Hypnea sp. were used to build three types of fixed-bed column for the removal of toxic heavy metal ions such as Cu(2+), Zn(2+), Mn(2+) and Ni(2+) from industrial effluent. In general, the highest efficiency of metal ion bioremoval was recorded for algal column of L. obtusa followed by G. acerosa and the lowest one was recorded for Hypnea sp., with mean removal values of 94%, 85% and 71%, respectively. The obtained results showed that biological treatments of industrial effluents with these algal columns, using standard algal biotest, Pseudokirchneriella subcapitata, were capable of reducing effluent toxicities from 75% to 15%, respectively. Red algal column may be considered as an inexpensive and efficient alternative treatment for conventional removal technology, for sequestering heavy metal ions from industrial effluents.

Development of a Low Strain-Rate Gun Propellant Bed Compression Test and its Use in Evaluating Mechanical Response

DTIC Science & Technology

2016-09-01

heuristics, die and propellant geometries from similar facilities reported in the literature [2,3] and the DST Group design .  bed* (mm) φbed...compliance curves from the experimental data. In UNCLASSIFIED DST- Group -TR-3291 UNCLASSIFIED 18 Figure 13, the red axial compliance traces were...UNCLASSIFIED DST- Group -TR-3291 UNCLASSIFIED 46 At a test temperature of -60˚C, the equivalent strain rates are within the 10 to 500 s-1 given in

Induction log responses to layered, dipping, and anisotropic formations: Induction log shoulder-bed corrections to anisotropic formations and the effect of shale anisotropy in thinly laminated sand/shale sequences

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

Hagiwara, Teruhiko

1996-12-31

Induction log responses to layered, dipping, and anisotropic formations are examined analytically. The analytical model is especially helpful in understanding induction log responses to thinly laminated binary formations, such as sand/shale sequences, that exhibit macroscopically anisotropic: resistivity. Two applications of the analytical model are discussed. In one application we examine special induction log shoulder-bed corrections for use when thin anisotropic beds are encountered. It is known that thinly laminated sand/shale sequences act as macroscopically anisotropic: formations. Hydrocarbon-bearing formations also act as macroscopically anisotropic formations when they consist of alternating layers of different grain-size distributions. When such formations are thick, inductionmore » logs accurately read the macroscopic conductivity, from which the hydrocarbon saturation in the formations can be computed. When the laminated formations are not thick, proper shoulder-bed corrections (or thin-bed corrections) should be applied to obtain the true macroscopic formation conductivity and to estimate the hydrocarbon saturation more accurately. The analytical model is used to calculate the thin-bed effect and to evaluate the shoulder-bed corrections. We will show that the formation resistivity and hence the hydrocarbon saturation are greatly overestimated when the anisotropy effect is not accounted for and conventional shoulder-bed corrections are applied to the log responses from such laminated formations.« less

Spectral analysis of Deccan intrabasaltic bole beds: Implications for the formation and alteration of phyllosilicates on Mars

NASA Astrophysics Data System (ADS)

Craig, Patricia; Chevrier, Vincent; Sayyed, M. R. G.; Islam, R.

2017-01-01

To fully understand phyllosilicates on Mars, it is beneficial to study analog deposits on Earth. One attractive candidate for martian phyllosilicates is the intrabasaltic bole beds (palaeosols) from the Deccan Volcanic Province of India. Eleven samples from the upper-layer red Deccan bole beds and underlying yellow and green Deccan bole beds were analyzed by X-ray diffraction (XRD), near-infrared (1.0-2.5 μm) and mid-infrared (5-15 μm) reflectance spectroscopy. Analysis of the bole beds indicated that the red boles are composed of a mixture of montmorillonite and hematite, yellow boles contain vermiculite and minor montmorillonite and green boles are composed mainly of nontronite (smectite) and celadonite (mica). While the bole beds are all chemically similar to each other and to the underlying basalt from which they were weathered, they are mineralogically different. This suggests transformation from one mineral to the next without ion transfer or loss which could be indicative of a limited-water environment. In fact, celadonite can transform into smectites (such as montmorillonite), often with vermiculite as an intermediate step. This not only explains the stratigraphy and mineralogy of the Deccan bole beds but may also explain the layered phyllosilicates identified in various, global locations on Mars. The transition observed in the Deccan bole beds suggests an evolution of the alteration process from deuteric alteration to low-temperature weathering, likely due to changes in temperature, in a closed system (no significant ion transfer) as evidenced by the minerals' similar chemistry. Thus, the Deccan bole beds are a good analog for the phyllosilicates layers on Mars and by studying the chemistry, mineralogy and spectral properties of the Deccan bole beds, we can link their formation and alteration processes to those of martian phyllosilicates. This will provide a clearer understanding of the environmental conditions on Mars at the time of the phyllosilicates' formation and hence during Mars' earliest history.

Stellar Activity at the End of the Main Sequence: GHRS Observations of the M8 Ve Star VB 10

NASA Technical Reports Server (NTRS)

Linsky, Jeffrey L.; Wood, Brian E.; Brown, Alexander; Giampapa, Mark S.; Ambruster, Carol

1995-01-01

We present Goddard High Resolution Spectrograph observations of the M8 Ve star VB 10 (equal to G1 752B), located very near the end of the stellar main sequence, and its dM3.5 binary companion G1 752A. These coeval stars provide a test bed for studying whether the outer atmospheres of stars respond to changes in internal structure as stars become fully convective near mass 0.3 solar mass (about spectral type M5), where the nature of the stellar magnetic dynamo presumably changes, and near the transition from red to brown dwarfs near mass 0.08 solar mass (about spectral type M9), when hydrogen burning ceases at the end of the main sequence. We obtain upper limits for the quiescent emission of VB 10 but observe a transition region spectrum during a large flare, which indicates that some type of magnetic dynamo must be present. Two indirect lines of evidence-scaling from the observed X-ray emission and scaling from a time-resolved flare on AD Leo suggest that the fraction of the stellar bolometric luminosity that heats the transition region of VB 10 outside of obvious flares is comparable to, or larger than, that for G1 752A. This suggests an increase in the magnetic heating rates, as measured by L(sub line)/L(sub bol) ratios, across the radiative/convective core boundary and as stars approach the red/brown dwarf boundary. These results provide new constraints for dynamo models and models of coronal and transition-region heating in late-type stars.

Lithofacies variation across the Mammoth Cave-Pope Megagroup boundary -- a sequence stratigraphic approach

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

McDonald, T.A.; Tabor, E.; Marzolf, J.E.

1994-04-01

Regional stratigraphic relations in southern Illinois suggest a major unconformity near the top of the St. Genevieve Limestone. Large exposures below the unconformity within the Anna quarries display a retrogradational parasequence-stacking pattern. Eight to 12 m-thick parasequences comprise thinning-upward marine bioclastic wackestone overlain by oolitic and bioclastic thickening-upward eolian( ) grainstone. An eolian origin for the bioclastic grainstones is supported by large scale cross stratification (0.5 to 2 m-thick sets), reworked character of rounded, coated bioclasts, and preserved duneforms. At the quarries, the unconformity is directly overlain by mudstones and sandstones. Thinning-upward mudstones interbedded with very thin (1 to 3more » cm thick) intraclastic packstone tempestites crop out in a roadcut about 500 m NE of the quarries. Small-scale ripples and absence of trace fossils in lower mudstone units suggest an estuarine or lagoonal, brackish-waver environment. The trace fossil Conostichus and horizontal burrows appear abruptly in the upper, thin mudstone units. Highly bioturbated green and red shales overlying a 1 to 4 m-thick covered interval in a roadcut 610 m farther north are interbedded with tidally deposited, medium- to coarse-grained, bioclastic grainstones. The shale-draped, medium cross-bedded grainstones document ten or more tidal bundles. The cross-bedded grainstone is overlain by wavy- to flaser-bedded very fine-grained sandstone suggestive of sand flat origin. These sandstones are overlain by the Aux Vases Sandstone. Numerous low-angle bounding surfaces within the Aux Vases enclose low-angle, wedge-planar cross-bedding. A single irregular surface coated by a few centimeters of poorly sorted unstratified sandstone defines a ravinement surface near the base of the Aux Vases Sandstone.« less

Tectonic significance of porosity and permeability regimes in the red beds formations of the South Georgia Rift Basin

NASA Astrophysics Data System (ADS)

Akintunde, Olusoga M.; Knapp, Camelia C.; Knapp, James H.

2014-09-01

A simple, new porosity/permeability-depth profile was developed from available laboratory measurements on Triassic sedimentary red beds (sandstone) from parts of the South Georgia Rift (SGR) basin in order to investigate the feasibility for long-term CO2 storage. The study locations were: Sumter, Berkeley, Dunbarton, Clubhouse Crossroad-3 (CC-3) and Norris Lightsey wells. As expected, both porosity and permeability show changes with depth at the regional scale that was much greater than at local scale. The significant changes in porosity and permeability with depth suggest a highly compacted, deformed basin, and potentially, a history of uplift and erosion. The permeability is generally low both at shallow (less than 1826 ft/556.56 m) and deeper depths (greater than 1826 ft/556.56 m). Both porosity and permeability follow the normal trend, decreasing linearly with depth for most parts of the study locations with the exception of the Norris Lightsey well. A petrophysical study on a suite of well logs penetrating the Norris Lightsey red beds at depths sampled by the core-derived laboratory measurements shows an abnormal shift (by 50%) in the acoustic travel time and/or in the sonic-derived P-wave velocity that indicates possible faulting or fracturing at depth. The departure of the Norris Lightsey's porosities and permeabilities from the normal compaction trend may be a consequence of the existence of a fault/fracture controlled abnormal pressure condition at depth. The linear and non-linear behaviors of the porosity/permeability distribution throughout the basin imply the composition of the SGR red beds, and by extension analog/similar Triassic-Jurassic formations within the Eastern North American Margin have been altered by compaction, uplift, erosion and possible faulting that have shaped the evolution of these Triassic formations following the major phase of rifting.

Paleomagnetic evidence that the central block of Salinia (California) is not a far-traveled terrane

USGS Publications Warehouse

Whidden, K.J.; Lund, S.P.; Bottjer, D.J.; Champion, D.; Howell, D.G.

1998-01-01

New paleomagnetic results from Late Cretaceous (75-85 m.y.) red beds on the central block of Salinia indicate that Salinia was located within 6?? (in latitude) of its current cratonal North American position during the Late Cretaceous (after correction for Neogene San Andreas Fault transport). The red beds formed as alluvial-fan overbank deposits with hematite cement deposited directly on Salinian granites in the La Panza Range. Paleomagnetic analysis shows two components of magnetization in the red beds, a low-blocking-temperature present-day overprint residing in goethite and a high-blocking-temperature (>600??) component residing in hematite. The hematite magnetization is a chemical remanent magnetization which formed soon after deposition during pedogenesis. The bedding-corrected hematite remanence contains a magnetic polarity stratigraphy with antipodal normal and reversed directions. Twenty-three Class I sites (??95 < 20??) have an average hematite direction with inclination = 54.4?? and declination = 18.2?? (??95 = 6.1??) after structural correction. These paleomagnetic data suggest that Salinia resided at about 35??N latitude during the Late Cretaceous, within 6?? of its current location adjacent to cratonal North America. By contrast, a summary of paleomagnetic data from the Peninsular Ranges terrane and the Sur-Obispo terrane, which are currently outboard of Salinia, shows northward transport of these terranes of 12,.o\\ to 22?? relative to their current locations in North America since the Cretaceous. The offsets increase systematically away from the craton with the most outboard Sur-Obispo terrane (which is composed of accretionary prism and distal forearc material) showing the largest degree of northward translation.

A Martian analog in Kansas: Comparing Martian strata with Permian acid saline lake deposits

NASA Astrophysics Data System (ADS)

Benison, Kathleen C.

2006-05-01

An important result of the Mars Exploration Rover's (MER) mission has been the images of sedimentary structures and diagenetic features in the Burns Formation at Meridiani Planum. Bedding, cross-bedding, ripple marks, mud cracks, displacive evaporite crystal molds, and hematite concretions are contained in these Martian strata. Together, these features are evidence of past saline groundwater and ephemeral shallow surface waters on Mars. Geochemical analyses of these Martian outcrops have established the presence of sulfates, iron oxides, and jarosite, which strongly suggests that these waters were also acidic. The same assemblage of sedimentary structures and diagenetic features is found in the salt-bearing terrestrial red sandstones and shales of the middle Permian (ca. 270 Ma) Nippewalla Group of Kansas, which were deposited in and around acid saline ephemeral lakes. These striking sedimentological and mineralogical similarities make these Permian red beds and evaporites the best-known terrestrial analog for the Martian sedimentary rocks at Meridiani Planum.

The Valley and Ridge Province of eastern Pennsylvania - stratigraphic and sedimentologic contributions and problems ( USA).

USGS Publications Warehouse

Epstein, J.B.

1986-01-01

The rocks in the area, which range from Middle Ordovician to Late Devonian in age, are more than 7620 m thick. This diversified group of sedimentary rocks was deposited in many different environments, ranging from deep sea, through neritic and tidal, to alluvial. In general, the Middle Ordovician through Lower Devonian strata are a sedimentary cycle related to the waxing and waning of Taconic tectonism. The sequence began with a greywacke-argillite suite (Martinsburg Formation) representing synorogenic basin deepening. This was followed by basin filling and progradation of a sandstone-shale clastic wedge (Shawangunk Formation and Bloomsburg Red Beds) derived from the erosion of the mountains that were uplifted during the Taconic orogeny. The sequence ended with deposition of many thin units of carbonate, sandstone, and shale on a shelf marginal to a land area of low relief. Another tectonic-sedimentary cycle, related to the Acadian orogeny, began with deposition of Middle Devonian rocks. Deep-water shales (Marcellus Shale) preceded shoaling (Mahantango Formation) and turbidite sedimentation (Trimmers Rock Formation) followed by another molasse (Catskill Formation). -from Author

Anomalously shallow inclination in middle-northern part of the South China block: palaeomagnetic study of Late Cretaceous red beds from Yichang area

NASA Astrophysics Data System (ADS)

Narumoto, Kazutoshi; Yang, Zhenyu; Takemoto, Kazuhiro; Zaman, Haider; Morinaga, Hayao; Otofuji, Yo-ichiro

2006-02-01

We present new palaeomagnetic results from Late Cretaceous red beds of the Paomagang Formation collected at 42 sites in the Yichang area (30.7°N, 111.7°E), middle-northern part of the South China Block. A high unblocking temperature component around 680°C was isolated from 26 sites by stepwise thermal demagnetization. Fold tests are positive at the 95 per cent confidence limit for 14 and 11 sites of the Paomagang and Wangdian areas, respectively. Normal and reversed polarity sequence found in the Wangdian area passed a reversal test at the 95 per cent confidence limit. The tilt-corrected mean direction for Yichang area is D= 3.8°, I= 23.3° (α95= 5.1°,N= 26), corresponding to a palaeopole at 71.5°N, 280.0°E with A95= 4.3°. Comparison with the expected inclination from the 80 Ma Eurasian APWP pole indicates a inclination flattening of 26.3°+/- 6.4°. Middle Cretaceous to Cenozoic NW-SE extension tectonics within the SCB contributes only 2.0° to the inclination flattening. While the massive samples of the Paomagang Formation show a moderate degree of anisotropy (1.017 < Pj < 1.086) and steeper inclination (I= 29.3°), the laminated samples, which form more than 75 per cent of the studied samples, show a higher degree of anisotropy (1.052 < Pj < 1.227) and shallower inclination value (I= 22.7°). A good correlation between remanence inclination and facies types indicates that depositional processes produced the observed shallow inclination in the Yichang area.

Outcrop shapes for correlation of Lower Mississippian carbonates in western North America

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

Haines, F.

1993-03-01

Examination of the sedimentary cycles in Mississippian carbonates in Iowa, Utah, Montana and Alberta shows a hierarchy of stratigraphic subdivisions: large sequences, cycles, rhythmic bands or marker beds, and couplets of laminated and dense beds. The 3 sequences shoal upward from dark mudstone to an oolitic or crinoidal cap beneath a disconformity. Sequence 1 (Horton Creek Member in Illinois, Upper Fitchville in Utah and Lower Banff oolite in Alberta) thins rapidly to fossiliferous limestone at a Waulsortian shelf margin on the southern edge of the Central Montana Trough. Sequence 2 (Hannibal-Chouteau in Missouri, Middle Banff in Alberta, lower Lodgepole cliffmore » in Montana and lower Chinese wall in Utah) thins at a shelf margin which is north-south in western Montana but swings east then northwest around an embayment in NW Montana and SW Alberta. Sequence 3 (Burlington-Keokuk in Iowa, Upper Banff and Pekisko in Alberta, and upper Lodgepole-massive lower Mission Canyon in Utah and Montana) marker beds lose their identity without a shelf margin in NW Montana and SW Alberta. Rhythmic bands, currently under study, demonstrate episodic deposition over large areas, band tops are sometimes bored, hardened and oxidized. Silty bands are used as marker beds. The S-4 marker (Dolby Creek) maintains a similar bed form despite facies changes. Laminated and dense limestone couplets are common in the basinal facies from Utah to Alberta and in the Chouteau formation of Missouri.« less

Tertiary geology and oil-shale resources of the Piceance Creek basin between the Colorado and White Rivers, northwestern Colorado

USGS Publications Warehouse

Donnell, John R.

1961-01-01

The area of the Piceance Creek basin between the Colorado and White Rivers includes approximately 1,600 square miles and is characterized by an extensive plateau that rises 1,000 to more than 4,000 feet above the surrounding lowlands. Relief is greatest in Naval Oil-Shale Reserves Nos. 1 and 3 near the south margin of the area, where the spectacular Roan Cliffs tower above the valley of the Colorado River. The oldest rocks exposed in the mapped area are sandstone, shale, and coal beds of the Mesaverde group of Late Cretaceous age, which crop out along the east margin of the area. Overlying the Mesaverde is an unnamed sequence of dark-colored sandstone and shale, Paleocene in age. The Ohio Creek conglomerate, composed of black and red chert and quartzite pebbles in a white sandstone matrix, is probably the basal unit in the Paleocene sequence. The Wasatch formation of early Eocene age overlies the Paleocene sedimentary rocks. It is composed of brightly colored shale, lenticular beds of sandstone, and a few thin beds of fresh-water limestone. The Kasatch formation interfingers with and is overlain by the Green River formation of middle Eocene age. The Green River formation has been divided into the Douglas Creek, Garden Gulch, Anvil Points, Parachute Creek, and Evacuation Creek members. The basal and uppermost members, the Douglas Creek and Evacuation Creek, respectively, are predominantly sandy units. The two middle members, the Garden Gulch and Parachute Creek, are composed principally of finer clastic rocks. The Anvil Points member is present only on the southeast, east, and northeast margins of the area. It is a nearshore facies composed principally of sandstone and is the equivalent of the Douglas Creek, Garden Gulch, and the lower part of the Parachute Creek members. All of the richer exposed oil-shale beds are found in the Parachute Creek member, which is divided into two oil-shale zones by a series of low-grade oilshale beds. The upper oil-shale zone has several key beds and zones which can be traced throughout most of the mapped area. One of these, the Mahogany ledge or zone, is a group of very rich oil-shale beds at the base of the upper oil-shale zone. Drilling for oil and gas in the northeastern part of the area has revealed rich oil-shale zones in the Garden Gulch member also.Local unconformities within and at the base of the Evacuation Creek member are exposed at several places along Piceance Creek and at one place near the mouth of Yellow Creek; otherwise, the rock sequence is conformable. The mapped area is the major part of a large syncline, modified by numerous smaller structural features. Fractures, probably associated genetically with the minor structural features, are present in the central part of the area. These fractures are high-angle normal faults with small displacement. They occur in pairs with the intervening block downdropped. Two sets of joints are prominent, one trending northwest and the other northeast. The joint systems control the drainage pattern in the south-central part of the area. More than 20,000 feet of sedimentary rocks underlies the area. Many of the formations yield oil or gas in northwestern Colorado, northeastern Utah, and southwestern Wyoming. The Piceance Creek gas field, in which gas occurs in the Douglas Creek member of the Green River formation, is the largest oil or gas field discovered thus far within the area. About 7,000 million barrels of oil is contained in oil shale that yields an average of 45 gallons per ton from a continuous sequence 5 or more feet thick in the Mahogany zone. Oil shale in the Mahogany zone and adjacent beds that yields an average of 30 gallons of oil per ton from a continuous sequence 15 or more feet thick contains about 91,000 million barrels of oil. Similar shale in deeper zones in the northern part of the area, for which detailed estimates have not been prepared, are now known to contain at least an additional 72,000 million barrels of oil. Oil shale in a sequence 15 or more feet thick that yields an average of 25 gallons of oil per ton contains about 154,000 million barrels of oil in the Mahogany zone and adjacent beds; such shale in deeper zones in the northern part of the area probably contains at least an additional 157,000 million barrels of oil, although detailed estimates were not made. Oil shale in a sequence greater than 15 feet thick that yields an average of 15 gallons of oil per ton contains more than 900,000 million barrels of oil. These estimates of the oil content of the deposit do not take into account any loss in mining or processing of the shale.

Exercise Training During Bed Rest Attenuates Deconditioning

NASA Technical Reports Server (NTRS)

Greenleaf, J. E.; Hargens, Alan R. (Technical Monitor)

1995-01-01

A 30-day 6 deg. head-down bed rest study was conducted to evaluate high-intensity, short-duration, alternating isotonic cycle ergometer exercise (ITE) training and high-intensity intermittent isokinetic exercise (IKE) training regiments designed to maintain peak VO2 and muscle mass, strength, and endurance at ambulatory control levels throughout prolonged bed rest. Other elements of the deconditioning (acclimation) syndrome, such as proprioception, psychological performance, hypovolemia, water balance, body composition, and orthostatic tolerance, were also measured. Compared with response during bed rest of the no exercise (NOE) control group: the ITE training regimen (a) maintained work capacity (peak VO2), (b) maintained plasma and red cell volume, (c) induced positive body water balance, (d) decreased quality of sleep and mental concentration, and (e) had no effect on the decrease in orthostatic tolerance; the IKE training regimen (a) attenuated the decrease in peak VO2 by 50%, (b) attenuated loss of red cell volume by 40%, but had no effect on loss of plasma volume, (c) induced positive body water balance, (d) had no adverse effect on quality of sleep or concentration, and (e) had no effect on the decrease in orthostatic tolerance. These findings suggest that various elements of the deconditioning syndrome can be manipulated by duration and intensity of ITE or IKE training regiments, and that several different training protocols will be required to maintain or restore physiological and psychological performance of individuals confined to prolonged bed rest.

Radioactivity and uranium content of the Sharon Springs member of the Pierre shale and associated rocks in western Kansas and eastern Colorado

USGS Publications Warehouse

Landis, Edwin R.

1955-01-01

As a part of the Geological Survey's program of investigating uranium-bearing carbonaceous rocks on behalf of the Division of Raw Materials of the U.S. Atomic Energy Commission, a reconnaissance of the Sharon Springs member of the Pierre shale in western Kansas and eastern Colorado was conducted during 1954. The Sharon Springs member of the Pierre shale and its lateral equivalents ranges from 155 to about 500 feet in thickness and generally contains about 0.001 percent uranium, but some beds contain larger amounts. A 6-foot thick shale bed in Cheyenne County, Colo., contains about 0.006 percent uranium, a 4 1/2-foot thick sequence of beds in Crowley County, Colo., is estimated to contain between 0.004 and 0.005 percent uranium, and a 3 1/2-foot thick sequence of beds in Kiowa County, Colo., contains about 0.004 percent uranium. At several outcrop localities, sequences of beds as much as 9 1/2 feet thick contain about 0.003 percent uranium. Data from wells indicate that the 4 1/2-foot thick sequence of beds in Crowley County, Colo., may have a lateral extent of at least 5 1/2 miles. A gamma-ray log of a well in Yuma County, Colo., indicates the presence of a sequence of beds 66 feet thick which contains 0.005 to 0.010 percent equivalent uranium. No definite pattern of areal distribution of radioactivity and uranium content in the Sharon Springs is indicated by available data. Lateral variation in uranium content of individual beds was not noted in outcrops, which seldom extend more than 150 feet, but subsurface data from gamma-ray logs of wells indicate that both the maximum radioactivity and the thickness of radioactive beds are variable within distances of a few miles. Vertical variation in radioactivity and uranium content of the more radioactive beds is usually abrupt, but in the rocks as a whole the range of uranium content is so small that large variations in content are absent. In most of the gamma-ray logs examined there is only part of the sequence of rocks comprising the Pierre shale and Niobrara formation that exhibits radioactivity in excess of the average radioactivity of the two formations. Comparison of features of gamma-ray logs of wells in north-eastern Colorado suggests that the most radioactive part referred to above is a laterally correlatable sequence of beds. The stratigraphic position of the radioactive unit relative to the Pierre shale-Niobrara formation contact in oil industry scout reports, as identified from electric logs and wells, is variable within short distances. This may indicate that some of the Pierre-Niobrara contacts picked from electric logs may not correspond to the boundary that would be selected by examination of the rocks themselves, or may indicate that there is a facies relationship between teh lowermost part of the Pierre shale and the uppermost part of the Niobrara formation.

Dating the upper Cenozoic sediments in Fisher Valley, southeastern Utah ( USA).

USGS Publications Warehouse

Colman, Steven M.; Choquette, Anne F.; Rosholt, J.M.; Miller, G.H.; Huntley, D.J.

1986-01-01

More than 140 m of upper Cenozoic basin-fill sediments were deposited and then deformed in Fisher Valley between about 2.5 and 0.25 m.y. ago, in response to uplift of the adjacent Onion Creek salt diapir. In addition to these basin-fill sediments, minor amounts of eolian and fluvial sand were depositd in Holocene time. The sediments, whose relative ages are known from the stratigraphy, are predominantly sandy, second-cycle red beds derived from nearby Mesozoic rocks; most were deposited in a vertical sequence, filling a sedimentary basin now exposed by fluvial dissection. We have applied a variety of established and experimental dating methods to the sediments in Fisher Valley to establish their age and to provide time control for the recent history of the Onion Creek salt diapir.-from Authors

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

Ghosh, S.K.; Zambrano, E.

The Trujillo Formation, overlying the Paleocene Cerro Verde and Valle Hondo formations, reveals a turbiditic origin in a lowstand shelf-edge and bathyal setting in two excellent road sections on the Valera-Carache road and many creek sections. The basal outcrop shows well developed fining upward (FU) sequences of proximal channel turbidite and overbank origin (abandonment phase) and minor coarsening upward (CU) sequences representing progradational pulse in overbank areas. The FU (and thinning-upward) sequence, overlying a shale, consists of: (a) basal stacked conglomeratic arenites (probably inner fan channels) with graded beds, imbricate casts and transported shells; (b) a sand/shale alternating unit (channelmore » margin/interchannel) with flame structure, lenticular bedding, infrequent Tb-d Sequence, rippled flats, and rare Planolites; and (c) a dark shale (overbank-interchannel lows) with scarce Chondrites and Scaladtuba traces. The CU sequence consists of thickening-upward heterolithic facies overlain by lenticular stacked pebbly arenites. The upper unit exposed near Puente Gomez is a typical progradational lobe starting with a basal shale, with intraformational diastems and slumped beds, and Tb-d and Tb-e sequences in thin intercalated sandstones; a heterolithic facies with flute/groove casts, Planolites, Thalassinoides and Neonereites occurs between the shale and a thick cross-stratified sandstone at the top. This CU lobe sequence is discordantly(?) overlain by a thin wedge of massive bedded pebbly sandstones of Middle Eocene(?) Misoa Formation. Unlike the southwesterly sourced subsurface turbidites, those in this area were probably sourced from both the south and north, though locally the southern source might have been more important.« less

The red-sequence of 72 WINGS local galaxy clusters

NASA Astrophysics Data System (ADS)

Valentinuzzi, T.; Poggianti, B. M.; Fasano, G.; D'Onofrio, M.; Moretti, A.; Ramella, M.; Biviano, A.; Fritz, J.; Varela, J.; Bettoni, D.; Vulcani, B.; Moles, M.; Couch, W. J.; Dressler, A.; Kjærgaard, P.; Omizzolo, A.; Cava, A.

2011-12-01

We study the color - magnitude red sequence and blue fraction of 72 X-ray selected galaxy clusters at z = 0.04-0.07 from the WINGS survey, searching for correlations between the characteristics of the red sequence (RS) and the environment. We consider the slope and scatter of the red sequence, the number ratio of red luminous-to-faint galaxies, the blue fraction, and the fractions of ellipticals, S0s, and spirals that compose the RS. None of these quantities correlate with the cluster velocity dispersion, X-ray luminosity, number of cluster substructures, BCG prevalence over next brightest galaxies, and the spatial concentration of ellipticals. The properties of the RS, instead, depend strongly on local galaxy density. Higher density regions have a smaller RS scatter, a higher luminous-to-faint ratio, a lower blue fraction, and a lower spiral fraction on the RS. Our results clearly illustrate the prominent effect of the local density in setting the epoch when galaxies become passive and join the red sequence, as opposed to the mass of the galaxy host structure.

A case study of rhodolith beds associated with offshore NW Gulf of Mexico hard banks: viewing rhodoliths as diversity-rich holobionts

NASA Astrophysics Data System (ADS)

Fredericq, S.; Sauvage, T.; Krayesky-Self, S.; Schmidt, W. E.

2016-02-01

Rhodolith beds offshore Louisiana in the NW Gulf of Mexico are associated with salt domes, unique deep bank habitats at 55-75m depth on the continental shelf. Seven sampling expeditions following the 2010 Deepwater Horizon (DWH) oil spill to 2 rhodolith bed habitats revealed a drastic macroalgal die-off that has persisted up to this day (last collections from September 2014) in locations that were diversity-rich pre-DWH. Laboratory observations of bare, denuded, and apparently "dead" rhodoliths collected post-DWH and placed in 75-liter microcosms in our lab, have shown macroalgal regeneration within 3 weeks. Metabarcoding of endolithic rhodolith environmental DNAs with newly designed primers for tufA recovered a wide microbiotal diversity of photosynthetic organisms including numerous seaweed species comprising red, green, brown (and other Ochrophyta) algae, as well as other phototrophic lineages (e.g. Cyanobacteria). Metabarcoding of 16S V4 from the same endolithic rhodolith DNAs used for tufA metabarcoding recovered in-depth microbiotal taxon coverage, including abundant prokaryotic (phototrophic Cyanobacteria, heterotrophic Bacteria and Archaea), and eukaryotic phototrophic diversity. 16S V4 recovered a similar proportion of phototrophs within rhodoliths pre- and post-DWH suggesting that although not visible in the field, seaweeds are still present in the NWGMx in the form of `resting' microscopic stages (dormant spores and filaments) within the CaCO3 of rhodoliths. Using tufA and 16S metabarcoding we were able to link the taxonomic identity of the "invisible," cryptic (hidden) parts of a macroalga that are part of a rhodolith's CaCO3 microbiota, with their corresponding "visible" macroscopic thalli through Sanger sequencing of plastid tufA and plastid 16S. We are continuing to characterize rhodoliths as holobionts critical for the cycling of macroalgal communities and as seedbank reservoirs and refugia of dormant microscopic stages of macroalgae. This research also illustrates and illuminates newly-found benthic life history stages of ecologically important primary producers that also cause harmful algal blooms (Dinoflagellata, Haptophyta), such as the formation of red tides, fish kills, or shellfish poisoning events in the Gulf of Mexico.

S-type rhyolites from the Tolmie Igneous Complex, Australia: deep crust origins and shallow crustal evolution

NASA Astrophysics Data System (ADS)

Clemens, J. D.; Birch, W. D.

2010-05-01

The Late Devonian Tolmie Igneous Complex, in Central Victoria, Australia, is composed mainly of Ba-rich (up to 3000 ppm) S-type rhyolite ignimbrites with SiO2 varying from 69 to 79 wt% and low Mg#s (1 to 43). Two main ignimbrite flows fill the Wabonga Caldera, the Ryans Creek and the overlying Toombullup Ignimbrites, totalling 750 to 1000 km3 in volume. The tectonic environment is late post-tectonic continental extension, with rifting and normal faulting. However, the volcanism was unimodal, without associated mafic lavas or pyroclastic rocks. Devonian red-beds underlie the Complex, Carboniferous, red-bed basins overlie the volcanic rocks, and some mafic lavas are present in the overlying red-bed sequences. The presence of almandine-rich garnet phenocrysts with rutile, in the Ryans Creek, implies minimum pressures of magma generation of 0.9 - 1.0 GPa. The Toombullup Ignimbrite contains two generations of garnet phenocrysts and three of orthopyroxene. Grt+Opx assemblages in the Toombullup imply early magmatic temperatures near 1000 ° C. The early phenocryst assemblage of Grt+Opx+Pl+Qtz constrains early magmatic crystallisation to around 0.4 GPa. Later Grt+Opx+Crd+Pl+Bt+Qtz assemblages suggest crystallisation at around 0.3 GPa and 750 to 800 ° C. The presence of ferroan Opx+Fa as late microphenocrysts suggest continued crystallisation at around 0.15 GPa and 800 ° C. Thus the magmas may were generated by high-T contact anatectic partial melting of Ba-enriched quartzofeldspathic metasediments near the base of the continental crust, during extension and mantle upwelling. There is then a record of partial crystallisation during ascent to shallow crustal pressures, where the felsic magmas evolved and interacted prior to eruption. Geochemical variations in the Complex suggest that there are at least 3 separate magma groups. Mafic-felsic magma mixing and restite unmixing can be ruled out as processes responsible for the variation. The chemistry of the magmas is interpreted to be the result of a complex interplay between partial melting of heterogeneous source rocks, variable entrainment of peritectic phases formed during the melting reactions and some crystal fractionation involving garnet, orthopyroxene, plagioclase and accessory minerals (Ap, Mon, Ilm, Zrn). The implication of these rocks for the local geology is that pre-Palaeozoic supracrustal rocks must have been carried to the base of the crust but escaped high-grade metamorphism and partial melting for 100s of millions of years after the orogenic events that brought them to those depths.

Intensive Exercise Training During Bed Rest Attenuates Deconditioning

NASA Technical Reports Server (NTRS)

Greenleaf, John E.

1997-01-01

Intensive exercise training during bed rest attenuates deconditioning. Med. Sci. Sports Exerc., Vol. 29, No. 2, pp. 207-215, 1997. A 30-d 6 deg head-down bed rest project was conducted to evaluate variable high-intensity, short-duration, isotonic cycle ergometer exercise (ITE) training and high-intensity intermittent resistive isokinetic exercise (IKE) training regimens designed to maintain peak VO2 and muscle mass, strength, and endurance at ambulatory control levels throughout prolonged bed rest. Other elements of the deconditioning (adaptive) syndrome, such as proprioception, psychological performance, hypovolemia, water balance, body composition, and orthostatic tolerance, were also measured. Major findings are summarized in this paper. Compared with response during bed rest of the no exercise (NOE) control group: the ITE training regimen (a) maintained work capacity (peak VO2), (b) maintained plasma and red cell volumes, (c) induced positive body water balance, (d) decreased quality of sleep and mental concentration, and (e) had no effect on the decrease in orthostatic tolerance; the IKE training regimen (f) attenuated the decrease in peak VO2 by 50%, (g) attenuated loss of red cell volume by 40% but had no effect on loss of plasma volume, (b) induced positive body water balance, (i) had no adverse effect on quality of sleep or concentration, and 0) had no effect on the decrease in orthostatic tolerance. These findings suggest that various elements of the deconditioning syndrome can be manipulated by duration and intensity of ITE or IKE training regimens and that several different training protocols will be required to maintain or restore physiological and psychological performance of individuals confined to prolonged bed rest.

Propagation of Southern Red Oak and Water Oak by Rooted Cuttings

Treesearch

Horace J. Duncan; Fred R. Matthews

1969-01-01

Southern red oak and water oak, needed in studies of fusiform rust of southern pines, were propagated from cuttings of rooted stump sprouts and mature tree branches placed in outdoor propagation beds in June. Root strike and root development were increased when cuttings with basal wounds were treated with both the hormone IBA and the fungicide folpet. Cuttings from...

Sequence Learning with Passive RFID Sensors for Real-Time Bed-Egress Recognition in Older People.

PubMed

Wickramasinghe, Asanga; Ranasinghe, Damith C; Fumeaux, Christophe; Hill, Keith D; Visvanathan, Renuka

2017-07-01

Getting out of bed and ambulating without supervision is identified as one of the major causes of patient falls in hospitals and nursing homes. Therefore, increased supervision is proposed as a key strategy toward falls prevention. An emerging generation of batteryless, lightweight, and wearable sensors are creating new possibilities for ambulatory monitoring, where the unobtrusive nature of such sensors makes them particularly adapted for monitoring older people. In this study, we investigate the use of a batteryless radio-frequency identification (RFID) tag response to analyze bed-egress movements. We propose a bed-egress movement detection framework that includes a novel sequence learning classifier with a set of features derived from bed-egress motion analysis. We analyzed data from 14 healthy older people (66-86 years old) who wore a wearable embodiment of a batteryless accelerometer integrated RFID sensor platform loosely attached over their clothes at sternum level, and undertook a series of activities including bed-egress in two clinical room settings. The promising results indicate the efficacy of our batteryless bed-egress monitoring framework.

Comparative analysis of myostatin gene and promoter sequences of Qinchuan and Red Angus cattle.

PubMed

He, Y L; Wu, Y H; Quan, F S; Liu, Y G; Zhang, Y

2013-09-04

To better understand the function of the myostatin gene and its promoter region in bovine, we amplified and sequenced the myostatin gene and promoter from the blood of Qinchuan and Red Angus cattle by using polymerase chain reaction. The sequences of Qinchuan and Red Angus cattle were compared with those of other cattle breeds available in GenBank. Exon splice sites were confirmed by mRNA sequencing. Compared to the published sequence (GenBank accession No. AF320998), 69 single nucleotide polymorphisms (SNPs) were identified in the Qinchuan myostatin gene, only one of which was an insertion mutation in Qinchuan cattle. There was a 16-bp insertion in the first 705-bp intron in 3 Qinchuan cattle. A total of 7 SNPs were identified in exon 3, in which the mutation occurred in the third base of the codon and was synonymous. On comparing the Qinchuan myostatin gene sequence to that of Red Angus cattle, a total of 50 SNPs were identified in the first and third exons. In addition, there were 18 SNPs identified in the Qinchuan cattle promoter region compared with those of other cattle compared to the Red Angus cattle myostatin promoter region. breeds (GenBank accession No. AF348479), but only 14 SNPs when compared to the Red Angus cattle myostatin promoter region.

Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia.

PubMed

Yu, Jeong-Nam; Han, Sang-Hoon; Kim, Bang-Hwan; Kryukov, Alexey P; Kim, Soonok; Lee, Byoung-Yoon; Kwak, Myounghai

2012-11-01

The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.

Quaternary geology and geomorphology of the Dinosaur Provincial Park area and surrounding plains, Alberta, Canada: the identification of former glacial lobes, drainage diversions and meltwater flood tracks

NASA Astrophysics Data System (ADS)

Evans, David J. A.

2000-06-01

The Quaternary geology and geomorphology of the lower Red Deer River drainage basin, centred on the Dinosaur Provincial Park badlands, provides information on pre-Late Wisconsinan drainage patterns and the dynamics of former lobes of the Laurentide Ice Sheet in western Canada. Patterns of deglaciation, proglacial lake evolution and spillway incision are also reconstructed based upon the distribution of surface materials and glacial/glaciofluvial landforms. The Empress Group fluvial and glaciolacustrine sediments, which could be as young as 27 ka BP, infill the precursor Red Deer River and its tributaries and document the initial advance of glacier ice into southern Alberta. Glaciotectonic disturbance of older sediments and bedrock, the production of deformation tills and the construction of a megafluting complex and cupola hills record the advances of a glacier lobe centred over the study area. Stratified inter- and intra-till beds record pulses of subglacial meltwater between phases of subsole deformation. The thickening of tills towards the margin of the lobe represents a till wedge, an expected product of sediment advection by glaciers moving over deformable beds. The eastern margin of the glacier lobe is demarcated by the interlobate Suffield hummocky moraine belt which contains overprinted thrust ridges, which record diachronous oscillations of neighbouring lobes within the ice sheet. Proglacial and glaciofluvial sediments were deposited in the area in association with proglacial Lake Bassano/Patricia, which drained eastwards when the Suffield moraine was dissected by spillways. Changes in the size of glacial lake Bassano/Patricia are clearly documented by a sequence of spillway incisions which culminated in the erosion of scabland topography and the initiation of a new course for the Red Deer River, a 15 km southward diversion of the main channel. In distinct contrast to the documented incision histories of other small rivers in Alberta, One Tree Creek and Little Sandhill Creek did not start major incisions of the Quaternary sediments over buried valley positions until the late-Holocene when environmental conditions were characterized by higher precipitation.

Par Pond vegetation status summer 1995 - July survey descriptive summary

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

Mackey, H.E. Jr.; Riley, R.S.

1995-07-01

A survey of the emergent shoreline aquatic plant, communities began in June 1995, three months after the refilling of Par Pond to approximately 200 feet (61 meters) above mean sea level, and continued with this July survey. Aquatic plant communities, similar to the pre-drawdown Par Pond communities, are becoming reestablished. Beds of maidencane (Panicum hemitomon), lotus (Nelumbo lutea), water lily (Nymphaea odorata), and watershield (Brasenia schreberi) are now extensive and well established. In addition, within isolated coves, extensive beds of water lilies and spike-rush (Eleocharis sp.) are common. Cattail occurrence has increased since refill, but large beds common to Parmore » Pond prior to the drawdown have not formed. Invasion of willow (Salix sp.) and red maple (Acer rubrum) occurred along the lake shoreline during drawdown. The red maples along the present shoreline are beginning to show evidence of stress and mortality from flooding over the past four months. Some of the willows appear to be stressed as well. The loblolly pines (Pinus taeda), which were flooded in all but the shallow shoreline areas, are now dead. Future surveys are planned for the growing seasons of 1995, 1996, and 1997, along with the evaluation of satellite data for mapping the areal extent of the macrophyte beds of Par Pond.« less

The Contribution of DNA Metabarcoding to Fungal Conservation: Diversity Assessment, Habitat Partitioning and Mapping Red-Listed Fungi in Protected Coastal Salix repens Communities in the Netherlands

PubMed Central

Geml, József; Gravendeel, Barbara; van der Gaag, Kristiaan J.; Neilen, Manon; Lammers, Youri; Raes, Niels; Semenova, Tatiana A.; de Knijff, Peter; Noordeloos, Machiel E.

2014-01-01

Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought. PMID:24937200

Effect Of Leg Exercise On Vascular Volumes During Bed Rest

NASA Technical Reports Server (NTRS)

Greenleaf, J. E.; Vernikos, J.; Wade, C. E.; Barnes, P. R.

1993-01-01

Report describes experiments on effects of no-exercise regimen and of two leg-exercise regimens on volumes of plasma, volumes of red blood cells, densities of bodies, and water balances of 19 men (32 to 42 years old) confined to minus 6 degrees-head-down bed rest for 30 days. Purpose of study to determine whether either or both exercise regimens maintain plasma volume and to relate levels of hypovolemia to body fluid balances. Results showed during bed rest, plasma volume maintained in isotomic group but not in other two groups, and no significant differences in body densities, body weights, or water balances among three groups. Concludes isotonic-exercise regimen better than isokinetic-exercise regimen for maintaining plasma volume during prolonged exposure to bed rest.

Effect of seed position and media on germination of black walnut and northern red oak: implications for nursery production and direct seeding

Treesearch

Anthony S. Davis; Barrett C. Wilson; Douglass F. Jacobs

2004-01-01

Germination of black walnut (Juglans nigra L.) and northern red oak (Quercus rubra L.) prior to sowing into containers or bareroot nursery beds can help maintain desired crop density and reduce nursery costs. Recommended techniques for germination of black walnut are labor intensive and require that walnuts be completely covered...

Red blood cell decreases of microgravity

NASA Technical Reports Server (NTRS)

Johnson, P. C.

1985-01-01

Postflight decreases in red blood cell mass (RBCM) have regularly been recorded after exposure to microgravity. These 5-25 percent decreases do not relate to the mission duration, workload, caloric intake or to the type of spacecraft used. The decrease is accompanied by normal red cell survivals, increased ferritin levels, normal radioactive iron studies, and increases in mean red blood cell volume. Comparable decreases in red blood cell mass are not found after bed rest, a commonly used simulation of the microgravity state. Inhibited bone marrow erythropoiesis has not been proven to date, although reticulocyte numbers in the peripheral circulation are decreased about 50 percent. To date, the cause of the microgravity induced decreases in RBCM is unknown. Increased splenic trapping of circulating red blood cells seem the most logical way to explain the results obtained.

The morphological transformation of red sequence galaxies in clusters since z ˜ 1

NASA Astrophysics Data System (ADS)

Cerulo, P.; Couch, W. J.; Lidman, C.; Demarco, R.; Huertas-Company, M.; Mei, S.; Sánchez-Janssen, R.; Barrientos, L. F.; Muñoz, R.

2017-11-01

The study of galaxy morphology is fundamental to understand the physical processes driving the structural evolution of galaxies. It has long been known that dense environments host high fractions of early-type galaxies and low fractions of late-type galaxies, indicating that the environment affects the structural evolution of galaxies. In this paper, we present an analysis of the morphological composition of red sequence galaxies in a sample of nine galaxy clusters at 0.8 < z < 1.5 drawn from the HAWK-I Cluster Survey (HCS), with the aim of investigating the evolutionary paths of galaxies with different morphologies. We classify galaxies according to their apparent bulge-to-total light ratio and compare with red sequence galaxies from the lower redshift WIde-field Nearby Galaxy-cluster Survey (WINGS) and ESO Distant Cluster Survey (EDisCS). We find that, while the HCS red sequence is dominated by elliptical galaxies at all luminosities and stellar masses, the WINGS red sequence is dominated by elliptical galaxies only at its bright end (MV < -21.0 mag), while S0s become the most frequent class at fainter luminosities. Disc-dominated galaxies comprise 10-14 per cent of the red sequence population in the low (WINGS) and high (HCS) redshift samples, although their fraction increases up to 40 per cent at 0.4 < z < 0.8 (EDisCS). We find a 20 per cent increase in the fraction of S0 galaxies from z ∼ 1.5 to 0.05 on the red sequence. These results suggest that elliptical and S0 galaxies follow different evolutionary histories and, in particular, that S0 galaxies result, at least at intermediate luminosities (-22.0 < MV < -20.0), from the morphological transformation of quiescent spiral galaxies.

The ecosystem service value of living versus dead biogenic reef

NASA Astrophysics Data System (ADS)

Sheehan, E. V.; Bridger, D.; Attrill, M. J.

2015-03-01

Mixed maerl beds (corralline red algae) comprise dead thalli with varying amounts of live maerl fragments, but previously it was not known whether the presence of the live maerl increases the ecosystem service 'habitat provision' of the dead maerl for the associated epibenthos. A 'flying array' towed sled with high definition video was used to film transects of the epibenthos in dead maerl and mixed maerl beds in two locations to the north and south of the English Channel (Falmouth and Jersey). Mixed maerl beds supported greater number of taxa and abundance than dead beds in Falmouth, while in Jersey, mixed and dead beds supported similar number of taxa and dead beds had a greater abundance of epifauna. Scallops tended to be more abundant on mixed beds than dead beds. Tube worms were more abundant on mixed beds in Falmouth and dead beds in Jersey. An increasing percentage occurrence of live maerl thalli correlated with increasing number of taxa in Falmouth but not Jersey. It was concluded that while live thalli can increase the functional role of dead maerl beds for the epibenthos, this is dependent on location and response variable. As a result of this work, maerl habitat in SE Jersey has been protected from towed demersal fishing gear.

Deep Sequencing of Pyrethroid-Resistant Bed Bugs Reveals Multiple Mechanisms of Resistance within a Single Population

PubMed Central

Adelman, Zach N.; Kilcullen, Kathleen A.; Koganemaru, Reina; Anderson, Michelle A. E.; Anderson, Troy D.; Miller, Dini M.

2011-01-01

A frightening resurgence of bed bug infestations has occurred over the last 10 years in the U.S. and current chemical methods have been inadequate for controlling this pest due to widespread insecticide resistance. Little is known about the mechanisms of resistance present in U.S. bed bug populations, making it extremely difficult to develop intelligent strategies for their control. We have identified bed bugs collected in Richmond, VA which exhibit both kdr-type (L925I) and metabolic resistance to pyrethroid insecticides. Using LD50 bioassays, we determined that resistance ratios for Richmond strain bed bugs were ∼5200-fold to the insecticide deltamethrin. To identify metabolic genes potentially involved in the detoxification of pyrethroids, we performed deep-sequencing of the adult bed bug transcriptome, obtaining more than 2.5 million reads on the 454 titanium platform. Following assembly, analysis of newly identified gene transcripts in both Harlan (susceptible) and Richmond (resistant) bed bugs revealed several candidate cytochrome P450 and carboxylesterase genes which were significantly over-expressed in the resistant strain, consistent with the idea of increased metabolic resistance. These data will accelerate efforts to understand the biochemical basis for insecticide resistance in bed bugs, and provide molecular markers to assist in the surveillance of metabolic resistance. PMID:22039447

Denitrification and Phosphorus Sequestration in Restored Oyster Beds in the Indian River Lagoon, Florida, USA

NASA Astrophysics Data System (ADS)

Gallagher, S. M.; Schmidt, C. A.; Walters, L.

2016-12-01

In 2016, an algae bloom in the St. Lucie River in Florida led the governor to declare a state of emergency. The river is part of a connected system of estuaries along the Atlantic coast of Florida called the Indian River Lagoon (IRL). As with many estuaries around the world, nutrient loading in the IRL has led to periodic eutrophication. As a result, much research has been done to address nutrients in these systems. Previous estuary studies have related oyster restoration to denitrification and phosphorus sequestration in their bed sediment. To this point, these studies have been inconclusive, and have only focused on seasonal variation in nutrient cycling. In 2007, yearly oyster bed installation and restoration began in a study area in the IRL. By 2016, beds aged up to eleven years were available for sampling. This unique advantage allowed investigation of bed sediment and nutrient cycling over long periods of time. Sediment from the IRL was measured for organic matter, microbial weight, carbon, nitrogen, and phosphorus. Denitrification was measured using an acetylene block technique. A statistical analysis was used to find differences in sediment characteristics and denitrification between restored beds and control sites over time. In addition, sequencing of 16S rRNA DNA and a variety of denitrifying genes was used to identify bacterial species and their denitrifying capability in the sediment. The ability to sequence denitrification genes in established oyster beds over a period of years was also unique to this study. Significant differences were found in soil properties, denitrification rates, and phosphorus sequestration between control sites and restored oyster beds. Gene sequencing also found differences in bacterial populations between the sites. Oyster bed restoration resulted in a rapid increase in nutrient removal as beds developed over three years, but additional benefits were limited as restoration progressed further. This study adds an investigation of IRL oysters to existing knowledge of nutrient removal by oysters in other estuaries. These results help clarify single year studies focused on seasonal changes by showing a rapid increase in oyster bed nutrient removal over a period of three years.

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox.

PubMed

Vozdova, Miluse; Kubickova, Svatava; Cernohorska, Halina; Fröhlich, Jan; Rubes, Jiri

2016-01-01

Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox. © 2017 S. Karger AG, Basel.

Positioning the red deer (Cervus elaphus) hunted by the Tyrolean Iceman into a mitochondrial DNA phylogeny.

PubMed

Olivieri, Cristina; Marota, Isolina; Rizzi, Ermanno; Ermini, Luca; Fusco, Letizia; Pietrelli, Alessandro; De Bellis, Gianluca; Rollo, Franco; Luciani, Stefania

2014-01-01

In the last years several phylogeographic studies of both extant and extinct red deer populations have been conducted. Three distinct mitochondrial lineages (western, eastern and North-African/Sardinian) have been identified reflecting different glacial refugia and postglacial recolonisation processes. However, little is known about the genetics of the Alpine populations and no mitochondrial DNA sequences from Alpine archaeological specimens are available. Here we provide the first mitochondrial sequences of an Alpine Copper Age Cervus elaphus. DNA was extracted from hair shafts which were part of the remains of the clothes of the glacier mummy known as the Tyrolean Iceman or Ötzi (5,350-5,100 years before present). A 2,297 base pairs long fragment was sequenced using a mixed sequencing procedure based on PCR amplifications and 454 sequencing of pooled amplification products. We analyzed the phylogenetic relationships of the Alpine Copper Age red deer's haplotype with haplotypes of modern and ancient European red deer. The phylogenetic analyses showed that the haplotype of the Alpine Copper Age red deer falls within the western European mitochondrial lineage in contrast with the current populations from the Italian Alps belonging to the eastern lineage. We also discussed the phylogenetic relationships of the Alpine Copper Age red deer with the populations from Mesola Wood (northern Italy) and Sardinia.

Bathing a patient in bed

MedlinePlus

... ed. American National Red Cross; 2013:chap 13. Smith SF, Duell DJ, Martin BC, Gonzalez L, Aebersold M. Bathing, bedmaking, and maintaining skin integrity. In: Smith SF, Duell DJ, Martin BC, Gonzalez L, Aebersold ...

Use of bed rest and head-down tilt to simulate spaceflight-induce immune system changes

NASA Technical Reports Server (NTRS)

Schmitt, D. A.; Schaffar, L.; Taylor, G. R.; Loftin, K. C.; Schneider, V. S.; Koebel, A.; Abbal, M.; Sonnenfeld, G.; Lewis, D. E.; Reuben, J. R.;

Improvements and validation of the erythropoiesis control model for bed rest simulation

NASA Technical Reports Server (NTRS)

Leonard, J. I.

1977-01-01

The most significant improvement in the model is the explicit formulation of separate elements representing erythropoietin production and red cell production. Other modifications include bone marrow time-delays, capability to shift oxyhemoglobin affinity and an algorithm for entering experimental data as time-varying driving functions. An area of model development is suggested by applying the model to simulating onset, diagnosis and treatment of a hematologic disorder. Recommendations for further improvements in the model and suggestions for experimental application are also discussed. A detailed analysis of the hematologic response to bed rest including simulation of the recent Baylor Medical College bed rest studies is also presented.

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.

Cambrian-lower Middle Ordovician passive carbonate margin, southern Appalachians: Chapter 14

USGS Publications Warehouse

Read, J. Fred; Repetski, John E.

2012-01-01

The southern Appalachian part of the Cambrian–Ordovician passive margin succession of the great American carbonate bank extends from the Lower Cambrian to the lower Middle Ordovician, is as much as 3.5 km (2.2 mi) thick, and has long-term subsidence rates exceeding 5 cm (2 in.)/k.y. Subsiding depocenters separated by arches controlled sediment thickness. The succession consists of five supersequences, each of which contains several third-order sequences, and numerous meter-scale parasequences. Siliciclastic-prone supersequence 1 (Lower Cambrian Chilhowee Group fluvial rift clastics grading up into shelf siliciclastics) underlies the passive margin carbonates. Supersequence 2 consists of the Lower Cambrian Shady Dolomite–Rome-Waynesboro Formations. This is a shallowing-upward ramp succession of thinly bedded to nodular lime mudstones up into carbonate mud-mound facies, overlain by lowstand quartzose carbonates, and then a rimmed shelf succession capped by highly cyclic regressive carbonates and red beds (Rome-Waynesboro Formations). Foreslope facies include megabreccias, grainstone, and thin-bedded carbonate turbidites and deep-water rhythmites. Supersequence 3 rests on a major unconformity and consists of a Middle Cambrian differentiated rimmed shelf carbonate with highly cyclic facies (Elbrook Formation) extending in from the rim and passing via an oolitic ramp into a large structurally controlled intrashelf basin (Conasauga Shale). Filling of the intrashelf basin caused widespread deposition of thin quartz sandstones at the base of supersequence 4, overlain by widespread cyclic carbonates (Upper Cambrian lower Knox Group Copper Ridge Dolomite in the south; Conococheague Formation in the north). Supersequence 5 (Lower Ordovician upper Knox in the south; Lower to Middle Ordovician Beekmantown Group in the north) has a basal quartz sandstone-prone unit, overlain by cyclic ramp carbonates, that grade downdip into thrombolite grainstone and then storm-deposited deep-ramp carbonates. Passive margin deposition was terminated by arc-continent collision when the shelf was uplifted over a peripheral bulge while global sea levels were falling, resulting in the major 0- to 10-m.y. Knox–Beekmantown unconformity. The supersequences and sequences appear to relate to regionally traceable eustatic sea level cycles on which were superimposed high-frequency Milankovitch sea level cycles that formed the parasequences under global greenhouse conditions.

Paleomagnetic and magnetic fabric studies of Lower Triassic red sandstones from the autochthonous cover of the Central Western Carpathians: new insights into paleogeographic setting and tectonic evolution of the area

NASA Astrophysics Data System (ADS)

Szaniawski, R.; Jankowski, L.; Ludwiniak, M.; Mazzoli, S.; Szczygieł, J.

2017-12-01

The Carpathian Mountains were formed through progressive collision and amalgamation of the Alcapa and Tisza-Dacia microplates with the European Platform. The Central Western Carpathians (CWC) tectonic unit analyzed in this study constitutes a fragment of the Alcapa microplate - research in this area is therefore of great importance in the context of the geotectonic evolution of the Carpathian orogen. Our paleomagnetic and magnetic fabric studies were focused on Lower Triassic red sandstones from the autochthonous cover of the crystalline basement. We present new results from three mountain massifs: Low Tatra, Velka Fatra and Strazovske Vrchy, comparing them with our earlier works performed in the Tatra Mts. Rockmagnetic studies reveal similar results in all four studied regions - the dominant ferromagnetic carrier in red sandstones is hematite, while the magnetic fabric is mostly controlled by paramagnetic minerals. AMS results outline a bedding parallel foliation and a tectonic lineation. This lineation lies in the bedding plane but is somewhat oblique to the present horizontal plane. The fact that the lineation is not exactly parallel to the strike of the beds is most likely due to multistage deformation: the lineation is related to bedding parallel shortening associated with the folding and thrusting stage, while present-day bedding attitude results at least partially from rotations associated with subsequent uplift and/or faulting. Paleomagnetic analysis indicate that hematite carrier records characteristic remanent component of high unblocking temperatures (680°C) and both normal (dominant) and reversed polarity. Paleomagnetic inclinations are similar to those expected from reference paleomagnetic data from the European Platform. Declination values are rather similar in all four studied areas and imply moderate counterclockwise rotations of the CWC. These results are incompatible with some of the previous paleomagnetic studies of younger rocks from the CWC suggesting large-scale counterclockwise rotations. Acknowledgements: this work was supported by Polish National Science Centre (NCN) (Grant nr. 2014/13/B/ST10/01151).

Sequence divergence of the red and green visual pigments in great apes and humans.

PubMed Central

Deeb, S S; Jorgensen, A L; Battisti, L; Iwasaki, L; Motulsky, A G

1994-01-01

We have determined the coding sequences of red and green visual pigment genes of the chimpanzee, gorilla, and orangutan. The deduced amino acid sequences of these pigments are highly homologous to the equivalent human pigments. None of the amino acid differences occurred at sites that were previously shown to influence pigment absorption characteristics. Therefore, we predict the spectra of red and green pigments of the apes to have wavelengths of maximum absorption that differ by < 2 nm from the equivalent human pigments and that color vision in these nonhuman primates will be very similar, if not identical, to that in humans. A total of 14 within-species polymorphisms (6 involving silent substitutions) were observed in the coding sequences of the red and green pigment genes of the great apes. Remarkably, the polymorphisms at 6 of these sites had been observed in human populations, suggesting that they predated the evolution of higher primates. Alleles at polymorphic sites were often shared between the red and green pigment genes. The average synonymous rate of divergence of red from green sequences was approximately 1/10th that estimated for other proteins of higher primates, indicating the involvement of gene conversion in generating these polymorphisms. The high degree of homology and juxtaposition of these two genes on the X chromosome has promoted unequal recombination and/or gene conversion that led to sequence homogenization. However, natural selection operated to maintain the degree of separation in peak absorbance between the red and green pigments that resulted in optimal chromatic discrimination. This represents a unique case of molecular coevolution between two homologous genes that functionally interact at the behavioral level. PMID:8041777

Paleomagnetism of Cretaceous Oceanic Red Beds (CORBs) from Gyangze, northern Tethys Himalaya: Evidence for Intra-oceanic Subduction System and Southern Paleolatitute Limit for the Lhasa Block

NASA Astrophysics Data System (ADS)

Tan, Xiaodong

2016-04-01

In the northern Tethys Himalaya, sporadically distributed Cretaceous oceanic red beds (CORBs, the Chuangde Formation) have been described. The sequence was interpreted to be firstly deposited in the outer continental shelf and upper slope, and later slumped into deep basin. Based on this model, and paleomagnetic data of shallow water deposits from the southern Tethys Himalaya, the CORBs were derived from the northern tip of the passive margin of the greater India. If so, the CORBs would provide more accurate record of the northern extent of the greater India, which is an important parameter for estimating the initial time of India-Asia continental collision and the amount of crustal shortening. The well studied and most accessible section is located in the Chuangde village, about 40km east from the Gyangze city. The formation is about 25m thick, ranging from 84 to 75Ma in age according to fossil records of planktonic foraminiferal species. The lower and upper parts are 2 and 5 meter thick marlstones, respectively, and the middle section is dominated by shale with a few layers of centimeter scale marlstones. Fifty cores were collected from the marlstones of the section, and for the purpose of fold test, 30 more cores were collected from the upper part of the formation from a second section located in the Pulong village, ~3km to the northeast of the Chuangde village. All samples were subject to stepwise thermal demagnetization. About 60% of the samples yielded interpretable demagnetization results. The bottom of the upper part of the formation show reversed high temperature component, and the rest of the upper part and the lower part show normal polarity. The Chuangde section data failed reversal test, because the normal polarity direction is likely not fully resolved from overprint component. However, the well resolved reversal direction from the Chuangde village and the normal direction from Pulong pass both reversal and fold tests. The mean paleomagnetic data indicate a paleolatitude of 10±2 degree north, ~2000 km distance from the southern Tethys Himalaya. Therefore, the formation is not deposited near the greater Indian continental margins. Based on recent plate tectonic reconstruction, the CORBs are very likely formed within a back-arc basin between the equatorial intra-oceanic subduction system and the Asian continental margin. Due to coeval development of abundant red beds in the Lhasa block, the characteristic pigments of hematite born in the CORBs are likely of terrestrial origin. In addition, the new data indicate that the Lhasa block is unlikely to be at low paleolatitude in the Late Cretaceous and Tertiary as some of the paleomagnetic results show.

Positioning the Red Deer (Cervus elaphus) Hunted by the Tyrolean Iceman into a Mitochondrial DNA Phylogeny

PubMed Central

Olivieri, Cristina; Marota, Isolina; Rizzi, Ermanno; Ermini, Luca; Fusco, Letizia; Pietrelli, Alessandro; De Bellis, Gianluca; Rollo, Franco; Luciani, Stefania

2014-01-01

In the last years several phylogeographic studies of both extant and extinct red deer populations have been conducted. Three distinct mitochondrial lineages (western, eastern and North-African/Sardinian) have been identified reflecting different glacial refugia and postglacial recolonisation processes. However, little is known about the genetics of the Alpine populations and no mitochondrial DNA sequences from Alpine archaeological specimens are available. Here we provide the first mitochondrial sequences of an Alpine Copper Age Cervus elaphus. DNA was extracted from hair shafts which were part of the remains of the clothes of the glacier mummy known as the Tyrolean Iceman or Ötzi (5,350–5,100 years before present). A 2,297 base pairs long fragment was sequenced using a mixed sequencing procedure based on PCR amplifications and 454 sequencing of pooled amplification products. We analyzed the phylogenetic relationships of the Alpine Copper Age red deer's haplotype with haplotypes of modern and ancient European red deer. The phylogenetic analyses showed that the haplotype of the Alpine Copper Age red deer falls within the western European mitochondrial lineage in contrast with the current populations from the Italian Alps belonging to the eastern lineage. We also discussed the phylogenetic relationships of the Alpine Copper Age red deer with the populations from Mesola Wood (northern Italy) and Sardinia. PMID:24988290

The Lower Triassic Sorkh Shale Formation of the Tabas Block, east central Iran: Succesion of a failed-rift basin at the Paleotethys margin

USGS Publications Warehouse

Lasemi, Y.; Ghomashi, M.; Amin-Rasouli, H.; Kheradmand, A.

2008-01-01

The Lower Triassic Sorkh Shale Formation is a dominantly red colored marginal marine succession deposited in the north-south trending Tabas Basin of east central Iran. It is correlated with the unconformity-bounded lower limestone member of the Elika Formation of the Alborz Mountains of northern Iran. The Sorkh Shale is bounded by the pre-Triassic and post-Lower Triassic interregional unconformities and consists mainly of carbonates, sandstones, and evaporites with shale being a minor constituent. Detailed facies analysis of the Sorkh Shale Formation resulted in recognition of several genetically linked peritidal facies that are grouped into restricted subtidal, carbonate tidal flat, siliciclastic tidal flat, coastal plain and continental evaporite facies associations. These were deposited in a low energy, storm-dominated inner-ramp setting with a very gentle slope that fringed the Tabas Block of east central Iran and passed northward (present-day coordinates) into deeper water facies of the Paleotethys passive margin of northern Cimmerian Continent. Numerous carbonate storm beds containing well-rounded intraclasts, ooids and bioclasts of mixed fauna are present in the Sorkh Shale Formation of the northern Tabas Basin. The constituents of the storm beds are absent in the fair weather peritidal facies of the Sorkh Shale Formation, but are present throughout the lower limestone member of the Elika Formation. The Tabas Block, a part of the Cimmerian continent in east central Iran, is a rift basin that developed during Early Ordovician-Silurian Paleotethys rifting. Facies and sequence stratigraphic analyses of the Sorkh Shale Formation has revealed additional evidence supporting the Tabas Block as a failed rift basin related to the Paleotethys passive margin. Absence of constituents of the storm beds in the fair weather peritidal facies of the Sorkh Shale Formation, presence of the constituents of the storm beds in the fair weather facies of the Elika Formation (the Sorkh Shale equivalent in the Alborz Paleotethys margin) and southward paleocurrent directions of carbonate storm beds suggest that the low topographic gradient of the ramp in the Tabas failed rift basin was facing the Paleotethys Ocean, where the storms were generated. In addition, northward paleocurrent directions of the fair weather facies and northward increase in carbonate content of the Sorkh Shale sequence further indicate that the Tabas Basin was tectonically a part of the Paleotethys passive margin. It is apparent that relative sea level, basin geometry and tectonic movements along the bounding faults played significant roles during deposition of the Sorkh Shale Formation by controlling accommodation space and facies variations along the Tabas failed rift basin.

Sedimentology and tectonics of the collision complex in the east arm of Sulawesi Indonesia

NASA Astrophysics Data System (ADS)

Simandjuntak, Tohap Oculair

An imbricated Mesozoic to Palaeogene continental margin sequence is juxtaposed with ophiolitic rocks in the East Arm of Sulawesi, Indonesia. The two tectonic terranes are bounded by the Batui Thrust and Balantak Fault System, which are considered to be the surface expression of the collision zone between the Banggai-Sula Platform and the Eastern Sulawesi Ophiolite Belt. The collision complex contains three distinctive sedimentary sequences : 1) Triassic-Palaeogene continental margin sediments, ii) Cretaceous pelagic sediments and iii) Neogene coarse clastic sediments and volcanogenic turbidites. (i) Late Triassic Lemo Beds consisting largely of carbonate-slope deposits and subsidiary clastics including quartz-rich lithic sandstones and lensoidal pebbly mudstone and conglomeratic breccia. The hemipelagic limestones are rich in micro-fossils. Some beds of the limestone contain bivalves and ammonites, including Misolia, which typifies the Triassic-Jurassic sequence of eastern Indonesia. The Jurassic Kapali Beds are dominated by quartzose arenites containing significant amounts of plant remains and lumps of coal. The Late Jurassic sediments consist of neritic carbonate deposits (Nambo Beds and Sinsidik Beds) containing ammonites and belemnites, including Belemnopsis uhligi Stevens, of Late Jurassic age. The Jurassic sediments are overlain unconformably by Late Cretaceous Luok Beds which are predominantly calcilutite with chert nodules rich in microfossils. The Luok Beds are unconformably overlain by the Palaeogene Salodik Limestones which consist of carbonate platform sediments rich in both benthic and planktonic foraminifera of Eocene to Early Miocene age. These sediments were deposited on the continental margin of the Banggai-Sula Platform. (ii) Deep-sea sediments (Boba Beds) consist largely of chert and subsidiary calcilutite rich in radiolaria of Cretaceous age. These rocks are part of an ophiolite suite. (iii) Coarse clastic sediments (Kolo Beds and Biak Conglomerates) are typical post-orogenic clastic rocks deposited on top of the collision complex. They are composed of material derived from both the continental margin sequence and ophiolite suite. Volcanogenic Lonsuit Turbidites occur in the northern part of the East Arm in Poh Head and unconformably overlie the ophiolite suite. Late Miocene to Pliocene planktonic foraminifera occur in the intercalated marlstone and marly sandstone beds within these rocks. The collision zone is marked by the occurrence of Kolokolo Melange, which contain exotic fragments detached from both the ophiolite suite and the continental margin sequence and a matrix of calcareous mudstone and marlstone rich in planktonic foraminifera of late Middle Miocene to Pliocene age. The melange is believed to have been formed during and after the collision of the Banggai-Sula Platform with the Eastern Sulawesi Ophiolite Belt. Hence, the collision event took place in Middle Miocene time. The occurrence of at least three terraces of Quaternary coraline reefs on the south coast of the East Arm of Sulawesi testifies to the rapid uplift of the region. Seismic data suggest that the collision might still be in progress at the present time.

Assessing the role of bed sediments in the persistence of red mud pollution in a shallow lake (Kinghorn Loch, UK).

PubMed

Olszewska, Justyna P; Heal, Kate V; Winfield, Ian J; Eades, Lorna J; Spears, Bryan M

2017-10-15

Red mud is a by-product of alumina production. Little is known about the long-term fate of red mud constituents in fresh waters or of the processes regulating recovery of fresh waters following pollution control. In 1983, red mud leachate was diverted away from Kinghorn Loch, UK, after many years of polluting this shallow and monomictic lake. We hypothesised that the redox-sensitive constituents of red mud leachate, phosphorus (P), arsenic (As) and vanadium (V), would persist in the Kinghorn Loch for many years following pollution control as a result of cycling between the lake bed sediment and the overlying water column. To test this hypothesis, we conducted a 12-month field campaign in Kinghorn Loch between May 2012 and April 2013 to quantify the seasonal cycling of P, As, and V in relation to environmental conditions (e.g., dissolved oxygen (DO) concentration, pH, redox chemistry and temperature) in the lake surface and bottom waters. To confirm the mechanisms for P, As and V release, a sediment core incubation experiment was conducted using lake sediment sampled in July 2012, in which DO concentrations were manipulated to create either oxic or anoxic conditions similar to the bed conditions found in the lake. The effects on P, As, and V concentrations and species in the water column were measured daily over an eight-day incubation period. Phosphate (PO 4 -P) and dissolved As concentrations were significantly higher in the bottom waters (75.9 ± 30.2 μg L -1 and 23.5 ± 1.83 μg L -1 , respectively) than in the surface waters (12.9 ± 1.50 μg L -1 and 14.1 ± 2.20 μg L -1 , respectively) in Kinghorn Loch. Sediment release of As and P under anoxic conditions was confirmed by the incubation experiment and by the significant negative correlations between DO and P and As concentrations in the bottom waters of the lake. In contrast, the highest dissolved V concentrations occurred in the bottom waters of Kinghorn Loch under oxic conditions (15.0 ± 3.35 μg L -1 ), with the release from the bed sediment apparently being controlled by a combination of competitive ion concentrations, pH and redox conditions. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fracture propagation through a layered shale and limestone sequence at Nash Point, South Wales: Implications on the development of fracture networks in layered sequences

NASA Astrophysics Data System (ADS)

Forbes Inskip, N.; Meredith, P. G.; Gudmundsson, A.

2017-12-01

While considerable effort has been expended on the study of fracture propagation in rocks in recent years, our understanding of how fractures propagate through sedimentary rocks composed of layers with different mechanical and elastic properties remains poor. Yet the mechanical layering is a key parameter controlling the propagation of fractures in sedimentary sequences. Here we report measurements of the contrasting properties of the Lower Lias at Nash Point, South Wales, which comprises a sequence of interbedded shale and limestone layers, and how those properties influence fracture propagation. The static Young's modulus (Estat) of both rock types has been measured parallel and normal to bedding. The shale is highly anisotropic, with Estat varying from 2.4 GPa, in the bedding-normal orientation, to 7.9 GPa, in the bedding-parallel orientation, yielding an anisotropy of 107%. By contrast the limestone has a very low anisotropy of 8%, with Estat values varying from 28.5 GPa, in the bedding-normal orientation, to 26.3 GPa in the bedding-parallel orientation. It follows that for a vertical fracture propagating in this sequence the modulus contrast is by a factor of about 12. This is important because the contrast in elastic properties is a key factor in controlling whether fractures arrest, deflect, or propagate across interfaces between layers in a sequence. Preliminary numerical modelling results (using a finite element modelling software) of induced fractures at Nash Point demonstrate a rotation of the maximum principal compressive stress across interfaces but also the concentration of tensile stress within the more competent (high Estat) limestone layers. The tensile strength (σT), using the Brazil-disk technique, and fracture toughness (KIc), using the semi-circular bend methodology, of both rock types have been measured. Measurements were made in the three principal orientations relative to bedding, Arrester, Divider, and Short-Transverse, and also at 15° intervals between these planes. Again, values for the shale show a high degree of anisotropy; with similar values in the Arrester and Divider orientations, but much lower values in the Short-Transverse orientation. σT and KIc values for the limestone are considerably higher than those for the shale and exhibit no significant anisotropy.

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar

USDA-ARS?s Scientific Manuscript database

A small fast neutron mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five Phaseolus vulgaris cv. Red Hawk fast neutron mutants wi...

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.

A sorting mechanism for a riffle-pool sequence

Treesearch

Thomas Lisle

1979-01-01

Transport of coarse, heterogeneous debris in a natural stream under a wide range of flows usually results in a remarkably stable, undulatory bed profile, which manifests an in transit sorting process of the bed material. In general, finer material representative of the bulk of the normal bed load resides in the deep sections, or pools, below flood stages. At high...

Hydrogeologic reconnaissance of the San Miguel River basin, southwestern Colorado

USGS Publications Warehouse

Ackerman, D.J.; Rush, F.E.

1984-01-01

The San Miguel River Basin encompasses 4,130 square kilometers of which about two-thirds is in the southeastern part of the Paradox Basin. The Paradox Basin is a part of the Colorado Plateaus that is underlain by a thick sequence of evaporite beds of Pennsylvanian age. The rock units that underlie the area have been grouped into hydrogeologic units based on their water-transmitting ability. Evaporite beds of mostly salt are both overlain and underlain by confining beds. Aquifers are present above and below the confining-bed sequence. The principal element of ground-water outflow from the upper aquifer is flow to the San Miguel River and its tributaries; this averages about 90 million cubic meters per year. A water budget for the lower aquifer has only two equal, unestimated elements, subsurface outflow and recharge from precipitation. The aquifers are generally isolated from the evaporite beds by the bounding confining beds; as a result, most ground water has little if any contact with the evaporites. No brines have been sampled and no brine discharges have been identified in the basin. Salt water has been reported for petroleum-exploration wells, but no active salt solution has been identified. (USGS)

The Importance of Splat Events to the Spatiotemporal Structure of Near-Bed Fluid Velocity and Bed Load Motion Over Bed Forms: Laboratory Experiments Downstream of a Backward Facing Step

NASA Astrophysics Data System (ADS)

Leary, K. C. P.; Schmeeckle, M. W.

2017-12-01

Flow separation/reattachment on the lee side of alluvial bed forms is known to produce a complex turbulence field, but the spatiotemporal details of the associated patterns of bed load sediment transported remain largely unknown. Here we report turbulence-resolving, simultaneous measurements of bed load motion and near-bed fluid velocity downstream of a backward facing step in a laboratory flume. Two synchronized high-speed video cameras simultaneously observed bed load motion and the motion of neutrally buoyant particles in a laser light sheet 6 mm above the bed at 250 frames/s downstream of a 3.8 cm backward facing step. Particle Imaging Velocimetry (PIV) and Acoustic Doppler Velocimetry (ADV) were used to characterize fluid turbulent patterns, while manual particle tracking techniques were used to characterize bed load transport. Octant analysis, conducted using ADV data, coupled with Markovian sequence probability analysis highlights differences in the flow near reattachment versus farther downstream. Near reattachment, three distinct flow patterns are apparent. Farther downstream we see the development of a dominant flow sequence. Localized, intermittent, high-magnitude transport events are more apparent near flow reattachment. These events are composed of streamwise and cross-stream fluxes of comparable magnitudes. Transport pattern and fluid velocity data are consistent with the existence of permeable "splat events," wherein a volume of fluid moves toward and impinges on the bed (sweep) causing a radial movement of fluid in all directions around the point of impingement (outward interaction). This is congruent with flow patterns, identified with octant analysis, proximal to flow reattachment.

Brown coal maceral distributions in a modern domed tropical Indonesian peat and a comparison with maceral distributions in Middle Pennsylvanian–age Appalachian bituminous coal beds

USGS Publications Warehouse

Grady, William C.; Eble, Cortland F.; Neuzil, Sandra G.

1993-01-01

Analyses of modern Indonesian peat samples reveal that the optical characteristics of peat constituents are consistent with the characteristics of macerals observed in brown coal and, as found by previous workers, brown-coal maceral terminology can be used in the analysis of modern peat. A core from the margin and one from near the center of a domed peat deposit in Riau Province, Sumatra, reveal that the volume of huminite macerals representing well-preserved cell structures (red, red-gray, and gray textinite; ulminite; and corpo/textinite) decreases upward. Huminite macerals representing severely degraded (<20 microns) cellular debris (degraded textinite, attrinite, and densinite) increase uniformly from the base to the surface. Greater degradation of the huminite macerals in the upper peat layers in the interior of the deposit is interpreted to be the result of fungal activity that increased in response to increasingly aerobic conditions associated with the doming of the peat deposit. Aerobic conditions concurrent with the activities of fungi may result in incipient oxidation of the severely degraded huminite macerals. This oxidation could lead to the formation of degradosemifusinite, micrinite, and macrinite maceral precursors in the peat, which may become evident only upon coalification. The core at the margin was petrographically more homogeneous than the core from the center and was dominated by well-preserved huminite macerals except in the upper 1 m, which showed signs of aerobic degradation and was similar to the upper 1 m of the peat in the interior of the deposit.The Stockton and other Middle Pennsylvanian Appalachian coal beds show analogous vertical trends in vitrinite maceral composition. The succession from telocollinite-rich, bright coal lithotypes in the lower benches upward to thin-banded/matrix collinite and desmocollinite in higher splint coal benches is believed to reflect a progression similar to that from the well-preserved textinite macerals in the lower portions of the peat cores to severely fragmented and degraded cellular materials (degraded textinite, attrinite, and densinite) in the upper portions of the cores. This petrographic sequence from bright to splint coal in the Stockton and other Middle Pennsylvanian coal beds supports previous interpretations of an upward transition from planar to domed swamp accumulations.

Insertion sequences enrichment in extreme Red sea brine pool vent.

PubMed

Elbehery, Ali H A; Aziz, Ramy K; Siam, Rania

2017-03-01

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Immobilized lysozyme for the continuous lysis of lactic bacteria in wine: Bench-scale fluidized-bed reactor study.

PubMed

Cappannella, Elena; Benucci, Ilaria; Lombardelli, Claudio; Liburdi, Katia; Bavaro, Teodora; Esti, Marco

2016-11-01

Lysozyme from hen egg white (HEWL) was covalently immobilized on spherical supports based on microbial chitosan in order to develop a system for the continuous, efficient and food-grade enzymatic lysis of lactic bacteria (Oenococcus oeni) in white and red wine. The objective is to limit the sulfur dioxide dosage required to control malolactic fermentation, via a cell concentration typical during this process. The immobilization procedure was optimized in batch mode, evaluating the enzyme loading, the specific activity, and the kinetic parameters in model wine. Subsequently, a bench-scale fluidized-bed reactor was developed, applying the optimized process conditions. HEWL appeared more effective in the immobilized form than in the free one, when the reactor was applied in real white and red wine. This preliminary study suggests that covalent immobilization renders the enzyme less sensitive to the inhibitory effect of wine flavans. Copyright © 2016 Elsevier Ltd. All rights reserved.

Geochemistry and diagenesis of Miocene lacustrine siliceous sedimentary and pyroclastic rocks, Mytilinii basin, Samos Island, Greece

USGS Publications Warehouse

Stamatakis, M.G.; Hein, J.R.; Magganas, A.C.

1989-01-01

A Late Miocene non-marine stratigraphic sequence composed of limestone, opal-CT-bearing limestone, porcelanite, marlstone, diatomaceous marlstone, dolomite, and tuffite crops out on eastern Samos Island. This lacustrine sequence is subdivided into the Hora Beds and the underlying Pythagorion Formation. The Hora Beds is overlain by the clastic Mytilinii series which contains Turolian (Late Miocene) mammalian fossils. The lacustrine sequence contains volcanic glass and the silica polymorphs opal-A, opal-CT, and quartz. Volcanic glass predominantly occurs in tuffaceous rocks from the lower and upper parts of the lacustrine sequence. Opal-A (diatom frustules) is confined to layers in the upper part of the Hora Beds. Beds rich in opal-CT underlie those containing opal-A. The occurrence of opal-CT is extensive, encompassing the lower Hora Beds and the sedimentary rocks and tuffs of the Pythagorion Formation. A transition zone between the opal-A and opal-CT zones is identified by X-ray diffraction patterns that are intermediate between those of opal-CT and opal-A, perhaps due to a mixture of the two polymorphs. Diagenesis was not advanced enough for opal-CT to transform to quartz or for volcanic glass to transform to opal-C. Based on geochemical and mineralogical data, we suggest that the rate of diagenetic transformation of opal-A to opal-CT was mainly controlled by the chemistry of pore fluids. Pore fluids were characterized by high salinity, moderately high alkalinity, and high magnesium ion activity. These pore fluid characteristics are indicated by the presence of evaporitic salts (halite, sylvite, niter), high boron content in biogenic silica, and by dolomite in both the opal-A and opal-CT-bearing beds. The absence of authigenic K-feldspar, borosilicates, and zeolites also support these pore fluid characteristics. Additional factors that influenced the rate of silica diagenesis were host rock lithology and the relatively high heat flow in the Aegean region from Miocene to Holocene. ?? 1989.

Accurate identification of RNA editing sites from primitive sequence with deep neural networks.

PubMed

Ouyang, Zhangyi; Liu, Feng; Zhao, Chenghui; Ren, Chao; An, Gaole; Mei, Chuan; Bo, Xiaochen; Shu, Wenjie

2018-04-16

RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed's state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.

The Accotink Schist, Lake Barcroft Metasandstone, and Popes Head Formation; keys to an understanding of the tectonic evolution of the northern Virginia Piedmont

USGS Publications Warehouse

Drake, Avery Ala; Lyttle, Peter T.

1981-01-01

The newly named Accotink Schist and Lake Barcroft Metasandstone of the Eastern Fairfax sequence are the structurally lowest metamorphic rocks in the northernmost Piedmont of Virginia. The Accotink consists of beds of pelitic schist that have thin basal intervals containing graded, very fine grained metasiltstone, as well as interbeds of metasandstone like that in the overlying Lake Barcroft Metasandstone. The unit is characterized by the Bouma turbidite sequences Te and Tde and can be assigned to turbidite facies D and E. The thickness of the Accotink is not known because its base is not exposed. The Accotink Schist grades up into the Lake Barcroft Metasandstone, which consists of two types of metasandstone. Type I metaarenite is quartzofeldspathic granofels which forms thick sequences of amalgamated beds that can best be described as belonging to the Bouma turbidite sequence Ta and to turbidite facies B 2 . Type II metagraywacke of the Lake Barcroft Metasandstone consists of micaceous metagraywacke in thin to medium beds, which can be described as belonging to the Buoma turbidite sequences Tabe and (or) Tae and to turbidite facies C. The Lake Barcroft Metasandstone appears to be about 400 m thick. It and the Accotink Schist are thought to represent a coarsening-upward sequence of an outer submarine-fan association of rocks. The Eastern Fairfax sequence is overlain by the Sykesville Formation. We believe that this contact is a movement surface upon which the Sykesville was emplaced by subaqueous sliding. The Sykesville contains isoclinally folded fragments, thought to be rip-ups, of Accotink and Lake Barcroft rocks. The Eastern Fairfax sequence is intruded by rocks of the Occoquan Granite batholith, which contains pendants of isoclinally folded schist and metagraywacke. Mter intrusion, the metasedimentary and plutonic rocks were folded together. Gamet and chlorite porphyroblasts within the Eastern Fairfax sequence appear to be related to the emplacement of the batholith. The minimum age of the Eastern Fairfax sequence is that of the Occoquan Granite batholith, currently thought to be about 560 m.y. The sequence, then, is considered to be of Early Cambrian age or older. The Accotink Schist and Lake Barcroft Metasandstone have some lithic similarity to the Loch Raven Schist and Oella Formation of Crowley (1976) of the Baltimore area, but a correlation is very uncertain at this time. The newly named Popes Head Formation overlies all other metasedimentary and transported meta-igneous rocks in northernmost Virginia west ofthe Occoquan Granite batholith and is intruded by the batholith. The Popes Head consists of a lower Old Mill Branch Metasiltstone Member and an upper Station Hills Phyllite Member. The Old Mill Branch consists largely of alternating coarser and finer grained strata that are mostly fine- to very fine grained, mineralogically quite mature graded metasiltstone, which can be described as belonging to Bouma turbidite sequence Tbde and (or) Tde, more rarely Tcde. The metasiltstone contains interbedded intervals in which both felsic and mafic metatuff contain pristine euhedral crystals of igneous minerals. We believe that the metatuff represents ash-fall deposits. The Old Mill Branch appears to be about 730 m thick. The Old Mill Branch grades up into the Station Hills Phyllite Member, which consists of thin- to medium-bedded pelitic phyllite and smaller amounts of very fine grained metasiltstone. The metasiltstone beds are graded, and many phyllite beds appear to have basal in- tervals containing graded, very fine grained metasiltstone. These beds can be described as belonging to Bouma turbidite sequence Tde. The Station Hills has intervals containing chlorite-rich phyllite, which probably represents mafic metatuff. No felsic metatuff has been recognized. The top of the Station Hills is not known, neither therefore, is its thickness. This unit appears to have a maximum thickness of about 300 m in northern

Magnetostratigraphy of The Astronomically-forced Alluvial Fan To Lacustrine Sequences of The Teruel Basin (late Miocene, Spain)

NASA Astrophysics Data System (ADS)

van Dam, J.; Aziz, H. Abdul; Hilgen, F. J.; Krijgsman, W.

During the last years, more and more examples of allocyclic, astronomical forced variations in the continental record have been documented. Sedimentary hiatuses, tra- ditionally regarded as the primary reason for the absence of clear patterns of orbital signature in the terrestrial domain, may be absent or short, given the appropriate set- ting. Spanish endoreic basins, for instance, form a ideal setting for the registration of orbital-forced climate change, as has been demonstrated for the Middle Miocene distal-alluvial fan-floodplain to lacustrine deposits of the Calatayud Basin. Astronom- ical forcing of sedimentary cycles has also been demonstrated in the Late Miocene distal alluvial fan to lacustrine sequences of the Teruel Basin. The early Late Miocene Cascante and Cañizar sections South of the town of Teruel show distinct cyclic bed- ding of red and/or green mottled mudstones alternating with white carbonate beds, whereby the alternation is mainly controlled by precession and eccentricity. The car- bonate beds are interpreted as (shallow) lake highstands, which occur in response to submergence of the alluvial fan distal plain. Small mammal teeth have been recov- ered from organic-richer layers at the base of the carbonate cycles in the Cascante and Cañizar sections. The recovery of mammal remains in terrestrial Milankovitch forced settings is crucial for several reasons: 1) it provides a first approximate age estimation for the sequence, thereby constraining other sources of temporal information such as magnetostratigraphy; 2) it infers very accurate ages of the mammal localities after as- tronomical tuning of the cyclic patterns; 3) it formulates hypotheses on the climatic regime and its variability using precise correlations to the insolation curve and in- terpretation of phase relations; and 4) it confronts the astronomically-based climatic reconstruction with the paleoecological reconstructions and faunal changes observed in the mammals themselves. This will lead to a better understanding of the nature of the response terrestrial organisms exhibit to climatic change. Based on the cyclo- and magnetostratigraphy, two age models for the sections (10.1-9.4 Ma; 10.3-9.6 Ma) are possible. However, spectral analysis results and estimated duration of subchrons indicate a preference for the younger age model. Additional sampling for mammals and paleomagnetism is needed to solve the problem of the age models, to date more 1 precisely mammal subzones J1, 2 and 3, and to establish the exact relations between changes in the mammal communities and short- and long-term astronomical cycles. 2

Correlation between high resolution sequence stratigraphy and mechanical stratigraphy for enhanced fracture characteristic prediction

NASA Astrophysics Data System (ADS)

Al Kharusi, Laiyyan M.

Sequence stratigraphy relates changes in vertical and lateral facies distribution to relative changes in sea level. These relative changes in carbonates effect early diagenesis, types of pores, cementation and dissolution patterns. As a result, in carbonates, relative changes in sea level significantly impact the lithology, porosity, diagenesis, bed and bounding surfaces which are all factors that control fracture patterns. This study explores these relationships by integrating stratigraphy with fracture analysis and petrophysical properties. A special focus is given to the relationship between mechanical boundaries and sequence stratigraphic boundaries in three different settings: (1) Mississippian strata in Sheep Mountain Anticline, Wyoming, (2) Mississippian limestones in St. Louis, Missouri, and (3) Pennsylvanian limestones intermixed with elastics in the Paradox Basin, Utah. The analysis of these sections demonstrate that a fracture hierarchy exists in relation to the sequence stratigraphic hierarchy. The majority of fractures (80%) terminate at genetic unit boundaries or the internal flooding surface that separates the transgressive from regressive hemicycle. Fractures (20%) that do not terminate at genetic unit boundaries or their internal flooding surface terminate at lower order sequence stratigraphic boundaries or their internal flooding surfaces. Secondly, the fracture spacing relates well to bed thickness in mechanical units no greater than 0.5m in thickness but with increasing bed thickness a scatter from the linear trend is observed. In the Paradox Basin the influence of strain on fracture density is illustrated by two sections measured in different strain regimes. The folded strata at Raplee Anticline has higher fracture densities than the flat-lying beds at the Honaker Trail. Cemented low porosity rocks in the Paradox Basin do not show a correlation between fracture pattern and porosity. However velocity and rock stiffness moduli's display a slight correlation to fracture spacing. Furthermore, bed thickness is found to be only one factor in determining fracture density but with increasing strain, internal bedforms and rock petrophysical heterogeneities influence fracture density patterns. This study illustrates how integrating sedimentologic and sequence stratigraphic interpretations with data on structural kinematics can lead to refined predictive understanding of fracture attributes.

Immobilized laccase mediated dye decolorization and transformation pathway of azo dye acid red 27.

PubMed

Chhabra, Meenu; Mishra, Saroj; Sreekrishnan, Trichur Ramaswamy

2015-01-01

Laccases have good potential as bioremediating agents and can be used continuously in the immobilized form like many other enzymes. In the present study, laccase from Cyathus bulleri was immobilized by entrapment in Poly Vinyl Alcohol (PVA) beads cross-linked with either nitrate or boric acid. Immobilized laccase was used for dye decolorization in both batch and continuous mode employing a packed bed column. The products of degradation of dye Acid Red 27 were identified by LC MS/MS analysis. The method led to very effective (90%) laccase immobilization and also imparted significant stability to the enzyme (more than 70% after 5 months of storage at 4°C). In batch decolorization, 90-95% decolorization was achieved of the simulated dye effluent for up to 10-20 cycles. Continuous decolorization in a packed bed bioreactor led to nearly 90% decolorization for up to 5 days. The immobilized laccase was also effective in decolorization and degradation of Acid Red 27 in the presence of a mediator. Four products of degradation were identified by LC-MS/MS analysis. The immobilized laccase in PVA-nitrate was concluded to be an effective agent in treatment of textile dye effluents.

New Cricetid Rodents from Strata near the Eocene-Oligocene Boundary in Erden Obo Section (Nei Mongol, China).

PubMed

Li, Qian; Meng, Jin; Wang, Yuanqing

2016-01-01

New cricetids (Eucricetodon wangae sp. nov., Eucricetodon sp. and Pappocricetodon siziwangqiensis sp. nov.) are reported from the lower and middle parts of the "Upper Red" beds of the Erden Obo section in Nei Mongol, China. Eucricetodon wangae is more primitive than other known species of the genus from lower Oligocene of Asia and Europe in having a single anterocone on M1, a single connection between the protocone and the paracone, the anterior metalophule connection in M1-2 and weaker anteroconid and ectomesolophid in lower molars. Pappocricetodon siziwangqiensis is more advanced than other species of the genus in permanently missing P4 and having posterior protolophule connection. These fossils suggest that the age of the "Upper Red" of the Erden Obo section is younger than the age of the Upper Eocene Houldjin and Caijiachong formations, but older than those containing the Shandgolian faunas; the "Upper Red" is most closely correlative to the Ergilian beds in age, and probably close to the Eocene/Oligocene boundary. Given the age estimate, Eucricetodon wangae provides the new evidence to support that cricetid dispersal from Asia to Europe occurred prior to the Eocene-Oligocene boundary.

Spectroscopic characterization of galaxy clusters in RCS-1: spectroscopic confirmation, redshift accuracy, and dynamical mass-richness relation

NASA Astrophysics Data System (ADS)

Gilbank, David G.; Barrientos, L. Felipe; Ellingson, Erica; Blindert, Kris; Yee, H. K. C.; Anguita, T.; Gladders, M. D.; Hall, P. B.; Hertling, G.; Infante, L.; Yan, R.; Carrasco, M.; Garcia-Vergara, Cristina; Dawson, K. S.; Lidman, C.; Morokuma, T.

2018-05-01

We present follow-up spectroscopic observations of galaxy clusters from the first Red-sequence Cluster Survey (RCS-1). This work focuses on two samples, a lower redshift sample of ˜30 clusters ranging in redshift from z ˜ 0.2-0.6 observed with multiobject spectroscopy (MOS) on 4-6.5-m class telescopes and a z ˜ 1 sample of ˜10 clusters 8-m class telescope observations. We examine the detection efficiency and redshift accuracy of the now widely used red-sequence technique for selecting clusters via overdensities of red-sequence galaxies. Using both these data and extended samples including previously published RCS-1 spectroscopy and spectroscopic redshifts from SDSS, we find that the red-sequence redshift using simple two-filter cluster photometric redshifts is accurate to σz ≈ 0.035(1 + z) in RCS-1. This accuracy can potentially be improved with better survey photometric calibration. For the lower redshift sample, ˜5 per cent of clusters show some (minor) contamination from secondary systems with the same red-sequence intruding into the measurement aperture of the original cluster. At z ˜ 1, the rate rises to ˜20 per cent. Approximately ten per cent of projections are expected to be serious, where the two components contribute significant numbers of their red-sequence galaxies to another cluster. Finally, we present a preliminary study of the mass-richness calibration using velocity dispersions to probe the dynamical masses of the clusters. We find a relation broadly consistent with that seen in the local universe from the WINGS sample at z ˜ 0.05.

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.

THE GALEX/S{sup 4}G UV–IR COLOR–COLOR DIAGRAM: CATCHING SPIRAL GALAXIES AWAY FROM THE BLUE SEQUENCE

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

Bouquin, Alexandre Y. K.; Gil de Paz, Armando; Gallego, Jesús

We obtained GALEX FUV, NUV, and Spitzer/IRAC 3.6 μm photometry for >2000 galaxies, available for 90% of the S{sup 4}G sample. We find a very tight GALEX blue sequence (GBS) in the (FUV–NUV) versus (NUV–[3.6]) color–color diagram, which is populated by irregular and spiral galaxies, and is mainly driven by changes in the formation timescale (τ) and a degeneracy between τ and dust reddening. The tightness of the GBS provides an unprecedented way of identifying star-forming galaxies and objects that are just evolving to (or from) what we call the GALEX green valley (GGV). At the red end of the GBS, atmore » (NUV–[3.6]) > 5, we find a wider GALEX red sequence (GRS) mostly populated by E/S0 galaxies that has a perpendicular slope to that of the GBS and of the optical red sequence. We find no such dichotomy in terms of stellar mass (measured by M{sub [3.6]}) since both massive (M{sub ⋆}>10{sup 11}M{sub ⊙}) blue- and red-sequence galaxies are identified. The type that is proportionally more often found in the GGV is the S0-Sa’s, and most of these are located in high-density environments. We discuss evolutionary models of galaxies that show a rapid transition from the blue to the red sequence on a timescale of 10{sup 8} yr.« less

The GALEX/S4G UV-IR Color-Color Diagram: Catching Spiral Galaxies Away from the Blue Sequence

NASA Astrophysics Data System (ADS)

Bouquin, Alexandre Y. K.; Gil de Paz, Armando; Boissier, Samuel; Muñoz-Mateos, Juan-Carlos; Sheth, Kartik; Zaritsky, Dennis; Laine, Jarkko; Gallego, Jesús; Peletier, Reynier F.; Röck, Benjamin R.; Knapen, Johan H.

2015-02-01

We obtained GALEX FUV, NUV, and Spitzer/IRAC 3.6 μm photometry for \\gt 2000 galaxies, available for 90% of the S4G sample. We find a very tight GALEX blue sequence (GBS) in the (FUV-NUV) versus (NUV-[3.6]) color-color diagram, which is populated by irregular and spiral galaxies, and is mainly driven by changes in the formation timescale (τ) and a degeneracy between τ and dust reddening. The tightness of the GBS provides an unprecedented way of identifying star-forming galaxies and objects that are just evolving to (or from) what we call the GALEX green valley (GGV). At the red end of the GBS, at (NUV-[3.6]) \\gt 5, we find a wider GALEX red sequence (GRS) mostly populated by E/S0 galaxies that has a perpendicular slope to that of the GBS and of the optical red sequence. We find no such dichotomy in terms of stellar mass (measured by {{M}[3.6]}) since both massive ({{M}\\star }\\gt {{10}11}{{M}⊙ }) blue- and red-sequence galaxies are identified. The type that is proportionally more often found in the GGV is the S0-Sa’s, and most of these are located in high-density environments. We discuss evolutionary models of galaxies that show a rapid transition from the blue to the red sequence on a timescale of 108 yr.

A Multiplex PCR assay to differentiate between dog and red fox.

PubMed

Weissenberger, M; Reichert, W; Mattern, R

2011-11-01

Foxes are frequently the cause of car accidents in Baden-Württemberg (BW, Germany). The domestic dog (Canis familiaris) is in close relation to the red fox (Vulpes vulpes) and the silver fox which is a coat colour variant of the red fox. As insurance claims that involve accidents with animals require authentication, we analyzed frequency distribution and allele sizes in two canine microsatellite loci in 26 dogs (different breeds) and 19 red foxes of the region of BW, Germany. Moreover, sequencing analysis was performed. Red foxes exhibited only 1 allele at each microsatellite locus, whereas in dog 7 alleles at the CPH4 locus and 6 alleles at the CPH12 locus were detected. Sequences of PCR products from the two species revealed several differences between dogs and foxes. We established a sequenced allelic ladder and give population data from dogs and red foxes from the region of BW, Germany. Using microsatellite polymorphisms is efficient in differentiating between dogs and foxes in forensic casework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

EVIDENCE FOR THE UNIVERSALITY OF PROPERTIES OF RED-SEQUENCE GALAXIES IN X-RAY- AND RED-SEQUENCE-SELECTED CLUSTERS AT z ∼ 1

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

Foltz, R.; Wilson, G.; DeGroot, A.

We study the slope, intercept, and scatter of the color–magnitude and color–mass relations for a sample of 10 infrared red-sequence-selected clusters at z ∼ 1. The quiescent galaxies in these clusters formed the bulk of their stars above z ≳ 3 with an age spread Δt ≳ 1 Gyr. We compare UVJ color–color and spectroscopic-based galaxy selection techniques, and find a 15% difference in the galaxy populations classified as quiescent by these methods. We compare the color–magnitude relations from our red-sequence selected sample with X-ray- and photometric-redshift-selected cluster samples of similar mass and redshift. Within uncertainties, we are unable tomore » detect any difference in the ages and star formation histories of quiescent cluster members in clusters selected by different methods, suggesting that the dominant quenching mechanism is insensitive to cluster baryon partitioning at z ∼ 1.« less

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.

The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana).

PubMed

Zhang, Jin; Zhang, Honghai; Zhao, Chao; Chen, Lei; Sha, Weilai; Liu, Guangshuai

2015-01-01

In this study, the complete mitochondrial genome of the Tibetan red fox (Vulpes Vulpes montana) was sequenced for the first time using blood samples obtained from a wild female red fox captured from Lhasa in Tibet, China. Qinghai--Tibet Plateau is the highest plateau in the world with an average elevation above 3500 m. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region (CR). The variable tandem repeats in CR is the main reason of the length variability of mitochondrial genome among canide animals.

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

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese

PubMed Central

Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-01-01

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. PMID:25767226

The effect of bedding system selected by manual muscle testing on sleep-related cardiovascular functions.

PubMed

Kuo, Terry B J; Li, Jia-Yi; Lai, Chun-Ting; Huang, Yu-Chun; Hsu, Ya-Chuan; Yang, Cheryl C H

2013-01-01

Different types of mattresses affect sleep quality and waking muscle power. Whether manual muscle testing (MMT) predicts the cardiovascular effects of the bedding system was explored using ten healthy young men. For each participant, two bedding systems, one inducing the strongest limb muscle force (strong bedding system) and the other inducing the weakest limb force (weak bedding system), were identified using MMT. Each bedding system, in total five mattresses and eight pillows of different firmness, was used for two continuous weeks at the participant's home in a random and double-blind sequence. A sleep log, a questionnaire, and a polysomnography were used to differentiate the two bedding systems. Heart rate variability and arterial pressure variability analyses showed that the strong bedding system resulted in decreased cardiovascular sympathetic modulation, increased cardiac vagal activity, and increased baroreceptor reflex sensitivity during sleep as compared to the weak bedding system. Different bedding systems have distinct cardiovascular effects during sleep that can be predicted by MMT.

The Effect of Bedding System Selected by Manual Muscle Testing on Sleep-Related Cardiovascular Functions

PubMed Central

Kuo, Terry B. J.; Li, Jia-Yi; Lai, Chun-Ting; Huang, Yu-Chun; Hsu, Ya-Chuan; Yang, Cheryl C. H.

2013-01-01

Background. Different types of mattresses affect sleep quality and waking muscle power. Whether manual muscle testing (MMT) predicts the cardiovascular effects of the bedding system was explored using ten healthy young men. Methods. For each participant, two bedding systems, one inducing the strongest limb muscle force (strong bedding system) and the other inducing the weakest limb force (weak bedding system), were identified using MMT. Each bedding system, in total five mattresses and eight pillows of different firmness, was used for two continuous weeks at the participant's home in a random and double-blind sequence. A sleep log, a questionnaire, and a polysomnography were used to differentiate the two bedding systems. Results and Conclusion. Heart rate variability and arterial pressure variability analyses showed that the strong bedding system resulted in decreased cardiovascular sympathetic modulation, increased cardiac vagal activity, and increased baroreceptor reflex sensitivity during sleep as compared to the weak bedding system. Different bedding systems have distinct cardiovascular effects during sleep that can be predicted by MMT. PMID:24371836

Mesoarchean Banded Iron Formation sequences in Dixon Island-Cleaverville Formation, Pilbara Australia: Oxygenic signal from DXCL project

NASA Astrophysics Data System (ADS)

Kiyokawa, S.; Ito, T.; Ikehara, M.; Yamaguchi, K. E.; Naraoka, H.; Onoue, T.; Horie, K.; Sakamoto, R.; Aihara, Y.; Miki, T.

2013-12-01

The 3.2-3.1 Ga Dixon island-Cleaverville formations are well-preserved Banded Iron Formation (BIF) within hydrothermal oceanic sequence at oceanic island arc setting (Kiyokawa et al., 2002, 2006, 2012). The stratigraphy of the Dixon Island (3195+15Ma) -Cleaverville (3108+13Ma) formations shows the well preserved environmental condition at the Mesoarchean ocean floor. The stratigraphy of these formations are formed about volcano-sedimentary sequences with hydrothermal chert, black shale and banded iron formation to the top. Based on the scientific drilling of DXCL project at 2007 and 2011, detail lithology between BIF sequence was clearly understood. Four drilling holes had been done at coastal sites; the Dixon Island Formation is DX site (100m) and the Cleaverville Formation is CL2 (40m), CL1 (60m) and CL3 (200m) sites and from stratigraphic bottom to top. Coarsening and thickening upward black shale-BIF sequences are well preserved of the stratigraphy form the core samples. The Dixon Island Formation consists komatiite-rhyolite sequences with many hydrothermal veins and very fine laminated cherty rocks above them. The Cleaverville Formation contains black shale, fragments-bearing pyroclastic beds, white chert, greenish shale and BIF. The CL3 core, which drilled through BIF, shows siderite-chert beds above black shale identified before magnetite lamination bed. U-Pb SHRIMP data of the tuff in lower Dixon Island Formation is 3195+15 Ma and the pyroclastic sequence below the Cleaverville BIF is 3108+13 Ma. Sedimentation rate of these sequence is 2-8 cm/ 1000year. The hole section of the organic carbon rich black shales below BIF are similar amount of organic content and 13C isotope (around -30per mill). There are very weak sulfur MIF signal (less 0.2%) in these black shale sequence. Our result show that thick organic rich sediments may be triggered to form iron rich siderite and magnetite iron beds. The stratigraphy in this sequence quite resemble to other Iron formation (eg. Hamersley BIF). So we investigate that the Cleaverville iron formation, which is one of the best well known Mesoarchean iron formation, was already started cyanobacteria oxygen production system to used pre-syn iron sedimentation at anoxic oceanic condition.

Late Jurassic-Early Cretaceous radiolarian age constraints from the sedimentary cover of the Amasia ophiolite (NW Armenia), at the junction between the Izmir-Ankara-Erzinçan and Sevan-Hakari suture zones

NASA Astrophysics Data System (ADS)

Danelian, T.; Asatryan, G.; Galoyan, Gh.; Sahakyan, L.; Stepanyan, J.

2016-01-01

The Amasia ophiolite, situated at the northernmost corner of Armenia, is part of the Sevan-Hakari suture zone which links with the Izmir-Ankara-Erzinçan suture zone in northern Turkey. Three new radiolarian assemblages have been extracted from siliceous sedimentary rocks that accumulated on the Amasia ophiolite in an oceanic setting. Two of these assemblages were extracted from red-brownish bedded cherts overlying basaltic lavas; one of these is likely to be middle Oxfordian to early Kimmeridgian in age, while the second correlates with the Berriasian. Similar time-equivalent lava-chert sequences have been dated recently using radiolarians from the Stepanavan, Vedi and Sevan ophiolite units, where they are considered to relate to submarine volcanic activity in the back-arc marginal basin in which the Armenian ophiolites were formed. The third radiolarian assemblage, of late Barremian age, was extracted from a more than 15-m-thick volcaniclastic-chert sequence. The related volcanic activity is likely to have been subaerial and probably relates to the formation of an oceanic volcanic plateau; no Cretaceous subaerial volcanism has been previously recorded in the Lesser Caucasus area.

THE RED SEQUENCE AT BIRTH IN THE GALAXY CLUSTER Cl J1449+0856 AT z = 2

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

Strazzullo, V.; Pannella, M.; Daddi, E.

We use Hubble Space Telescope /WFC3 imaging to study the red population in the IR-selected, X-ray detected, low-mass cluster Cl J1449+0856 at z = 2, one of the few bona fide established clusters discovered at this redshift, and likely a typical progenitor of an average massive cluster today. This study explores the presence and significance of an early red sequence in the core of this structure, investigating the nature of red-sequence galaxies, highlighting environmental effects on cluster galaxy populations at high redshift, and at the same time underlining similarities and differences with other distant dense environments. Our results suggest thatmore » the red population in the core of Cl J1449+0856 is made of a mixture of quiescent and dusty star-forming galaxies, with a seedling of the future red sequence already growing in the very central cluster region, and already characterizing the inner cluster core with respect to lower-density environments. On the other hand, the color–magnitude diagram of this cluster is definitely different from that of lower-redshift z ≲ 1 clusters, as well as of some rare particularly evolved massive clusters at similar redshift, and it is suggestive of a transition phase between active star formation and passive evolution occurring in the protocluster and established lower-redshift cluster regimes.« less

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes).

PubMed

Kutschera, Verena E; Lecomte, Nicolas; Janke, Axel; Selva, Nuria; Sokolov, Alexander A; Haun, Timm; Steyer, Katharina; Nowak, Carsten; Hailer, Frank

2013-06-05

Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)

PubMed Central

2013-01-01

Background Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Results Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. Conclusions The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan’s northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories. PMID:23738594

Regional hydrology of the Green River-Moab area, northwestern Paradox Basin, Utah

USGS Publications Warehouse

Rush, F.E.; Whitfield, M.S.; Hart, I.M.

1984-01-01

The Green River-Moab area encompasses about 7,800 square kilometers or about 25 percent of the Paradox basin. The entire Paradox basin is a part of the Colorado Plateaus that is underlain by a thick sequence of evaporite (salt) beds of Pennsylvanian age. The rock units that underlie the area have been grouped into hydrogeologic units based on their water-transmitting ability. Confining beds consist of evaporite beds of mostly salt, and over- lying and underlying thick sequences of rocks with minimal permeability; above and below these confining beds are aquifers. The upper Mesozoic sand- stone aquifer, probably is the most permeable hydrogeologic unit of the area and is the subject of this investigation. The principal component of ground- water outflow from this aquifer probably is subsurface flow to regional streams (the Green and Colorado Rivers) and is about 100 million cubic meters per year. All other components of outflow are relatively small. The average annual recharge to the aquifer is about 130 million cubic meters, of which about 20 million cubic meters is from local precipitation. For the lower aquifer, all recharge and discharge probably is by subsurface flow and was not estimated.The aquifers are generally isolated from the evaporite beds by the bounding confining beds; as a result, most ground water has little if any contact with the evaporites. Brines are present in the confining beds, but solution of beds o£ salt probably is very slow in most parts of the area. No brine discharges' have been identified.

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.

PubMed

Storari, Michelangelo; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-03-12

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. Copyright © 2015 Storari et al.

Genome sequence of "Candidatus Mycoplasma haemolamae" strain purdue, a red blood cell pathogen of alpacas (Vicugna pacos) and llamas (Lama glama).

PubMed

Guimaraes, Ana M S; Toth, Balazs; Santos, Andrea P; do Nascimento, Naíla C; Kritchevsky, Janice E; Messick, Joanne B

2012-11-01

We report the complete genome sequence of "Candidatus Mycoplasma haemolamae," an endemic red-cell pathogen of camelids. The single, circular chromosome has 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation.

Validation of a model for investigating red cell mass changes during weightlessness

NASA Technical Reports Server (NTRS)

Leonard, J. I.

1976-01-01

The model, both the conceptual model and simulation model, provided a convenient framework on which to demonstrate the commonality between such diverse stresses as descent from altitude, red cell infusions, bed rest, and weightlessness. The results suggest that all of these stresses induce an increased blood hematocrit leading to tissue hyperoxia and eventual inhibition of the erythyocyte producing circuit until the hyperoxic condition is relieved. The erythropoietic system was acting, in these situations, as if it were an hematocrit sensor and regulator. In these terms the decreases in red cell mass during Skylab may be explained in terms of normal feedback regulation of the erythropoietic system in the face of sustained decreases in plasma colume.

Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala).

PubMed

Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H

2013-04-02

Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.

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

Hurst, J.M.; Lapointe, P.A.; Nyein, U.K.

Three Oligocene-Miocene carbonate depositional morphologies commonly occur: shoals, reefs, and isolated platforms. Lenticular shoals (0-25 m thick, 1 km long) are stacked and intercalated with siliciclastic mudstones. Facies include trough/festoon cross-bedded benthic foram grainstones passing laterally and vertically into red-algal dominated graded-laminated beds, bioturbated silty calcareous mudstone, and siliciclastic sandy foram wackestone and packstone. The morphology and facies are hydrodynamically controlled. Pinnacle reefs (1-2 km[sup 2]) dominated by red-algae, branching corals, and large mollusks occur on structure or aligned within shelf mudstones. The latter location reflects low sedimentation rates and hydrodynamic control. Isolated platforms (up to 150 km[sup 2]) aremore » environmental mosaics of marginal path reefs and shoals, interior lagoons, and islands plus marginal slopes. Facies are similar to shoals and reefs except there are more muddy fabrics and less high-energy facies. They develop on tilted fault blocks or eroded submerged arcs in the offshore Gulf of Martaban, distal to the ancestral Irrawaddy delta.« less

The Spatial-Temporal Analysis of Ecological Environment of Red Bed Hills in East Sichuan - Taking LU County as a Case

NASA Astrophysics Data System (ADS)

Liu, H.; Liu, Y.; Wang, X.; Liu, J.

2018-04-01

Good ecological environment is the foundation of human existence and development, the development of society and economy must be based on the premise of maintaining the stability and balance of the ecological environment. RS and GIS technology are used in this paper while the red-bed hills of Sichuan Province-Lu County have been taken as an example. According to the ecological environment characteristics of the study areas and the principle of choosing evaluation index, this paper selected six evaluation indicators (elevation, slope, aspect, vegetation cover, land use, gully density) to establish evaluation index system of ecological environment of Lu County. This paper determine the weight of each evaluation index by AHP (Analytic Hierarchy Process) and establishes a comprehensive evaluation model by the weighted comprehensive evaluation method. This model is used to divide the ecological environment quality of Lu County into excellent, good, middle, poor and worse, and to analyze the ecological environment change in Lu County in recent ten years.

Late-summer food of red-winged blackbirds in a fresh tidal-river marsh

USGS Publications Warehouse

Meanley, B.

1961-01-01

During late summer in the Delaware Valley and Chesapeake Bay region, hundreds of thousands of Red-winged Blackbirds feed in wild rice beds of fresh tidal-river marshes. The period during which wild rice seed is available coincides with the ripening period of a part of the corn crop, and there is evidence to indicate that the availability of the wild rice reduces bird feeding pressure on corn in the area. The importance of wild rice and other marsh plants to the redwing during the period when wild rice seed is available was studied further by field observations and by analysis of stomach contents of 130 birds collected in wild rice beds of the Patuxent River in southern Maryland. Seeds of marsh plants formed the bulk of the food of redwings collected. Dotted smartweed, wild rice, and Walter?s millet were the most important food plants. Corn was the fourth most important item. It occurred in 35, approximately one-fourth, of the stomachs

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

Friis Hills Drilling Project - Coring an Early to mid-Miocene terrestrial sequence in the Transantarctic Mountains to examine climate gradients and ice sheet variability along an inland-to-offshore transect

NASA Astrophysics Data System (ADS)

Lewis, A. R.; Levy, R. H.; Naish, T.; Gorman, A. R.; Golledge, N.; Dickinson, W. W.; Kraus, C.; Florindo, F.; Ashworth, A. C.; Pyne, A.; Kingan, T.

2015-12-01

The Early to mid-Miocene is a compelling interval to study Antarctic ice sheet (AIS) sensitivity. Circulation patterns in the southern hemisphere were broadly similar to present and reconstructed atmospheric CO2 concentrations were analogous to those projected for the next several decades. Geologic records from locations proximal to the AIS are required to examine ice sheet response to climate variability during this time. Coastal and offshore drill core records recovered by ANDRILL and IODP provide information regarding ice sheet variability along and beyond the coastal margin but they cannot constrain the extent of inland retreat. Additional environmental data from the continental interior is required to constrain the magnitude of ice sheet variability and inform numerical ice sheet models. The only well-dated terrestrial deposits that register early to mid-Miocene interior ice extent and climate are in the Friis Hills, 80 km inland. The deposits record multiple glacial-interglacial cycles and fossiliferous non-glacial beds show that interglacial climate was warm enough for a diverse biota. Drifts are preserved in a shallow valley with the oldest beds exposed along the edges where they terminate at sharp erosional margins. These margins reveal drifts in short stratigraphic sections but none is more than 13 m thick. A 34 m-thick composite stratigraphic sequence has been produced from exposed drift sequences but correlating beds in scattered exposures is problematic. Moreover, much of the sequence is buried and inaccessible in the basin center. New seismic data collected during 2014 reveal a sequence of sediments at least 50 m thick. This stratigraphic package likely preserves a detailed and more complete sedimentary sequence for the Friis Hills that can be used to refine and augment the outcrop-based composite stratigraphy. We aim to drill through this sequence using a helicopter-transportable diamond coring system. These new cores will allow us to obtain continuous measurements on unweathered material through the terrestrial sequence. Beds of tephra are exposed in outcrop and we expect to encounter these key age markers in the cored sequence. These new high quality, well-dated terrestrial data will be directly compared to marine cores to provide environmental data across a broad onshore-offshore transect.

The Optical Gravitational Lensing Experiment. Ellipsoidal Variability of Red Giants in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Soszynski, I.; Udalski, A.; Kubiak, M.; Szymanski, M. K.; Pietrzynski, G.; Zebrun, K.; Szewczyk, O.; Wyrzykowski, L.; Dziembowski, W. A.

2004-12-01

We used the OGLE-II and OGLE-III photometry of red giants in the Large Magellanic Cloud to select and study objects revealing ellipsoidal variability. We detected 1546 candidates for long period ellipsoidal variables and 121 eclipsing binary systems with clear ellipsoidal modulation. The ellipsoidal red giants follow a period--luminosity (PL) relationship (sequence E), and the scatter of the relation is correlated with the amplitude of variability: the larger the amplitude, the smaller the scatter. We note that some of the ellipsoidal candidates exhibit simultaneously OGLE Small Amplitude Red Giants pulsations. Thus, in some cases the Long Secondary Period (LSP) phenomenon can be explained by the ellipsoidal modulation. We also select about 1600 red giants with distinct LSP, which are not ellipsoidal variables. We discover that besides the sequence D in the PL diagram known before, the LSP giants form additional less numerous sequence for longer periods. We notice that the PL sequence of the ellipsoidal candidates is a direct continuation of the LSP sequence toward fainter stars, what might suggest that the LSP phenomenon is related to binarity but there are strong arguments against such a possibility. About 10% of the presented light curves reveal clear deformation by the eccentricity of the system orbits. The largest estimated eccentricity in our sample is about 0.4. All presented data, including individual BVI observations and finding charts are available from the OGLE Internet archive.

Genome Sequence of “Candidatus Mycoplasma haemolamae” Strain Purdue, a Red Blood Cell Pathogen of Alpacas (Vicugna pacos) and Llamas (Lama glama)

PubMed Central

Toth, Balazs; Santos, Andrea P.; do Nascimento, Naíla C.; Kritchevsky, Janice E.

2012-01-01

We report the complete genome sequence of “Candidatus Mycoplasma haemolamae,” an endemic red-cell pathogen of camelids. The single, circular chromosome has 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation. PMID:23105057

Tonian paleomagnetism of the red beds of Madiyi Formation, lower Banxi Group in South China: implications for pre-Sturtian climate, Rodinia reconstruction and true polar wander

NASA Astrophysics Data System (ADS)

Hanbiao, X.; Zhang, S.; Xiao, Q.; Li, H.; Chang, L.; Fu, H.; Liu, R.

2017-12-01

We present a new Tonian paleomagnetic pole from the red beds of ca. 810 Ma Madiyi Formation, lower Banxi Group in the central South China Block (SCB). Detailed thermal demagnetization reveals two distinct magnetic components among the samples. A low temperature component (LTC), removed from almost all the samples below 580°C, yielded a paleopole at 68.0°N, 211.7°E (A95=1.9) that is close to the pole of late Jurassic. The high temperature component (HTC), isolated between 580-690°C, gave a mean direction of D=310.0°, I=57.4°, α95=3.7 (108 samples of 13 sites) after bedding correction, corresponding to a paleomagnetic pole at 47.6°N, 46.7°E (A95=5.6°). The HTC passed a reversal test on 95% and 99% confidence level. Directional distribution of the HTC show significant elongation which may indicate inclination shallowing, and the inclination was corrected to 75.1° using E/I technique, corresponding to a paleolatitude at 60.8±3.4° of research area. The paleopole calculated from the E/I-corrected HTC is at 44.8°N, 80.2°E (A95=3.4°), being significantly distinct from any younger poles of the SCB. This new pole plus existing high quality paleomagnetic poles from the SCB demonstrate that the SCB experienced a polar-equatorial region drifting tendency from 825 Ma to Cambrian. The high-paleolatitude red beds rather than glacial sediments deposited in the SCB, combined with coeval widespread evaporative in other continents, possibly suggest pre-Cryogenian global greenhouse climate. In our reconstruction at 800 Ma, the SCB was placed on the northwest periphery of Rodinia, with its western margin adjacent to the northern India, rather than occupying a central position of Rodinia. The distribution of 825-750 Ma poles of the SCB, East Svalbard, Australia, Laurentia, India along a great arc may be associated with true polar wander around 800 Ma.

The rDNA ITS region in the lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): intragenomic variability and putative pseudogenic sequences.

PubMed

Ruggiero, Maria Valeria; Procaccini, Gabriele

2004-01-01

Halophila stipulacea is a dioecious marine angiosperm, widely distributed along the western coasts of the Indian Ocean and the Red Sea. This species is thought to be a Lessepsian immigrant that entered the Mediterranean Sea from the Red Sea after the opening of the Suez Canal (1869). Previous studies have revealed both high phenotypic and genetic variability in Halophila stipulacea populations from the western Mediterranean basin. In order to test the hypothesis of a Lessepsian introduction, we compare genetic polymorphism between putative native (Red Sea) and introduced (Mediterranean) populations through rDNA ITS region (ITS1-5.8S-ITS2) sequence analysis. A high degree of intraindividual variability of ITS sequences was found. Most of the intragenomic polymorphism was due to pseudogenic sequences, present in almost all individuals. Features of ITS functional sequences and pseudogenes are described. Possible causes for the lack of homogenization of ITS paralogues within individuals are discussed.

Volatile organic compound adsorption in a gas-solid fluidized bed.

PubMed

Ng, Y L; Yan, R; Tsen, L T S; Yong, L C; Liu, M; Liang, D T

2004-01-01

Fluidization finds many process applications in the areas of catalytic reactions, drying, coating, combustion, gasification and microbial culturing. This work aims to compare the dynamic adsorption characteristics and adsorption rates in a bubbling fluidized bed and a fixed bed at the same gas flow-rate, gas residence time and bed height. Adsorption with 520 ppm methanol and 489 ppm isobutane by the ZSM-5 zeolite of different particle size in the two beds enabled the differentiation of the adsorption characteristics and rates due to bed type, intraparticle mass transfer and adsorbate-adsorbent interaction. Adsorption of isobutane by the more commonly used activated carbon provided the comparison of adsorption between the two adsorbent types. With the same gas residence time of 0.79 seconds in both the bubbling bed and fixed bed of the same bed size of 40 mm diameter and 48 mm height, the experimental results showed a higher rate of adsorption in the bubbling bed as compared to the fixed bed. Intraparticle mass transfer and adsorbent-adsorbate interaction played significant roles in affecting the rate of adsorption, with intraparticle mass transfer being more dominant. The bubbling bed was observed to have a steeper decline in adsorption rate with respect to increasing outlet concentration compared to the fixed bed. The adsorption capacities of zeolite for the adsorbates studied were comparatively similar in both beds; fluidizing, and using smaller particles in the bubbling bed did not increase the adsorption capacity of the ZSM-5 zeolite. The adsorption capacity of activated carbon for isobutane was much higher than the ZSM-5 zeolite for isobutane, although at a lower adsorption rate. Fourier transform infra-red (FTIR) spectroscopy was used as an analytical tool for the quantification of gas concentration. Calibration was done using a series of standards prepared by in situ dilution with nitrogen gas, based on the ideal gas law and relating partial pressure to gas concentration. Concentrations up to 220 ppm for methanol and 75 ppm for isobutane were prepared using this method.

Ages of intermediate-age Magellanic Cloud star clusters

NASA Technical Reports Server (NTRS)

Flower, P. J.

1984-01-01

Ages of intermediate-age Large Magellanic Cloud star clusters have been estimated without locating the faint, unevolved portion of cluster main sequences. Six clusters with established color-magnitude diagrams were selected for study: SL 868, NGC 1783, NGC 1868, NGC 2121, NGC 2209, and NGC 2231. Since red giant photometry is more accurate than the necessarily fainter main-sequence photometry, the distributions of red giants on the cluster color-magnitude diagrams were compared to a grid of 33 stellar evolutionary tracks, evolved from the main sequence through core-helium exhaustion, spanning the expected mass and metallicity range for Magellanic Cloud cluster red giants. The time-dependent behavior of the luminosity of the model red giants was used to estimate cluster ages from the observed cluster red giant luminosities. Except for the possibility of SL 868 being an old globular cluster, all clusters studied were found to have ages less than 10 to the 9th yr. It is concluded that there is currently no substantial evidence for a major cluster population of large, populous clusters greater than 10 to the 9th yr old in the Large Magellanic Cloud.

Mechanical stratigraphic controls on natural fracture spacing and penetration

NASA Astrophysics Data System (ADS)

McGinnis, Ronald N.; Ferrill, David A.; Morris, Alan P.; Smart, Kevin J.; Lehrmann, Daniel

2017-02-01

Fine-grained low permeability sedimentary rocks, such as shale and mudrock, have drawn attention as unconventional hydrocarbon reservoirs. Fracturing - both natural and induced - is extremely important for increasing permeability in otherwise low-permeability rock. We analyze natural extension fracture networks within a complete measured outcrop section of the Ernst Member of the Boquillas Formation in Big Bend National Park, west Texas. Results of bed-center, dip-parallel scanline surveys demonstrate nearly identical fracture strikes and slight variation in dip between mudrock, chalk, and limestone beds. Fracture spacing tends to increase proportional to bed thickness in limestone and chalk beds; however, dramatic differences in fracture spacing are observed in mudrock. A direct relationship is observed between fracture spacing/thickness ratio and rock competence. Vertical fracture penetrations measured from the middle of chalk and limestone beds generally extend to and often beyond bed boundaries into the vertically adjacent mudrock beds. In contrast, fractures in the mudrock beds rarely penetrate beyond the bed boundaries into the adjacent carbonate beds. Consequently, natural bed-perpendicular fracture connectivity through the mechanically layered sequence generally is poor. Fracture connectivity strongly influences permeability architecture, and fracture prediction should consider thin bed-scale control on fracture heights and the strong lithologic control on fracture spacing.

GEOCHEMICAL MODELING OF ARSENIC SPECIATION AND MOBILIZATION: IMPLICATIONS FOR BIOREMEDIATION

EPA Science Inventory

Geochemical modeling techniques were used to examine the biogeochemical linkages between Fe, S, and As in shallow alluvial aquifers. We modeled: 1) the adsorption and desorption of As on the surface of hydrous ferric oxides (HFO’s) in stream beds under aerobic conditions; 2) red...

Association of MC3R gene polymorphisms with body weight in the red fox and comparative gene organization in four canids.

PubMed

Skorczyk, A; Flisikowski, K; Szydlowski, M; Cieslak, J; Fries, R; Switonski, M

2011-02-01

There are five genes encoding melanocortin receptors. Among canids, the genes have mainly been studied in the dog (MC1R, MC2R and MC4R). The MC4R gene has also been analysed in the red fox. In this report, we present a study of chromosome localization, comparative sequence analysis and polymorphism of the MC3R gene in the dog, red fox, arctic fox and Chinese raccoon dog. The gene was localized by FISH to the following chromosome: 24q24-25 in the dog, 14p16 in the red fox, 18q13 in the arctic fox and NPP4p15 in the Chinese raccoon dog. A high identity level of the MC3R gene sequences was observed among the species, ranging from 96.0% (red fox--Chinese raccoon dog) to 99.5% (red fox--arctic fox). Altogether, eight polymorphic sites were found in the red fox, six in the Chinese raccoon dog and two in the dog, while the arctic fox appeared to be monomorphic. In addition, association of several polymorphisms with body weight was analysed in red foxes (the number of genotyped animals ranged from 319 to 379). Two polymorphisms in the red fox, i.e. a silent substitution c.957A>C and c.*185C>T in the 3'-flanking sequence, showed a significant association (P < 0.01) with body weight. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

Fixed-bed operation for manganese removal from water using chitosan/bentonite/MnO composite beads.

PubMed

Muliwa, Anthony M; Leswifi, Taile Y; Maity, Arjun; Ochieng, Aoyi; Onyango, Maurice S

2018-04-24

In the present study, a new composite adsorbent, chitosan/bentonite/manganese oxide (CBMnO) beads, cross-linked with tetraethyl-ortho-silicate (TEOS) was applied in a fixed-bed column for the removal of Mn (II) from water. The adsorbent was characterised by scanning electron microscopy (SEM), Fourier transform infra-red (FT-IR), N 2 adsorption-desorption and X-ray photoelectron spectroscopy (XPS) techniques, and moreover the point of zero charge (pH pzc ) was determined. The extend of Mn (II) breakthrough behaviour was investigated by varying bed mass, flow rate and influent concentration, and by using real environmental water samples. The dynamics of the column showed great dependency of breakthrough curves on the process conditions. The breakthrough time (t b ), bed exhaustion time (t s ), bed capacity (q e ) and the overall bed efficiency (R%) increased with an increase in bed mass, but decreased with the increase in both influent flow rate and concentration. Non-linear regression suggested that the Thomas model effectively described the breakthrough curves while large-scale column performance could be estimated by the bed depth service time (BDST) model. Experiments with environmental water revealed that coexisting ions had little impact on Mn (II) removal, and it was possible to achieve 6.0 mg/g breakthrough capacity (q b ), 4.0 L total treated water and 651 bed volumes processed with an initial concentration of 38.5 mg/L and 5.0 g bed mass. The exhausted bed could be regenerated with 0.001 M nitric acid solution within 1 h, and the sorbent could be reused twice without any significant loss of capacity. The findings advocate that CBMnO composite beads can provide an efficient scavenging pathway for Mn (II) in polluted water.

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

USDA-ARS?s Scientific Manuscript database

The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the last two decades. This global resurgence is likely linked to increased international travel and commerce and widespread insecticide resistance. Analyses of the C. le...

Investigating the Effect of Ligand Amount and Injected Therapeutic Activity: A Simulation Study for 177Lu-Labeled PSMA-Targeting Peptides

PubMed Central

Schuchardt, Christiane; Kulkarni, Harshad R.; Shahinfar, Mostafa; Singh, Aviral; Glatting, Gerhard; Baum, Richard P.; Beer, Ambros J.

2016-01-01

In molecular radiotherapy with 177Lu-labeled prostate specific membrane antigen (PSMA) peptides, kidney and/or salivary glands doses limit the activity which can be administered. The aim of this work was to investigate the effect of the ligand amount and injected activity on the tumor-to-normal tissue biologically effective dose (BED) ratio for 177Lu-labeled PSMA peptides. For this retrospective study, a recently developed physiologically based pharmacokinetic model was adapted for PSMA targeting peptides. General physiological parameters were taken from the literature. Individual parameters were fitted to planar gamma camera measurements (177Lu-PSMA I&T) of five patients with metastasizing prostate cancer. Based on the estimated parameters, the pharmacokinetics of tumor, salivary glands, kidneys, total body and red marrow was simulated and time-integrated activity coefficients were calculated for different peptide amounts. Based on these simulations, the absorbed doses and BEDs for normal tissue and tumor were calculated for all activities leading to a maximal tolerable kidney BED of 10 Gy2.5/cycle, a maximal salivary gland absorbed dose of 7.5 Gy/cycle and a maximal red marrow BED of 0.25 Gy15/cycle. The fits yielded coefficients of determination > 0.85, acceptable relative standard errors and low parameter correlations. All estimated parameters were in a physiologically reasonable range. The amounts (for 25−29 nmol) and pertaining activities leading to a maximal tumor dose, considering the defined maximal tolerable doses to organs of risk, were calculated to be 272±253 nmol (452±420 μg) and 7.3±5.1 GBq. Using the actually injected amount (235±155 μg) and the same maximal tolerable doses, the potential improvement for the tumor BED was 1–3 fold. The results suggest that currently given amounts for therapy are in the appropriate order of magnitude for many lesions. However, for lesions with high binding site density or lower perfusion, optimizing the peptide amount and activity might improve the tumor-to-kidney and tumor-to-salivary glands BED ratio considerably. PMID:27611841

Investigating the Effect of Ligand Amount and Injected Therapeutic Activity: A Simulation Study for 177Lu-Labeled PSMA-Targeting Peptides.

PubMed

Kletting, Peter; Schuchardt, Christiane; Kulkarni, Harshad R; Shahinfar, Mostafa; Singh, Aviral; Glatting, Gerhard; Baum, Richard P; Beer, Ambros J

2016-01-01

In molecular radiotherapy with 177Lu-labeled prostate specific membrane antigen (PSMA) peptides, kidney and/or salivary glands doses limit the activity which can be administered. The aim of this work was to investigate the effect of the ligand amount and injected activity on the tumor-to-normal tissue biologically effective dose (BED) ratio for 177Lu-labeled PSMA peptides. For this retrospective study, a recently developed physiologically based pharmacokinetic model was adapted for PSMA targeting peptides. General physiological parameters were taken from the literature. Individual parameters were fitted to planar gamma camera measurements (177Lu-PSMA I&T) of five patients with metastasizing prostate cancer. Based on the estimated parameters, the pharmacokinetics of tumor, salivary glands, kidneys, total body and red marrow was simulated and time-integrated activity coefficients were calculated for different peptide amounts. Based on these simulations, the absorbed doses and BEDs for normal tissue and tumor were calculated for all activities leading to a maximal tolerable kidney BED of 10 Gy2.5/cycle, a maximal salivary gland absorbed dose of 7.5 Gy/cycle and a maximal red marrow BED of 0.25 Gy15/cycle. The fits yielded coefficients of determination > 0.85, acceptable relative standard errors and low parameter correlations. All estimated parameters were in a physiologically reasonable range. The amounts (for 25-29 nmol) and pertaining activities leading to a maximal tumor dose, considering the defined maximal tolerable doses to organs of risk, were calculated to be 272±253 nmol (452±420 μg) and 7.3±5.1 GBq. Using the actually injected amount (235±155 μg) and the same maximal tolerable doses, the potential improvement for the tumor BED was 1-3 fold. The results suggest that currently given amounts for therapy are in the appropriate order of magnitude for many lesions. However, for lesions with high binding site density or lower perfusion, optimizing the peptide amount and activity might improve the tumor-to-kidney and tumor-to-salivary glands BED ratio considerably.

Y-Chromosome Markers for the Red Fox.

PubMed

Rando, Halie M; Stutchman, Jeremy T; Bastounes, Estelle R; Johnson, Jennifer L; Driscoll, Carlos A; Barr, Christina S; Trut, Lyudmila N; Sacks, Benjamin N; Kukekova, Anna V

2017-09-01

The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over 2 scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside 2 markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from 4 populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern United States), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the 2 previously known markers alone would have identified only 10 haplotypes. The haplotypes from the 4 populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Sedimentary facies and depositional history of the Swan Islands, Honduras

NASA Astrophysics Data System (ADS)

Ivey, Marvin L.; Breyer, John A.; Britton, Joseph C.

1980-10-01

Swan Island is a Honduran possession in the western Caribbean, located on the southeastern side of the Cayman Trench. Two sedimentary assemblages are found on the island: an older bedded sequence of mid-Tertiary age (Aquitanian or Burdigalian) and a younger sedimentary sequence of Late Pleistocene age. The older sequence is composed of a series of calcarenites, calcilutites, and siliciclastic mudstones; capping these are cliff-forming reefal carbonates of the younger sequence. The rocks of the older bedded sequence accumulated in deep water. Sedimentation consisted of a constant rain of pyroclastic debris interrupted by the episodic introduction of upslope carbonate material by turbidity currents. Uplift and deformation of this sequence was initiated sometime after the Early Miocene. By the Late Pleistocene, uplift had brought the rocks into water depths conducive to coral growth. Pleistocene sedimentation on the island was controlled by the interaction between tectonic uplift and eustatic sea-level changes. The primary controlling force on the tectonic history of the island is its proximity to the boundary between the North American and Caribbean plates.

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.

Geology of the Southern Guadalupe Mountains, Texas

USGS Publications Warehouse

King, Philip B.

1948-01-01

This report deals with an area of 425 square miles in the western part of Texas, immediately south of the New Mexico line. The area comprises the south end of the Guadalupe Mountains and the adjacent part of the Delaware Mountains; it includes the highest peaks in the State of Texas. The area is a segment of a large mountain mass that extends 50 miles or more northward and southward. The report describes the geology of the area, that is, the nature of its rocks, tectonics, and surface features, and the evidence that they give as to the evolution of the area through geologic time. Incidental reference is made to the geology of surrounding regions in order to place the area in its environment. The Permian system of the southwestern United States has been until recently one of the intriguing but little known subjects of American stratigraphy. In the latter half of the nineteenth century after the western. United States was settled, the "red bed" sections of the Permian were studied and reported on by many geologists, but up to 1920 the existence of a contemporaneous marine sequence in western Texas and southeastern New Mexico was little appreciated. Since that year the discovery of extensive oil fields and potash beds in this region gave an impetus to the study of the Permian rocks, and furnished the geologist with records of hundreds of drill holes from which to deduce the nature of the strata not exposed at the surface. At the same time geologists have studied the rocks in the outcropping areas, and have compared them with the strata encountered by drilling.Much remains to be done in order to understand the history of Permian time in the region. The physical and chemical conditions that caused. the deposition of .the various and often complexly related deposits need to be better understood. More of the fossils of the rich and interesting marine faunas should be described, and the relations of the fossils to their environments should be determined. Further, a satisfactory scheme of correlation is needed, and also a subdivision into series that will express the contemporaneity of strata in different areas. One useful contribution to the solution of these problems is the detailed study of sequences of rocks exposed at the surface in the different mountain ranges of Texas and New Mexico.This report deals with one such sequence of rocks in western Texas, the one exposed in the southern Guadalupe Mountains (fig. 1). Here, the Permian rocks are magnificently exposed, to a thickness of about 4,000 feet (pl. 1). They are all of marine origin, and belong to the middle part of the system, with the base concealed and the top absent. Overlying and underlying beds, however, are found in nearby areas.

RED TAPE AND CLEAN AIR: TITLE V AIR POLLUTION PERMITTING IMPLEMENTATION AS A TEST BED FOR THEORY DEVELOPMENT. (R824753)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

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

10Be concentrations of Red soils in Southwest Japan and its possibility of dating

NASA Astrophysics Data System (ADS)

Maejima, Y.; Matsuzaki, H.; Nakano, C.

2004-08-01

10Be concentrations of six Red soils distributed in Southwest Japan ranged from 0.8 × 108 to 2.7 × 109 atoms g-1, and minimum absolute ages were estimated by inventory of meteoric 10Be. The results are follows: Red soils on Toyota derived from granite (⩽25 ka), Kashii derived from Tertiary shale (⩽24 ka), Akiyoshidai derived from limestone (⩽110 ka), Okinawa Island derived from Kunigami gravel bed (⩽9 ka) and Ogasawara Island derived from agglomerate and Boninite (⩽22 and ⩽7 ka) were obtained, respectively. Soil age except with Akiyoshidai indicated younger age. It suggested that the loss of 10Be from the soil was caused by leaching of 10Be or by soil erosion, and 10Be is susceptible to leaching out from these Red soils under the humid climate condition such as Southwest Japan.

Ecology of red maple swamps in the glaciated northeast: A community profile

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

Golet, F.C.; Calhoun, A.J.K.; DeRagon, W.R.

1993-06-01

The report is part of a series of profiles on the ecology of wetland and deepwater habitats. This particular profile addresses red maple swamps in the glaciated northeastern United States. Red maple (Acer rubrum) swamp is a dominant wetland type in most of the region; it reaches the greatest abundance in southern New England and northern New Jersey; where it comprises 60-80% of all inland wetlands. Red maple swamps occur in a wide variety of hydrogeologic settings, from small, isolated basins in till or glaciofluvial deposits to extensive wetland complexes on glacial lake beds, and from hillside seeps to streammore » floodplains and lake edges. Individual swamps may be seasonally flooded, temporarily flooded, or seasonally saturated, and soils may be mineral or organic. As many as five distinct vegetation layers may occur in these swamps, including trees, saplings, shrubs, herbs, and ground cover plants such as bryophytes and clubmosses.« less

Development of a trickle bed reactor of electro-Fenton process for wastewater treatment.

PubMed

Lei, Yangming; Liu, Hong; Shen, Zhemin; Wang, Wenhua

2013-10-15

To avoid electrolyte leakage and gas bubbles in the electro-Fenton (E-Fenton) reactors using a gas diffusion cathode, we developed a trickle bed cathode by coating a layer composed of carbon black and polytetrafluoroethylene (C-PTFE) onto graphite chips instead of carbon cloth. The trickle bed cathode was optimized by single-factor and orthogonal experiments, in which carbon black, PTFE, and a surfactant were considered as the determinant of the performance of graphite chips. In the reactor assembled by the trickle bed cathode, H2O2 was generated with a current of 0.3A and a current efficiency of 60%. This performance was attributed to the fine distribution of electrolyte and air, as well as the effective oxygen transfer from the gas phase to the electrolyte-cathode interface. In terms of H2O2 generation and current efficiency, the developed trickle bed reactor had a performance comparable to that of the conventional E-Fenton reactor using a gas diffusion cathode. Further, 123 mg L(-1) of reactive brilliant red X-3B in aqueous solution was decomposed in the optimized trickle bed reactor as E-Fenton reactor. The decolorization ratio reached 97% within 20 min, and the mineralization reached 87% within 3h. Copyright © 2013 Elsevier B.V. All rights reserved.

Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea

NASA Astrophysics Data System (ADS)

DiBattista, Joseph D.; Coker, Darren J.; Sinclair-Taylor, Tane H.; Stat, Michael; Berumen, Michael L.; Bunce, Michael

2017-12-01

Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.

Controls on Middle Pennsylvanian peat-forming floras in the Eastern United States

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

Eble, C.F.

1992-01-01

Middle Pennsylvanian strata in the Central Appalachian Basin contain numerous coal beds that provide an opportunity to study changes in coal-spore floras on an intra- and inter-bed scale. Vertical spore abundance patterns within individual coal beds record the ecological dynamics, both biologic and edaphic, of peat-forming systems in this interval. Coal palynofloras of this interval show a stratigraphic change in composition. Early to Middle Pennsylvanian spore floras are largely dominated by Lycospora. Species of Densosporites, a small lycopsid genus, Granulatisporites, a fern/pteridosperm( )-allied genus, and Laevigatosporites, a calamite-related genus, commonly displace Lycospora vertically within these beds, reflecting patterns of ecologicalmore » succession. Spore floras from stratigraphically younger coal beds in this sequence exhibit similar intra-bed spore variation, but contain increased percentages of tree-fern spores, and tend to be more florally heterogeneous overall. Areas of clastic deposition within the swamps are also marked by changes in spore composition. These changes in coal palynology are paralleled by stratigraphic changes in coal appearance and associated strata composition. The proportion of dull'' coal lithotypes, frequency of clastic partings, and amount of coarse clastics in the enclosing strata all increase toward the top of this sequence. Climate may have been more important in determining the floral composition of Early through mid-Middle Pennsylvanian peat swamps, whereas climate, tectonics, and eustasy interacted to determine sediment volume and type in this interval.« less

Using Green and Red Fluorescent Proteins to Teach Protein Expression, Purification, and Crystallization

ERIC Educational Resources Information Center

Wu, Yifeng; Zhou, Yangbin; Song, Jiaping; Hu, Xiaojian; Ding, Yu; Zhang, Zhihong

2008-01-01

We have designed a laboratory curriculum using the green and red fluorescent proteins (GFP and RFP) to visualize the cloning, expression, chromatography purification, crystallization, and protease-cleavage experiments of protein science. The EGFP and DsRed monomer (mDsRed)-coding sequences were amplified by PCR and cloned into pMAL (MBP-EGFP) or…

Red, green, blue equals 1, 2, 3: Digit-color synesthetes can use structured digit information to boost recall of color sequences.

PubMed

Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

2015-01-01

Digit-color synesthetes report experiencing colors when perceiving letters and digits. The conscious experience is typically unidirectional (e.g., digits elicit colors but not vice versa) but recent evidence shows subtle bidirectional effects. We examined whether short-term memory for colors could be affected by the order of presentation reflecting more or less structure in the associated digits. We presented a stream of colored squares and asked participants to report the colors in order. The colors matched each synesthete's colors for digits 1-9 and the order of the colors corresponded either to a sequence of numbers (e.g., [red, green, blue] if 1 = red, 2 = green, 3 = blue) or no systematic sequence. The results showed that synesthetes recalled sequential color sequences more accurately than pseudo-randomized colors, whereas no such effect was found for the non-synesthetic controls. Synesthetes did not differ from non-synesthetic controls in recall of color sequences overall, providing no evidence of a general advantage in memory for serial recall of colors.

Molecular characterization of Wolbachia infection in bed bugs (Cimex lectularius) collected from several localities in France

PubMed Central

Akhoundi, Mohammad; Cannet, Arnaud; Loubatier, Céline; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Delaunay, Pascal

2016-01-01

Wolbachia symbionts are maternally inherited intracellular bacteria that have been detected in numerous insects including bed bugs. The objective of this study, the first epidemiological study in Europe, was to screen Wolbachia infection among Cimex lectularius collected in the field, using PCR targeting the surface protein gene (wsp), and to compare obtained Wolbachia strains with those reported from laboratory colonies of C. lectularius as well as other Wolbachia groups. For this purpose, 284 bed bug specimens were caught and studied from eight different regions of France including the suburbs of Paris, Bouches-du-Rhône, Lot-et-Garonne, and five localities in Alpes-Maritimes. Among the samples, 166 were adults and the remaining 118 were considered nymphs. In all, 47 out of 118 nymphs (40%) and 61 out of 166 adults (37%) were found positive on wsp screening. Among the positive cases, 10 samples were selected randomly for sequencing. The sequences had 100% homology with wsp sequences belonging to the F-supergroup strains of Wolbachia. Therefore, we confirm the similarity of Wolbachia strains detected in this epidemiological study to Wolbachia spp. reported from laboratory colonies of C. lectularius. PMID:27492563

Amelogenin Evolution and Tetrapod Enamel Structure

PubMed Central

Diekwisch, Thomas G.H.; Jin, Tianquan; Wang, Xinping; Ito, Yoshihiro; Schmidt, Marcella; Druzinsky, Robert; Yamane, Akira; Luan, Xianghong

2009-01-01

Amelogenins are the major proteins involved in tooth enamel formation. In the present study we have cloned and sequenced four novel amelogenins from three amphibian species in order to analyze similarities and differences between mammalian and non-mammalian amelogenins. The newly sequenced amphibian amelogenin sequences were from a Red-eyed tree frog (Litoria chloris) and a Mexican axolotl (Ambystoma mexicanum). We identified two amelogenin isoforms in the Eastern Red-backed Salamander (Plethodon cinereus). Sequence comparisons confirmed that non-mammalian amelogenins are overall shorter than their mammalian counterparts, contain less proline and less glutamine, and feature shorter polyproline tripeptide repeat stretches than mammalian amelogenins. We propose that unique sequence parameters of mammalian amelogenins might be a pre-requisite for complex mammalian enamel prism architecture. PMID:19828974

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.

OUTCROP-BASED LITHOFACIES AND DEPOSITIONAL SETTING OF ARSENIC-BEARING PERMIAN RED BEDS IN THE CENTRAL OKLAHOMA AQUIFER (COA), CLEVELAND COUNTY, OKLAHOMA

EPA Science Inventory

In January 2001, the Environmental Protection Agency established safe drinking water standards for arsenic at a maximum concentration of 10 mg/L. Results from the National Water-Quality Assessment Program (USGS), however, document the occurrence of arsenic concentrations in drin...

Geology of the Azacualpa geothermal site, Departamento de Comayagua Honduras, Central America: Field report. Geologia del area geotermica de Azacualpa Departamento de Comayagua, Honduras, America Central: Informe de camps (in English and Spanish)

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

Eppler, D.; Baldridge, S.; Perry, F.

1987-03-01

Thermal waters at the Azacualpa geothermal site are surfacing along fractures in the Atima Formation associated with the main north-south-trending Zacapa fault and the subordinate north-south-trending splays of the main fault. Permeability appears to be related to these fractures rather than to formation permeability in either the limestones of the Atima Formation or the Valle de Angeles Group red beds. Attitudes of lower Valle de Angeles Group red beds do not vary appreciably with distance away from the Zacapa fault, suggesting that the system is not behaving like a listric normal fault at depth. The ''Jaitique structure,'' as conjectured bymore » R. Fakundiny (1985), does not appear to have any manifestation at the surface in terms of structures that can be seen or measured in the bedrock. Its existence is considered unlikely at the present time. Calorimetry calculations indicate that the thermal anomaly at the Azacualpa site is producing approx.4.4 thermal megawatts.« less

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.

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.

Blood volume responses of men and women to bed rest

NASA Technical Reports Server (NTRS)

Fortney, S. M.; Turner, C.; Steinmann, L.; Driscoll, T.; Alfrey, C.

1994-01-01

This paper reviews a series of studies that indicate that estrogens play an important role in blood volume regulation. The first study illustrates that the plasma volume (PV) of ambulatory women fluctuates during the menstrual cycle, increasing during periods of elevated estrogens. In the second study, it was shown that exogenous and endogenous elevations in blood estrogens attenuate the decrease in PV during bed rest. In the third study, the hypothesis was tested that women, who naturally have a higher blood estrogen content compared with men, will have a smaller loss of PV during bed rest. Ten men and ten women underwent a 13-day, 6 degrees head-down bed rest. Plasma volume and red cell mass (RCM) were measured before and after bed rest using 125I and 51Cr labeling, respectively. Before bed rest, the men and women had similar blood volume (BV) and PV (mL/kg body weight), but the women had a smaller (P < .01) RCM (22.2 +/- 0.9 versus 26.2 +/- 0.8 mL/kg, mean +/- SE). During bed rest, the decrease in RCM (mL/kg) was similar in men and women. However, the decrease in BV was greater in men (8.0 +/- 0.8 mL/kg versus 5.8 +/- 0.8 mL/kg), because of a greater reduction in PV (6.3 +/- 0.6 mL/kg versus 4.1 +/- 0.6 mL/kg). Because the decline in BV has been proposed to contribute to the cardiovascular deconditioning after bed rest, it is possible that women may experience less cardiac and circulatory strain on reambulation.

Shallow high-resolution geophysical investigation along the western segment of the Victoria Lines Fault (island of Malta)

NASA Astrophysics Data System (ADS)

Villani, Fabio; D'Amico, Sebastiano; Panzera, Francesco; Vassallo, Maurizio; Bozionelos, George; Farrugia, Daniela; Galea, Pauline

2018-01-01

The Victoria Lines Fault (island of Malta) is a >15 km-long and N260°-striking segmented normal fault-system, which is probably inactive since the late Pliocene. In the westernmost part, the Fomm Ir-Rih segment displays comparable geologic throw and escarpment height ( 150-170 m), moreover its hangingwall hosts thin patches of Middle Pleistocene clastic continental deposits (red beds), which are poorly preserved elsewhere. We acquired two seismic transects, by collecting ambient vibration recordings, processed by using horizontal-to-vertical spectral ratios, complemented by one high-resolution 2-D refraction tomography survey crossing this fault where it is locally covered by red beds and recent colluvial deposits. We found a resonance peak at 1.0 Hz in the hangingwall block, whereas clear peaks in the range 5.0-10.0 Hz appear when approaching the subsurface fault, and we relate them to the fractured bedrock within the fault zone. The best-fit tomographic model shows a relatively high-Vp shallow body (Vp 2200-2400 m/s) that we relate to the weathered top of the Miocene Upper Coralline Limestone Fm., bounded on both sides by low-Vp regions (<1400 m/s). The latter are the smeared images of steep fault zones. Tomography further reveals a thick ( 15-20 m) low-Vp (<1000 m/s) zone, which could be a syn-tectonic wedge of colluvial deposits developed in the downthrown block. Surface waves analysis indicates lateral changes of the average shallow shear wave velocity, with Vs 130 m/s within the inferred fault zone, and Vs >230 m/s above the weathered top-bedrock. Our results depict a clear seismic signature of the Victoria Lines Fault, characterized by low seismic velocity and high amplification of ground motion. We hypothesize that, during the Middle Pleistocene, faulting may have affected the basal part of the red beds, so that this part of the investigated complex fault-system may be considered inactive since 0.6 Myr ago.

[Molecular cloning of the DNA sequence of activin beta A subunit gene mature peptides from panda and related species and its application in the research of phylogeny and taxonomy].

PubMed

Wang, Xiao-Jing; Wang, Xiao-Xing; Wang, Ya-Jun; Wang, Xi-Zhong; He, Guang-Xin; Chen, Hong-Wei; Fei, Li-Song

2002-09-01

Activin, which is included in the transforming growth factor-beta (TGF beta) superfamily of proteins and receptors, is known to have broad-ranging effects in the creatures. The mature peptide of beta A subunit of this gene, one of the most highly conserved sequence, can elevate the basal secretion of follicle-stimulating hormone (FSH) in the pituitary and FSH is pivotal to organism's reproduction. Reproduction block is one of the main reasons which cause giant panda to extinct. The sequence of Activin beta A subunit gene mature peptides has been successfully amplified from giant panda, red panda and malayan sun bear's genomic DNA by using polymerase chain reaction (PCR) with a pair of degenerate primers. The PCR products were cloned into the vector pBlueScript+ of Esherichia coli. Sequence analysis of Activin beta A subunit gene mature peptides shows that the length of this gene segment is the same (359 bp) and there is no intron in all three species. The sequence encodes a peptide of 119 amino acid residues. The homology comparison demonstrates 93.9% DNA homology and 99% homology in amino acid among these three species. Both GenBank blast search result and restriction enzyme map reveal that the sequences of Activin beta A subunit gene mature peptides of different species are highly conserved during the evolution process. Phylogeny analysis is performed with PHYLIP software package. A consistent phylogeny tree has been drawn with three different methods. The software analysis outcome accords with the academic view that giant panda has a closer relationship to the malayan sun bear than the red panda. Giant panda should be grouped into the bear family (Uersidae) with the malayan sun bear. As to the red panda, it would be better that this animal be grouped into the unique family (red panda family) because of great difference between the red panda and the bears (Uersidae).

Multiple sources for late-Holocene tsunamis at Discovery Bay, Washington State, USA

USGS Publications Warehouse

Williams, H.F.L.; Hutchinson, I.; Nelson, A.R.

2005-01-01

Nine muddy sand beds interrupt a 2500-yr-old sequence of peat deposits beneath a tidal marsh at the head of Discovery Bay on the south shore of the Strait of Juan de Fuca, Washington. An inferred tsunami origin for the sand beds is assessed by means of six criteria. Although all the sand beds contain marine diatoms and almost all the beds display internal stratification, the areal extent of the oldest beds is too limited to confirm their origin as tsunami deposits. The ages of four beds overlap with known late-Holocene tsunamis generated by plate-boundary earthquakes at the Cascadia subduction zone. Diatom assemblages in peat deposits bracketing these four beds do not indicate concurrent change in elevation at Discovery Bay. Diatoms in the peat bracketing a tsunami bed deposited about 1000 cal. yr BP indicate a few decimeters of submergence, suggesting deformation on a nearby upper-plate fault. Other beds may mark tsunamis caused by more distant upper-plate earthquakes or local submarine landslides triggered by earthquake shaking. Tsunamis from both subduction zone and upper-plate sources pose a significant hazard to shoreline areas in this region.

Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea.

PubMed

Kochzius, Marc; Blohm, Dietmar

2005-03-14

The aim of this study is to reveal gene flow between populations of the coral reef dwelling lionfish Pterois miles in the Gulf of Aqaba and northern Red Sea. Due to the fjord-like hydrography and topology of the Gulf of Aqaba, isolation of populations might be possible. Analysis of 5' mitochondrial control region sequences from 94 P. miles specimens detected 32 polymorphic sites, yielding 38 haplotypes. Sequence divergence among different haplotypes ranged from 0.6% to 9.9% and genetic diversity was high (h=0.85, pi=1.9%). AMOVA indicates panmixia between the Gulf of Aqaba and northern Red Sea, but analysis of migration pattern shows an almost unidirectional migration originating from the Red Sea.

Quantitative Sequencing for the Determination of Kdr-type Resistance Allele (V419L, L925I, I936F) Frequencies in Common Bed Bug (Hemiptera: Cimicidae) Populations Collected from Israel.

PubMed

Palenchar, Daniel J; Gellatly, Kyle J; Yoon, Kyong Sup; Mumcuoglu, Kosta Y; Shalom, Uri; Clark, J Marshall

2015-09-01

Human bed bug infestations have dramatically increased worldwide since the mid-1990s. A similar phenomenon was also observed in Israel since 2005, when infestations were reported from all over the country. Two single nucleotide polymorphisms (V419L and L925I) in the bed bug voltage-sensitive sodium channel confer kdr-type resistance to pyrethroids. Using quantitative sequencing (QS), the resistance allele frequencies of Israeli bed bug populations from across the country were determined. Genomic DNA was extracted from samples of 12 populations of bed bugs collected from Israel and DNA fragments containing the V419L or L925I and I936F mutations sites were PCR amplified. The PCR products were analyzed by QS and the nucleotide signal ratios calculated and used to predict the resistance allele frequencies of the unknown populations. Results of the genetic analysis show that resistant nucleotide signals are highly correlated to resistance allele frequencies for both mutations. Ten of the 12 tested populations had 100% of the L925I mutation and 0% of the V419L mutation. One population was heterogeneous for the L925I mutation and had 0% of the V419L mutation and another population was heterogeneous for the V419L mutation and had 100% of the L925I mutation. I936F occurred only at low levels. These results indicate that bed bugs in Israel are genetically resistant to pyrethroids. Thus, pyrethroids should only be used for bed bug management with caution using effective application and careful monitoring procedures. Additionally, new and novel-acting insecticides and nonchemical means of controlling bed bugs should be explored. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red Stripe in Argentina

PubMed Central

Fontana, Cecilia A.; Bassi, Daniela; Puglisi, Edoardo; Salazar, Sergio M.; Vignolo, Graciela M.; Coccocelli, Pier S.

2016-01-01

Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax avenae. The genome sequence from the first isolate of this bacterium in Argentina is presented here. The draft genome of the A. avenae T10_61 strain contains 5,646,552 bp and has a G+C content of 68.6 mol%. PMID:26847889

A unique Middle Ordovician K-bentonite bed succession at Röstånga, S. Sweden

USGS Publications Warehouse

Bergstrom, Stig M.; Huff, Warren D.; Kolata, Dennis R.; Yost, Deborah A.; Hart, Charles P.

1997-01-01

An approximately 8.5 m thick sequence of upper Viruan (upper Middle Ordovician) shales, mudstones, and limestones in an outcrop at Kyrkbäcken near Röstånga in W‐central Skåne contains 19 K‐bentonite beds, several of which are as much as 40–67 cm thick. Thirteen of these beds are in the upper part of the Sularp Fm., four in the Skagen Fm., and two questionable beds in the Mossen Fm. Evidence from macrofossils, chitinozoans, and conodonts are used for biostratigraphic age assessment of the K‐bentonite succession. Regional comparison of the sequence with those at Kinnekulle (Kullatorp), Koängen, and Tommarp suggests that its total stratigraphie thickness is smaller than those at the two former sites but the thicknesses of several of the Kyrkbacken ash beds are greater than those in similar stratigraphic positions in the other successions. The K‐bentonites at Kyrkbacken have a similar clay mineralogy and major and trace element composition as other Ordovician K‐bentonites, and these data indicate that the parental magma was of felsic, probably rhyolitic composition. Based on amphibole geoba‐rometry, the magma chamber is interpreted to have been at a depth of 14–20 km. The relatively large number of unusually thick ash beds of Middle Ordovician age makes the easily accessible Kyrkbäcken outcrop unique not only in Baltoscandia but, as far as we are aware, also on the entire northern hemisphere, and only one comparable exposure is known in the southern hemisphere, namely in the Precordillera of northern Argentina.

Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings.

PubMed

Schabereiter-Gurtner, C; Piñar, G; Vybiral, D; Lubitz, W; Rölleke, S

2001-11-01

A molecular approach was chosen to analyse the correlation between bacterial colonisation and rosy discolouration of masonry and lime wall paintings of two historically important buildings in Austria and Germany. The applied molecular method included PCR amplification of genes encoding the small subunit rRNA of bacteria (16S rDNA), genetic fingerprinting by denaturing gradient gel electrophoresis (DGGE), construction of 16S rDNA clone libraries, and comparative phylogenetic sequence analyses. The bacterial community of one red-pigmented biofilm sampled in Herberstein (Austria) contained bacteria phylogenetically related to the genera Saccharopolyspora, Nocardioides, Pseudonocardia, Rubrobacter, and to a Kineococcus-like bacterium. The bacterial community of the second red-pigmented biofilm sampled in Herberstein contained bacteria related to Arthrobacter, Comamonas, and to Rubrobacter. Rubrobacter-related 16S rDNA sequences were the most abundant. In the red-pigmented biofilm sampled in Burggen (Germany), only Rubrobacter-related bacteria were identified. No Rubrobacter-related bacteria were detected in non-rosy biofilms. The majority of sequences (70%) obtained from the bacterial communities of the three investigated rosy biofilms were related to sequences of the genus Rubrobacter (red-pigmented bacteria), demonstrating a correlation between Rubrobacter-related bacteria and the phenomenon of rosy discolouration of masonry and lime wall paintings.

Geologic summary of the Appalachian Basin, with reference to the subsurface disposal of radioactive waste solutions

USGS Publications Warehouse

Colton, G.W.

1962-01-01

The Appalachian basin is an elongate depression in the crystalline basement complex< which contains a great volume of predominantly sedimentary stratified rocks. As defined in this paper it extends from the Adirondack Mountains in New York to central Alabama. From east to west it extends from the west flank of the Blue Ridge Mountains to the crest of the Findlay and Cincinnati arches and the Nashville dome. It encompasses an area of about 207,000 square miles, including all of West Virginia and parts of New York, New Jersey, Pennsylvania, Ohio, Maryland, Virginia, Kentucky, Tennessee, North Carolina, Georgia, and Alabama. The stratified rocks that occupy the basin constitute a wedge-shaped mass whose axis of greatest thickness lies close to and parallel to the east edge of the basin. The maximum thickness of stratified rocks preserved in any one part of the basin today is between 35,000 and 40,000 feet. The volume of the sedimentary rocks is approximately 510,000 cubic miles and of volcanic rocks is a few thousand cubic miles. The sedimentary rocks are predominantly Paleozoic in age, whereas the volcanic rocks are predominantly Late Precambrian. On the basis of gross lithology the stratified rocks overlying the crystalline basement complex can be divided into nine vertically sequential units, which are designated 'sequences' in this report. The boundaries between contiguous sequences do not necessarily coincide with the commonly recognized boundaries between systems or series. All sequences are grossly wedge shaped, being thickest along the eastern margin of the basin and thinnest along the western margin. The lowermost unit--the Late Precambrian stratified sequence--is present only along part of the eastern margin of the basin, where it lies unconformably on the basement complex. It consists largely of volcanic tuffs and flows but contains some interbedded sedimentary rocks. The Late Precambrian sequence is overlain by the Early Cambrian clastic sequence. Where the older sequence is absent, the Early Cambrian sequence rests on the basement complex. Interbedded fine- to coarse-grained noncarbonate detrital rocks comprise the bulk of the sequence, but some volcanic and carbonate rocks are included. Next above is the Cambrian-Ordovician carbonate sequence which consists largely of limestone and dolomite. Some quartzose sandstone is present in the lower part in the western half of the basin, and much shale is present in the upper part in the southeast part of the basin. The next higher sequence is the Late Ordovician clastic sequence, which consists largely of shale, siltstone, and sandstone. Coarse-grained light-gray to red rocks are common in the sequence along the eastern side of the basin, whereas fine-grained dark-gray to black calcareous rocks are common along the west side. The Late Ordovician clastic sequence is overlain--unconformably in many places--by the Early Silurian clastic sequence. The latter comprises a relatively thin wedge of coarse-grained clastic rocks. Some of the most prolific oil- and gas-producing sandstones in the Appalachian basin are included. Among these are the 'Clinton' sands of Ohio, the Medina Sandstones of New York and Pennsylvania, and the Keefer or 'Big Six' Sandstone of West Virginia and Kentucky. Conformably overlying the Early Silurian clastic sequence is the Silurian-Devonian carbonate sequence, which consists predominantly of limestone and dolomite. It also contains a salt-bearing unit in the north-central part of the basin and a thick wedge of coarse-grained red beds in the northeastern part. The sequence is absent in much of the southern part of the basin. Large volumes of gas and much oil are obtained from some of its rocks, especially from the Oriskany Sandstone and the Huntersville Chert. The Silurian-Devonian carbonate sequence is abruptly overlain by the Devonian clastic sequence--a thick succession of interbedded shale, mudrock, siltstone, and sandstone. Colors range f

Tests of two convection theories for red giant and red supergiant envelopes

NASA Technical Reports Server (NTRS)

Stothers, Richard B.; Chin, Chao-Wen

1995-01-01

Two theories of stellar envelope convection are considered here in the context of red giants and red supergiants of intermediate to high mass: Boehm-Vitense's standard mixing-length theory (MLT) and Canuto & Mazzitelli's new theory incorporating the full spectrum of turbulence (FST). Both theories assume incompressible convection. Two formulations of the convective mixing length are also evaluated: l proportional to the local pressure scale height (H(sub P)) and l proportional to the distance from the upper boundary of the convection zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red phase of core helium burning. Since the theoretically predicted effective temperatures for cool stars are known to be sensitive to the assigned value of the mixing length, this quantity has been individually calibrated for each evolutionary sequence. The calibration is done in a composite Hertzsprung-Russell diagram for the red giant and red supergiant members of well-observed Galactic open clusters. The MLT model requires the constant of proportionality for the convective mixing length to vary by a small but statistically significant amount with stellar mass, whereas the FST model succeeds in all cases with the mixing lenghth simply set equal to z. The structure of the deep stellar interior, however, remains very nearly unaffected by the choices of convection theory and mixing lenghth. Inside the convective envelope itself, a density inversion always occurs, but is somewhat smaller for the convectively more efficient MLT model. On physical grounds the FST model is preferable, and seems to alleviate the problem of finding the proper mixing length.

Contribution of Primordial Binary Evolution to the Two Blue-straggler Sequences in Globular Cluster M30

NASA Astrophysics Data System (ADS)

Jiang, Dengkai; Chen, Xuefei; Li, Lifang; Han, Zhanwen

2017-11-01

Two blue-straggler sequences discovered in globular cluster M30 provide a strong constraint on the formation mechanisms of blue stragglers. We study the formation of blue-straggler binaries through binary evolution, and find that binary evolution can contribute to the blue stragglers in both of the sequences. Whether a blue-straggler is located in the blue sequence or red sequence depends on the contribution of the mass donor to the total luminosity of the binary, which is generally observed as a single star in globular clusters. The blue stragglers in the blue sequence have a cool white dwarf companion, while the majority (˜60%) of the objects in the red sequence are binaries that are still experiencing mass transfer. However, there are also some objects for which the donors have just finished the mass transfer (the stripped-core stars, ˜10%) or the blue stragglers (the accretors) have evolved away from the blue sequence (˜30%). Meanwhile, W UMa contact binaries found in both sequences may be explained by various mass ratios, that is, W UMa contact binaries in the red sequence have two components with comparable masses (e.g., mass ratio q ˜ 0.3-1.0), while those in the blue sequence have low mass ratios (e.g., q< 0.3). However, the fraction of the blue sequence in M30 cannot be reproduced by binary population synthesis if we assumed the initial parameters of a binary sample to be the same as those of the field. This possibly indicates that dynamical effects on binary systems are very important in globular clusters.

The development of the red giant branch. I - Theoretical evolutionary sequences

NASA Technical Reports Server (NTRS)

Sweigart, Allen V.; Greggio, Laura; Renzini, Alvio

1989-01-01

A grid of 100 evolutionary sequences extending from the zero-age main sequence to the onset of helium burning has been computed for stellar masses between 1.4 and 3.4 solar masses, helium abundances of 0.20 and 0.30, and heavy-element abundances of 0.004, 0.01, and 0.04. Using these computations the transition in the morphology of the red giant branch (RGB) between low-mass stars, which have an extended and luminous first RGB phase prior to helium ignition, and intermediate-mass stars, which do not, is investigated. Extensive tabulations of the numerical results are provided to aid in applying these sequences. The effects of the first dredge-up on the surface helium and CNO abundances of the sequences is discussed.

Toxigenic Corynebacterium ulcerans isolated from a free-roaming red fox (Vulpes vulpes).

PubMed

Sting, Reinhard; Ketterer-Pintur, Sandra; Contzen, Matthias; Mauder, Norman; Süss-Dombrowski, Christine

2015-01-01

Corynebacterium (C.) ulcerans could be isolated from the spleen of a red fox (Vulpes vulpes) that had been found dead in the state of Baden-Württemberg, Germany. Pathohistological examination suggested that the fox had died of distemper, as was confirmed by PCR. The isolate was identified biochemically, by MALDI-TOF MS, FT-IR and by partial 16S rRNA, rpoB and tox gene sequencing. Using the Elek test the C. ulcerans isolate demonstrated diphtheria toxin production. FT-IR and sequencing data obtained from the C. ulcerans isolate from the red fox showed higher similarity to isolates from humans than to those from wild game.

Hepatozoon canis in German red foxes (Vulpes vulpes) and their ticks: molecular characterization and the phylogenetic relationship to other Hepatozoon spp.

PubMed

Najm, Nour-Addeen; Meyer-Kayser, Elisabeth; Hoffmann, Lothar; Pfister, Kurt; Silaghi, Cornelia

2014-07-01

In this study, the prevalence of Hepatozoon spp. in red foxes (Vulpes vulpes) and their ticks from Germany, as well as molecular characterizations and phylogenetic relationship to other Hepatozoon spp. were investigated. DNA extracts of 261 spleen samples and 1,953 ticks were examined for the presence of Hepatozoon spp. by a conventional polymerase chain reaction (PCR) targeting the 18S rRNA gene. The ticks included four tick species: Ixodes ricinus, Ixodes canisuga, Ixodes hexagonus and Dermacentor reticulatus. A total of 118/261 foxes (45.2%) and 148/1,953 ticks (7.5%) were Hepatozoon PCR-positive. Amplicons from 36 positive foxes and 41 positive ticks were sequenced. All sequences obtained from foxes and 39/41 from ticks had a 99% similarity to Hepatozoon canis, whereas two ticks' sequences had a 99% identity to Hepatozoon sp. The obtained Hepatozoon sequences in this study were phylogenetically related to other Hepatozoon sequences detected in other countries, which may represent strain variants. The high prevalence of H. canis DNA in red foxes in this study supports the suggested role of those animals in distribution of this parasite. Furthermore, detection of DNA of H. canis in foxes and all examined tick species collected from those foxes allows speculating about previously undescribed potential vectors for H. canis and suggests a potential role of the red fox in its natural endemic cycles.

Energetic Aspects of Non-Radial Solar-Like Oscillations in Red Giants

NASA Astrophysics Data System (ADS)

Dupret, Marc-Antoine; Belkacem, Kévin

The non-radial oscillations discovered by CoRoT (see e.g. de Ridder et al. (2009)) and by Kepler(see e.g. Bedding et al. (2010)) in thousands of red giants constitute a wonderful mine of information to determine their global characteristics and probe their internal structure. A. Miglio and J. Montalbán have presented in detail in this conference the seismic structure of red giants, the information hold by their oscillation frequencies, and how it can be used. An adiabatic analysis of the oscillations was sufficient at this level as the frequencies are mainly determined by the deep layers were the oscillatons are quasi-adiabatic. We consider here energetic aspects of non-radial oscillations in red-giants. Non-adiabatic models of solar-like oscillations are required to determine the theoretical amplitude and lifetimes of the modes. These parameters allow us to determine how power spectra are expected to look like, depending on the structure of the red giant. Comparison with the observed measures gives thus additional constraints on the models.

In Brief: Red tide Web site

NASA Astrophysics Data System (ADS)

Showstack, Randy; Kumar, Mohi

2008-06-01

The U.S. National Oceanic and Atmospheric Administration has established the NOAA New England Red Tide Information Center to help people understand the significant red tides that are predicted to form there later this spring. The site (http://www.oceanservice.noaa.gov/redtide) will provide a summary of the current red tide situation and its potential harmful impacts on humans and animals and will serve as a central repository of information. The site also will have direct links to news releases, changes to relevant federal fishing regulations, links to closures of shellfish waters, and links to state agency Web sites with localized information. In addition, the site will have information about NOAA's scientific response effort as well as information from several other sources including NOAA's major response partner, the Woods Hole Oceanographic Institution (WHOI). On 24 April, WHOI scientists, using forecast models developed with NOAA funding support, predicted ``that excess winter precipitation has set the stage for a harmful algal bloom similar to the historic red tide of 2005.'' That bloom shut down shellfish beds from the Bay of Fundy to Martha's Vineyard for several months.

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.

The evolution of the cluster optical galaxy luminosity function between z = 0.4 and 0.9 in the DAFT/FADA survey

NASA Astrophysics Data System (ADS)

Martinet, Nicolas; Durret, Florence; Guennou, Loïc; Adami, Christophe; Biviano, Andrea; Ulmer, Melville P.; Clowe, Douglas; Halliday, Claire; Ilbert, Olivier; Márquez, Isabel; Schirmer, Mischa

2015-03-01

Context. There is some disagreement about the abundance of faint galaxies in high-redshift clusters, with contradictory results in the literature arising from studies of the optical galaxy luminosity function (GLF) for small cluster samples. Aims: We compute GLFs for one of the largest medium-to-high-redshift (0.4 ≤ z < 0.9) cluster samples to date in order to probe the abundance of faint galaxies in clusters. We also study how the GLF depends on cluster redshift, mass, and substructure and compare the GLFs of clusters with those of the field. We separately investigate the GLFs of blue and red-sequence (RS) galaxies to understand the evolution of different cluster populations. Methods: We calculated the GLFs for 31 clusters taken from the DAFT/FADA survey in the B,V,R, and I rest-frame bands. We used photometric redshifts computed from BVRIZJ images to constrain galaxy cluster membership. We carried out a detailed estimate of the completeness of our data. We distinguished the red-sequence and blue galaxies using a V - I versus I colour-magnitude diagram. We studied the evolution of these two populations with redshift. We fitted Schechter functions to our stacked GLFs to determine average cluster characteristics. Results: We find that the shapes of our GLFs are similar for the B,V,R, and I bands with a drop at the red GLF faint ends that is more pronounced at high redshift: αred ~ -0.5 at 0.40 ≤ z < 0.65 and αred > 0.1 at 0.65 ≤ z < 0.90. The blue GLFs have a steeper faint end (αblue ~ -1.6) than the red GLFs, which appears to be independent of redshift. For the full cluster sample, blue and red GLFs meet at MV = -20, MR = -20.5, and MI = -20.3. A study of how galaxy types evolve with redshift shows that late-type galaxies appear to become early types between z ~ 0.9 and today. Finally, the faint ends of the red GLFs of more massive clusters appear to be richer than less massive clusters, which is more typical of the lower redshift behaviour. Conclusions: Our results indicate that these clusters form at redshifts higher than z = 0.9 from galaxy structures that already have an established red sequence. Late-type galaxies then appear to evolve into early types, enriching the red sequence between this redshift and today. This effect is consistent with the evolution of the faint-end slope of the red sequence and the galaxy type evolution that we find. Finally, faint galaxies accreted from the field environment at all redshifts might have replaced the blue late-type galaxies that converted into early types, explaining the lack of evolution in the faint-end slopes of the blue GLFs. Appendix is available in electronic form at http://www.aanda.org

Middle Stone Age bedding construction and settlement patterns at Sibudu, South Africa.

PubMed

Wadley, Lyn; Sievers, Christine; Bamford, Marion; Goldberg, Paul; Berna, Francesco; Miller, Christopher

2011-12-09

The Middle Stone Age (MSA) is associated with early behavioral innovations, expansions of modern humans within and out of Africa, and occasional population bottlenecks. Several innovations in the MSA are seen in an archaeological sequence in the rock shelter Sibudu (South Africa). At ~77,000 years ago, people constructed plant bedding from sedges and other monocotyledons topped with aromatic leaves containing insecticidal and larvicidal chemicals. Beginning at ~73,000 years ago, bedding was burned, presumably for site maintenance. By ~58,000 years ago, bedding construction, burning, and other forms of site use and maintenance intensified, suggesting that settlement strategies changed. Behavioral differences between ~77,000 and 58,000 years ago may coincide with population fluctuations in Africa.

Design and assembly of a catalyst bed gas generator for the catalytic decomposition of high concentration hydrogen peroxide propellants and the catalytic combustion of hydrocarbon/air mixtures

NASA Technical Reports Server (NTRS)

Lohner, Kevin A. (Inventor); Mays, Jeffrey A. (Inventor); Sevener, Kathleen M. (Inventor)

2004-01-01

A method for designing and assembling a high performance catalyst bed gas generator for use in decomposing propellants, particularly hydrogen peroxide propellants, for use in target, space, and on-orbit propulsion systems and low-emission terrestrial power and gas generation. The gas generator utilizes a sectioned catalyst bed system, and incorporates a robust, high temperature mixed metal oxide catalyst. The gas generator requires no special preheat apparatus or special sequencing to meet start-up requirements, enabling a fast overall response time. The high performance catalyst bed gas generator system has consistently demonstrated high decomposition efficiency, extremely low decomposition roughness, and long operating life on multiple test articles.

Middle Jurassic incised valley fill (eolian/estuarine) and nearshore marine petroleum reservoirs, Powder River Basin

USGS Publications Warehouse

Ahlbrandt, T.S.; Fox, J.E.

1997-01-01

Paleovalleys incised into the Triassic Spearfish Formation (Chugwater equivalent) are filled with a vertical sequence of eolian, estuarine, and marine sandstones of the Middle Jurassic (Bathonian age) Canyon Springs Sandstone Member of the Sundance Formation. An outcrop exemplifying this is located at Red Canyon in the southern Black Hills, Fall River County, South Dakota. These paleovalleys locally have more than 300 ft of relief and are as much as several miles wide. Because they slope in a westerly direction, and Jurassic seas transgressed into the area from the west there was greater marine-influence and more stratigraphic complexity in the subsurface, to the west, as compared to the Black Hills outcrops. In the subsurface two distinctive reservoir sandstone beds within the Canyon Springs Sandstone Member fill the paleovalleys. These are the eolian lower Canyon Springs unit (LCS) and the estuarine upper Canyon Springs unit (UCS), separated by the marine "Limestone Marker" and estuarine "Brown Shale". The LCS and UCS contain significant proven hydrocarbon reservoirs in Wyoming (about 500 MMBO in-place in 9 fields, 188 MMBO produced through 1993) and are prospective in western South Dakota, western Nebraska and northern Colorado. Also prospective is the Callovian-age Hulett Sandstone Member which consists of multiple prograding shoreface to foreshore parasequences, as interpreted from the Red Canyon locality. Petrographic, outcrop and subsurface studies demonstrate the viability of both the Canyon Springs Sandstone and Hulett Sandstone members as superior hydrocarbon reservoirs in both stratigraphic and structural traps. Examples of fields with hydrocarbon production from the Canyon Springs in paleovalleys include Lance Creek field (56 MMBO produced) and the more recently discovered Red Bird field (300 MBO produced), both in Niobrara County, Wyoming. At Red Bird field the primary exploration target was the Pennsylvanian "Leo sands" of the Minnelusa Formation, and production from the Canyon Springs was not anticipated. Canyon Springs reservoirs are easily bypassed because they are relatively unconsolidated, underpressured, low-resistivity, and difficult to evaluate from petrophysics, drill-stem tests, or well cuttings.

The Germination of Several Tree Species in Plastic Greenhouses

Treesearch

Howard M. Phipps

1969-01-01

The technique of growing tree seedlings in plastic greenhouses is being evaluated for red pine, jack pine, white spruce, and yellow birch at the Chittenden Nursery in northern Lower Michigan. Both a long growing season and a normal-length growing season in plastic greenhouses were compared with standard outdoor nursery beds (control). First-year results showed that...

Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species.

PubMed

Zhong, Hua-Ming; Zhang, Hong-Hai; Sha, Wei-Lai; Zhang, Cheng-De; Chen, Yu-Cai

2010-04-01

The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

Missense polymorphisms in the MC1R gene of the dog, red fox, arctic fox and Chinese raccoon dog.

PubMed

Nowacka-Woszuk, J; Salamon, S; Gorna, A; Switonski, M

2013-04-01

Coat colour variation is determined by many genes, one of which is the melanocortin receptor type 1 (MC1R) gene. In this study, we examined the whole coding sequence of this gene in four species belonging to the Canidae family (dog, red fox, arctic fox and Chinese raccoon dog). Although the comparative analysis of the obtained nucleotide sequences revealed a high conservation, which varied between 97.9 and 99.1%, we altogether identified 22 SNPs (10 in dogs, six in farmed red foxes, two in wild red foxes, three in arctic foxes and one in Chinese raccoon dog). Among them, seven appeared to be novel: one silent in the dog, three missense and one silent in the red fox, one in the 3'-flanking region in the arctic fox and one silent in the Chinese raccoon dog. In dogs and red foxes, the SNPs segregated as 10 and four haplotypes, respectively. Taking into consideration the published reports and results of this study, the highest number of missense polymorphisms was until now found in the dog (9) and red fox (7). © 2012 Blackwell Verlag GmbH.

Genome Sequence of Streptomyces caatingaensis CMAA 1322, a New Abiotic Stress-Tolerant Actinomycete Isolated from Dried Lake Bed Sediment in the Brazilian Caatinga Biome

PubMed Central

Gacesa, Ranko; Taketani, Rodrigo Gouvêa; Long, Paul F.; Melo, Itamar Soares

2015-01-01

The genome sequence of the first Streptomyces species isolated from the Brazilian Caatinga is reported here. Genes related to environmental stress tolerance were prevalent and included many secondary metabolic gene clusters. PMID:26358601

Hierarchy of sedimentary discontinuity surfaces and condensed beds from the middle Paleozoic of eastern North America: Implications for cratonic sequence stratigraphy

USGS Publications Warehouse

McLaughlin, P.I.; Brett, Carlton E.; Wilson, M.A.

2008-01-01

Sedimentological analyses of middle Paleozoic epeiric sea successions in North America suggest a hierarchy of discontinuity surfaces and condensed beds of increasing complexity. Simple firmgrounds and hardgrounds, which are comparatively ephemeral features, form the base of the hierarchy. Composite hardgrounds, reworked concretions, authigenic mineral crusts and monomictic intraformational conglomerates indicate more complex histories. Polymictic intraformational conglomerates, ironstones and phosphorites form the most complex discontinuity surfaces and condensed beds. Complexity of discontinuities is closely linked to depositional environments duration of sediment starvation and degree of reworking which in turn show a relationship to stratigraphic cyclicity. A model of cratonic sequence stratigraphy is generated by combining data on the complexity and lateral distribution of discontinuities in the context of facies successions. Lowstand, early transgressive and late transgressive systems tracts are representative of sea-level rise. Early and late transgressive systems tracts are separated by the maximum starvation surface (typically a polymictic intraformational conglomerate or condensed phosphorite), deposited during the peak rate of sea-level rise. Conversely the maximum flooding surface, representing the highest stand of sea level, is marked by little to no break in sedimentation. The highstand and falling stage systems tracts are deposited during relative sea-level fall. They are separated by the forced-regression surface, a thin discontinuity surface or condensed bed developed during the most rapid rate of sea-level fall. The lowest stand of sea level is marked by the sequence boundary. In subaerially exposed areas it is occasionally modified as a rockground or composite hardground.

Development of a microcapillary column for detecting targeted messenger RNA molecules.

PubMed

Ohnishi, Michihiro

2006-03-24

A capillary column in a rapid-flow system has been developed for detecting targeted messenger RNA (mRNA) molecules. The column has a structure made of two beds-one bed of porous microbeads and one bed of microbeads with a polythymidine base sequence. The targeted eukaryotic mRNA molecules are detected by two-step hybridization (sandwich hybridization) composed of polyadenosine selection of mRNA molecules and formation of a probe-target (targeted mRNA) hybrid. The sandwich hybridization, which is accomplished within 1 h, was tested using synthetic polydeoxynucleotides. Ten picomoles of the targeted polydeoxynucleotide were detected.

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.).

PubMed

Bushakra, Jill M; Lewers, Kim S; Staton, Margaret E; Zhebentyayeva, Tetyana; Saski, Christopher A

2015-10-26

Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs.  Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.

Isolation, sequencing and expression of RED, a novel human gene encoding an acidic-basic dipeptide repeat.

PubMed

Assier, E; Bouzinba-Segard, H; Stolzenberg, M C; Stephens, R; Bardos, J; Freemont, P; Charron, D; Trowsdale, J; Rich, T

1999-04-16

A novel human gene RED, and the murine homologue, MuRED, were cloned. These genes were named after the extensive stretch of alternating arginine (R) and glutamic acid (E) or aspartic acid (D) residues that they contain. We term this the 'RED' repeat. The genes of both species were expressed in a wide range of tissues and we have mapped the human gene to chromosome 5q22-24. MuRED and RED shared 98% sequence identity at the amino acid level. The open reading frame of both genes encodes a 557 amino acid protein. RED fused to a fluorescent tag was expressed in nuclei of transfected cells and localised to nuclear dots. Co-localisation studies showed that these nuclear dots did not contain either PML or Coilin, which are commonly found in the POD or coiled body nuclear compartments. Deletion of the amino terminal 265 amino acids resulted in a failure to sort efficiently to the nucleus, though nuclear dots were formed. Deletion of a further 50 amino acids from the amino terminus generates a protein that can sort to the nucleus but is unable to generate nuclear dots. Neither construct localised to the nucleolus. The characteristics of RED and its nuclear localisation implicate it as a regulatory protein, possibly involved in transcription.

Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis).

PubMed

Hu, Guang-Fu; Liu, Xiang-Jiang; Li, Zhong; Liang, Hong-Wei; Hu, Shao-Na; Zou, Gui-Wei

2016-01-01

The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.

Evaluation of eelgrass beds mapping using a high-resolution airborne multispectral scanner

USGS Publications Warehouse

Su, H.; Karna, D.; Fraim, E.; Fitzgerald, M.; Dominguez, R.; Myers, J.S.; Coffland, B.; Handley, L.R.; Mace, T.

2006-01-01

Eelgrass (Zostera marina) can provide vital ecological functions in stabilizing sediments, influencing current dynamics, and contributing significant amounts of biomass to numerous food webs in coastal ecosystems. Mapping eelgrass beds is important for coastal water and nearshore estuarine monitoring, management, and planning. This study demonstrated the possible use of high spatial (approximately 5 m) and temporal (maximum low tide) resolution airborne multispectral scanner on mapping eelgrass beds in Northern Puget Sound, Washington. A combination of supervised and unsupervised classification approaches were performed on the multispectral scanner imagery. A normalized difference vegetation index (NDVI) derived from the red and near-infrared bands and ancillary spatial information, were used to extract and mask eelgrass beds and other submerged aquatic vegetation (SAV) in the study area. We evaluated the resulting thematic map (geocoded, classified image) against a conventional aerial photograph interpretation using 260 point locations randomly stratified over five defined classes from the thematic map. We achieved an overall accuracy of 92 percent with 0.92 Kappa Coefficient in the study area. This study demonstrates that the airborne multispectral scanner can be useful for mapping eelgrass beds in a local or regional scale, especially in regions for which optical remote sensing from space is constrained by climatic and tidal conditions. ?? 2006 American Society for Photogrammetry and Remote Sensing.

Corrigendum.

PubMed

2016-01-01

Jakubowski, T.L., Perron, T.J., and Teixeira, E. (2015). Rashes in school: Can they stay, or should they go? NASN School Nurse, 30(5): 274-282. (Original DOI: 10.1177/1942602X15596815)In the September 2015 issue of NASN School Nurse, the images for Lyme Disease and Spider bites were reversed. The correct order appears below.spnas;31/1/61/TABLE11942602X15621761T1table1-1942602X15621761Table 5.Bites/Stings in ChildrenDiagnosis(Bites, Stings, cutaneous infestations)Rash DescriptionSigns and SymptomsStay in School or Go Home?PhotoLyme Disease (Borrelia burgdorferi)Transmitted by deer tickErythema rash when present, "Bull's eye rash" distinct red borders with central clearing.Rash at site of bite but can have multiple rashesFever, joint pain, malaise, headache, single swollen joint usually knee usually accompany the rash.Not Contagious: Can stay at school.Incubation: 1-32 days median is 11 days. April through October with more than 50% of the cases presenting in June and July.Rocky Mountain Spotted Fever (RMSF) Rickettial infection transmitted by wood ticks.Characteristic spotted rash, maculopapular and sometimes petechial rash.Triad of fever, rash, and history of tick exposure, headache, vomiting, sore throatNot Contagious: Can stay at school.Rash initially appears on wrists and ankles and spreads to trunk within hours. Palms of hands and soles of feet are also involved.Incubation: Average time frame one week. Can range 2-14 days. August through September highest prevalence.Scabies(Mites)Papules and burrows, excoriation secondary to scratching.Intense itching especially at night. Commonly seen between the fingers and toes.Is Contagious: Should go home.Skin-to-skin contact. Mites can remain alive for > 2 days on clothing and bedding.Incubation: 4-6 weeksIf the child had it previously 1-4 days.*Can return to school with medical clearance.Bee stingsLocalized swelling, redness. If allergic can spread rapidly. Raised pink wheel.Pain, redness, swelling, hives if allergic, respiratory distress if highly allergic.Not Contagious: Can stay at school.Spider bitesLocalized redness, swelling, can spread if infection - cellulitis can occur.Pain, redness, swelling. Bites are commonly seen on thighs, buttocks and abdomen.Not Contagious: Can stay at school.Bed Bugs(Cimex Lectularius)Red itchy welts that appear in a row. Numerous bites appear as a red itchy wide spread rash. Often mistaken for mosquito bites.Red, itchy, swellingAppear on face neck and extremities, areas exposed during sleep.Not Contagious: Can stay at school.Incubation: Bites may not appear for several days after exposure.Flea BitesRed spots surrounded by reddened haloes.Red, itchy.Commonly seen on the feet and ankles.Not Contagious: Can stay at school. © 2015 The Author(s).

Increasing the Energy Efficiency of the Cyclic Action Mechanisms in Rolling for a Roller Bed Used as an Example

NASA Astrophysics Data System (ADS)

andreev, A. N.; Kolesnichenko, D. A.

2017-12-01

The possibility of increasing the energy efficiency of the production cycle in a roller bed is briefly reviewed and justified. The sequence diagram of operation of the electrical drive in a roller bed is analyzed, and the possible increase in the energy efficiency is calculated. A method for energy saving is described for the application of a frequency-controlled asynchronous electrical drive of drive rollers in a roller bed with an increased capacitor capacity in a dc link. A fine mathematical model is developed to describe the behavior of the electrical drive during the deceleration of a roller bed. An experimental setup is created and computer simulation and physical modeling are performed. The basic information flows of the general hierarchical automatic control system of an enterprise are described and determined with allowance for the proposed method of increasing the energy efficiency.

Red soil as a regenerable sorbent for high temperature removal of hydrogen sulfide from coal gas.

PubMed

Ko, Tzu-Hsing; Chu, Hsin; Lin, Hsiao-Ping; Peng, Ching-Yu

2006-08-25

In this study, hydrogen sulfide (H(2)S) was removed from coal gas by red soil under high temperature in a fixed-bed reactor. Red soil powders were collected from the northern, center and southern of Taiwan. They were characterized by XRPD, porosity analysis and DCB chemical analysis. Results show that the greater sulfur content of LP red soils is attributed to the higher free iron oxides and suitable sulfidation temperature is around 773K. High temperature has a negative effect for use red soil as a desulfurization sorbent due to thermodynamic limitation in a reduction atmosphere. During 10 cycles of regeneration, after the first cycle the red soil remained stable with a breakthrough time between 31 and 36 min. Hydrogen adversely affects sulfidation reaction, whereas CO exhibits a positive effect due to a water-shift reaction. COS was formed during the sulfidation stage and this was attributed to the reaction of H(2)S and CO. Results of XRPD indicated that, hematite is the dominant active species in fresh red soil and iron sulfide (FeS) is a product of the reaction between hematite and hydrogen sulfide in red soils. The spinel phase FeAl(2)O(4) was found during regeneration, moreover, the amount of free iron oxides decreased after regeneration indicating the some of the free iron oxide formed a spinel phase, further reducting the overall desulfurization efficiency.

Late pleistocene aggradation and degradation of the lower colorado river: Perspectives from the Cottonwood area and other reconnaissance below Boulder Canyon

USGS Publications Warehouse

Lundstrom, S.C.; Mahan, S.A.; Paces, J.B.; Hudson, M.R.; House, P.K.; Malmon, D.V.; Blair, J.L.; Howard, K.A.

2008-01-01

Where the lower Colorado River traverses the Basin and Range Province below the Grand Canyon, significant late Pleistocene aggradation and subsequent degrada tion of the river are indicated by luminescence, paleomagnetic, and U-series data and stratigraphy. Aggradational, finely bedded reddish mud, clay, and silt are underlain and overlain by cross-bedded to plane-bedded fine sand and silt. That sequence is commonly disconformably overlain by up to 15 m of coarse sand, rounded exotic gravel, and angular, locally derived gravel. Luminescence dates on the fine sediments range from ca. 40 ka to 70 ka, considering collective uncertainties. A section of fine grained sediments over a vertical range of 15 m shows normal polarity magnetization and little apparent secular variation beyond dispersion that can be explained by com paction. Aggradation on large local tributaries such as Las Vegas Wash appears to have been coeval with that of the Colorado River. The upper limits of erosional rem nants of the sequence define a steeper grade above the historical river, and these late Pleistocene deposits are greater than 100 m above the modern river north of 35??N. Ter race gravels inset below the upper limit of the aggradational sequence yield 230Th dates that range from ca. 32 ka to 60 ka and indicate that degradation of the river system in this area closely followed aggradation. The thick sequence of rhythmically bedded mud and silt possibly indicates set tings that were ponded laterally between valley slopes and levees of the aggrading river. Potential driving mechanisms for such aggradation and degradation include sediment-yield response to climate change, drought, fire, vegetation-ecosystem dynam ics, glaciation, paleofloods, groundwater discharge, and building and destruction of natural dams produced by volcanism and landslides. ?? 2008 The Geological Society of America.

Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs.

PubMed

Bugno-Poniewierska, Monika; Solek, Przemysław; Wronski, Mariusz; Potocki, Leszek; Jezewska-Witkowska, Grażyna; Wnuk, Maciej

2014-12-01

The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects. © 2014 The Authors.

Development and transferability of black and red raspberry microsatellite markers from short-read sequences

USDA-ARS?s Scientific Manuscript database

The advent of next-generation sequencing technologies has been a boon to the cost-effective development of molecular markers, particularly in non-model species. Here, we demonstrate the efficiency of microsatellite or simple sequence repeat (SSR) marker development from short-read sequences using th...

Cardiovascular consequences of bed rest: effect on maximal oxygen uptake

NASA Technical Reports Server (NTRS)

Convertino, V. A.

1997-01-01

Maximal oxygen uptake (VO2max) is reduced in healthy individuals confined to bed rest, suggesting it is independent of any disease state. The magnitude of reduction in VO2max is dependent on duration of bed rest and the initial level of aerobic fitness (VO2max), but it appears to be independent of age or gender. Bed rest induces an elevated maximal heart rate which, in turn, is associated with decreased cardiac vagal tone, increased sympathetic catecholamine secretion, and greater cardiac beta-receptor sensitivity. Despite the elevation in heart rate, VO2max is reduced primarily from decreased maximal stroke volume and cardiac output. An elevated ejection fraction during exercise following bed rest suggests that the lower stroke volume is not caused by ventricular dysfunction but is primarily the result of decreased venous return associated with lower circulating blood volume, reduced central venous pressure, and higher venous compliance in the lower extremities. VO2max, stroke volume, and cardiac output are further compromised by exercise in the upright posture. The contribution of hypovolemia to reduced cardiac output during exercise following bed rest is supported by the close relationship between the relative magnitude (% delta) and time course of change in blood volume and VO2max during bed rest, and also by the fact that retention of plasma volume is associated with maintenance of VO2max after bed rest. Arteriovenous oxygen difference during maximal exercise is not altered by bed rest, suggesting that peripheral mechanisms may not contribute significantly to the decreased VO2max. However reduction in baseline and maximal muscle blood flow, red blood cell volume, and capillarization in working muscles represent peripheral mechanisms that may contribute to limited oxygen delivery and, subsequently, lowered VO2max. Thus, alterations in cardiac and vascular functions induced by prolonged confinement to bed rest contribute to diminution of maximal oxygen uptake and reserve capacity to perform physical work.

Long Duration Head-Down Tilt Bed Rest Studies: Safety Considerations Regarding Vision Health

NASA Technical Reports Server (NTRS)

Cromwell, Ronita L.; Zanello, S. B.; Yarbough, P. O.; Ploutz-Snyder, Robert; Taibbi, G.; Vizzeri, G.

2012-01-01

Visual symptoms reported in astronauts returning from long duration missions in low Earth orbit, including hyperopic shift, choroidal folds, globe flattening and papilledema, are thought to be related to fluid shifts within the body due to microgravity exposure. Because of this possible relation to fluid shifts, safety considerations have been raised regarding the ocular health of head-down tilt (HDT) bed rest subjects. HDT is a widely used ground ]based analog that simulates physiological changes of spaceflight, including fluid shifts. Thus, vision monitoring has been performed in bed rest subjects in order to evaluate the safety of HDT with respect to vision health. Here we report ocular outcomes in 9 healthy subjects (age range: 27-48 years; Male/Female ratio: 8/1) completing bed rest Campaign 11, an integrated, multidisciplinary 70-day 6 degrees HDT bed rest study. Vision examinations were performed on a weekly basis, and consisted of office-based (2 pre- and 2 post-bed rest) and in-bed testing. The experimental design was a repeated measures design, with measurements for both eyes taken for each subject at each planned time point. Findings for the following tests were all reported as normal in each testing session for every subject: modified Amsler grid, red dot test, confrontational visual fields, color vision and fundus photography. Overall, no statistically significant differences were observed for any of the measures, except for both near and far visual acuity, which increased during the course of the study. This difference is not considered clinically relevant as may result from the effect of learning. Intraocular pressure results suggest a small increase at the beginning of the bed rest phase (p=0.059) and lesser increase at post-bed rest with respect to baseline (p=0.046). These preliminary results provide the basis for further analyses that will include correlations between intraocular pressure change pre- and post-bed rest, and optical coherence tomography measurements of the retina.

Clinical sequencing in leukemia with the assistance of artificial intelligence.

PubMed

Tojo, Arinobu

2017-01-01

Next generation sequencing (NGS) of cancer genomes is now becoming a prerequisite for accurate diagnosis and proper treatment in clinical oncology. Because the genomic regions for NGS expand from a certain set of genes to the whole exome or whole genome, the resulting sequence data becomes incredibly enormous and makes it quite laborious to translate the genomic data into medicine, so-called annotation and curation. We organized a clinical sequencing team and established a bidirectional (bed-to-bench and bench-to-bed) system to integrate clinical and genomic data for hematological malignancies. We also started a collaborative research project with IBM Japan to adopt the artificial intelligence Watson for Genomics (WfG) to the pipeline of medical informatics. Genomic DNA was prepared from malignant as well as normal tissues in each patient and subjected to NGS. Sequence data was analyzed using an in-house semi-automated pipeline in combination with WfG, which was used to identify candidate driver mutations and relevant pathways from which applicable drug information was deduced. Currently, we have analyzed more than 150 patients with hematological disorders, including AML and ALL, and obtained many informative findings. In this presentation, I will introduce some of the achievements we have made so far.

Long period astronomical cycles from the Triassic to Jurassic bedded chert sequence (Inuyama, Japan); Geologic evidences for the chaotic behavior of solar planets

NASA Astrophysics Data System (ADS)

Ikeda, Masayuki; Tada, Ryuji

2013-04-01

Astronomical theory predicts that ~2 Myr eccentricity cycle have changed its periodicity and amplitude through time because of the chaotic behavior of solar planets, especially Earth-Mars secular resonance. Although the ~2 Myr eccentricity cycle has been occasionally recognized in geological records, their frequency transitions have never been reported. To explore the frequency evolution of ~2 Myr eccentricity cycle, we used the bedded chert sequence in Inuyama, Japan, of which rhythms were proven to be of astronomical origin, covering the ~30 Myr long spanning from the Triassic to Jurassic. The frequency modulation of ~2 Myr cycle between ~1.6 and ~1.8 Myr periodicity detected from wavelet analysis of chert bed thickness variation are the first geologic record of chaotic transition of Earth-Mars secular resonance. The frequency modulation of ~2 Myr cycle will provide new constraints for the orbital models. Additionally, ~8 Myr cycle detected as chert bed thickness variation and its amplitude modulation of ~2 Myr cycle may be related to the amplitude modulation of ~2 Myr eccentricity cycle through non-linear process(es) of Earth system dynamics, suggesting possible impact of the chaotic behavior of Solar planets on climate change.

An overview of the issues: physiological effects of bed rest and restricted physical activity

NASA Technical Reports Server (NTRS)

Convertino, V. A.; Bloomfield, S. A.; Greenleaf, J. E.

1997-01-01

Reduction of exercise capacity with confinement to bed rest is well recognized. Underlying physiological mechanisms include dramatic reductions in maximal stroke volume, cardiac output, and oxygen uptake. However, bed rest by itself does not appear to contribute to cardiac dysfunction. Increased muscle fatigue is associated with reduced muscle blood flow, red cell volume, capillarization and oxidative enzymes. Loss of muscle mass and bone density may be reflected by reduced muscle strength and higher risk for injury to bones and joints. The resultant deconditioning caused by bed rest can be independent of the primary disease and physically debilitating in patients who attempt to reambulate to normal active living and working. A challenge to clinicians and health care specialists has been the identification of appropriate and effective methods to restore physical capacity of patients during or after restricted physical activity associated with prolonged bed rest. The examination of physiological responses to bed rest deconditioning and exercise training in healthy subjects has provided significant information to develop effective rehabilitation treatments. The successful application of acute exercise to enhance orthostatic stability, daily endurance exercise to maintain aerobic capacity, or specific resistance exercises to maintain musculoskeletal integrity rather than the use of surgical, pharmacological, and other medical treatments for clinical conditions has been enhanced by investigation and understanding of underlying mechanisms that distinguish physical deconditioning from the disease. This symposium presents an overview of cardiovascular and musculoskeletal deconditioning associated with reduced physical work capacity following prolonged bed rest and exercise training regimens that have proven successful in ameliorating or reversing these adverse effects.

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

Treesearch

Lisa W. Alexander; Keith E. Woeste

2014-01-01

Given the low intraspecific chloroplast diversity detected in northern red oak (Quercus rubra L.), more powerful genetic tools are necessary to accurately characterize Q. rubra chloroplast diversity and structure. We report the sequencing, assembly, and annotation of the chloroplast genome of northern red oak via pyrosequencing and...

Amplification of North American Red Oak Microsatellite Markers in European White Oaks and Chinese Chestnut

Treesearch

P. R. Aldrich; M. Jagtap; C. H. Michler; J. Romero-Severson

2003-01-01

We examined the cross-species amplification success of thirty microsatellite markers developed from North American northern red oak (Quercus rubra) in other members of the family Fagaceae. Sixteen of these markers are newly developed and we report primer sequences and amplification conditions here. Twelve of the thirty (40.0%) red oak markers...

Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome.

PubMed

Rousvoal, Sylvie; Bouyer, Betty; López-Cristoffanini, Camilo; Boyen, Catherine; Collén, Jonas

2016-08-01

Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named C. crispus virus (CcV). It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A nonidentical gag gene was also found in the nuclear genome of C. crispus, with associated expressed sequence tags (EST) and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographic locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. Neither phenotype caused by the infection nor any virus particles or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae. © 2016 Phycological Society of America.

Evaluation of Municipal Wastewater Treatment Plant Activated Sludge for Biodegradation of Propylene Glycol as an Aircraft Deicing Fluid

DTIC Science & Technology

2012-03-01

Propylene Glycol Deicer Biodegredation Kinetics: Complete-Mix Stirred Tank Reactors , Filter, and Fluidized Bed . Journal of Environmental...scale sequencing batch reactor containing municipal waste water treatment facility activated sludge (AS) performing simultaneous organic carbon...Sequencing Batch Reactor Operation ..................................................................... 13 PG extraction from AS

Genome Sequence of Streptomyces caatingaensis CMAA 1322, a New Abiotic Stress-Tolerant Actinomycete Isolated from Dried Lake Bed Sediment in the Brazilian Caatinga Biome.

PubMed

Santos, Suikinai Nobre; Gacesa, Ranko; Taketani, Rodrigo Gouvêa; Long, Paul F; Melo, Itamar Soares

2015-09-10

The genome sequence of the first Streptomyces species isolated from the Brazilian Caatinga is reported here. Genes related to environmental stress tolerance were prevalent and included many secondary metabolic gene clusters. Copyright © 2015 Santos et al.

Impulsivity in binge eating disorder: food cues elicit increased reward responses and disinhibition.

PubMed

Schag, Kathrin; Teufel, Martin; Junne, Florian; Preissl, Hubert; Hautzinger, Martin; Zipfel, Stephan; Giel, Katrin Elisabeth

2013-01-01

Binge eating disorder (BED) represents a distinct eating disorder diagnosis. Current approaches assume increased impulsivity to be one factor leading to binge eating and weight gain. We used eye tracking to investigate both components of impulsivity, namely reward sensitivity and rash-spontaneous behaviour towards food in BED for the first time. Overweight and obese people with BED (BED+; n = 25), without BED (BED-; n = 26) and healthy normal-weight controls (NWC; n = 25) performed a free exploration paradigm measuring reward sensitivity (experiment 1) and a modified antisaccade paradigm measuring disinhibited, rash-spontaneous behaviour (experiment 2) using food and nonfood stimuli. Additionally, trait impulsivity was assessed. In experiment 1, all participants located their initial fixations more often on food stimuli and BED+ participants gazed longer on food stimuli in comparison with BED- and NWC participants. In experiment 2, BED+ participants had more difficulties inhibiting saccades towards food and nonfood stimuli compared with both other groups in first saccades, and especially towards food stimuli in second saccades and concerning sequences of first and second saccades. BED- participants did not differ significantly from NWC participants in both experiments. Additionally, eye tracking performance was associated with self-reported reward responsiveness and self-control. According to these results, food-related reward sensitivity and rash-spontaneous behaviour, as the two components of impulsivity, are increased in BED in comparison with weight-matched and normal-weight controls. This indicates that BED represents a neurobehavioural phenotype of obesity that is characterised by increased impulsivity. Interventions for BED should target these special needs of affected patients.

Coupling channel evolution monitoring and RFID tracking in a large, wandering, gravel-bed river: Insights into sediment routing on geomorphic continuity through a riffle-pool sequence

NASA Astrophysics Data System (ADS)

Chapuis, Margot; Dufour, Simon; Provansal, Mireille; Couvert, Bernard; de Linares, Matthieu

2015-02-01

Bedload transport and bedform mobility in large gravel-bed rivers are not easily monitored, especially during floods. Large reaches present difficulties in bed access during flows for flow measurements. Because of these logistical issues, the current knowledge about bedload transport processes and bedform mobility lacks field-based information, while this missing information would precisely match river management needs. The lack of information linking channel evolution and particle displacements is even more striking in wandering reaches. The Durance River is a large, wandering, gravel-bed river (catchment area: 14,280 km2; mean width: 240 m), located in the southern French Alps and highly impacted by flow diversion and gravel mining. In order to improve current understanding of the link between sediment transport processes and river bed morphodynamics, we set up a sediment particle survey in the channel using Radio Frequency Identification (RFID) tracking and topographic surveys (GPS RTK and scour chains) for a 4-year recurrence interval flood. By combining topographic changes before and after a flood, intraflood erosion/deposition patterns from scour chains, differential routing of tracer particles, and spatial distribution of bed shear stress through a complex reach, this paper aims to define the critical shear stress for significant sediment mobility in this setting. Gravel tracking highlights displacement patterns in agreement with bar downstream migration and transport of particles across the riffle within this single flood event. Because no velocity measurements were possible during flood, a TELEMAC three-dimensional model helped interpret particle displacements by estimating spatial distribution of shear stresses and flow directions at peak flow. Although RFID tracking in a large, wandering, gravel-bed river does have some technical limitations (burial, recovery process time-consuming), it provides useful information on sediment routing through a riffle-pool sequence.

Germination and early growth of coastal tree species on organic seed beds.

Treesearch

Don Minore

1972-01-01

Germination and early growth on rotten wood and duff under several shade levels were observed for Douglas-fir, Sitka spruce, western hemlock, western redcedar, lodgepole pine, Pacific silver fir, and red alder. Nutrients were more abundant in duff than in rotten wood. Seedlings usually were larger and more abundant on duff-covered rotten logs than on duff-covered...

Unaltered cosmic spherules in a 1.4-Gyr-old sandstone from Finland.

PubMed

Deutsch, A; Greshake, A; Pesonen, L J; Pihlaja, P

1998-09-10

Micrometeorites-submillimetre-sized particles derived from asteroids and comets-occur in significant quantities in deep sea sediments, and the ice sheets of Greenland and Antarctica. The most abundant micrometeorites are cosmic spherules, which contain nickel-rich spinels that were crystallized and oxidized during atmospheric entry, therefore recording the oxygen content in the uppermost atmosphere. But the use of micrometeorites for detecting past changes in the flux of incoming extraterrestrial matter, and as probes of the evolution of the atmosphere, has been hampered by the fact that most objects with depositional ages higher than 0.5 Myr show severe chemical alteration. Here we report the discovery of unaltered cosmic spherules in a 1.4-Gyr-old sandstone (red bed) from Finland. From this we infer that red beds, a common lithology in the Earth's history, may contain substantial unbiased populations of fossil micrometeorites. The study of such populations would allow systematic research on variations in the micrometeorite flux from the early Proterozoic era to recent times (a time span of about 2.5 Gyr), and could help to better constrain the time when the atmospheric oxygen content was raised to its present level.

Photocatalytic discoloration of Acid Red 14 aqueous solution using titania nanoparticles immobilized on graphene oxide fabricated plate.

PubMed

Akerdi, Abdollah Gholami; Bahrami, S Hajir; Arami, Mokhtar; Pajootan, Elmira

2016-09-01

Textile industry consumes remarkable amounts of water during various operations. A significant portion of the water discharge to environment is in the form of colored contaminant. The present research reports the photocatalytic degradation of anionic dye effluent using immobilized TiO2 nanoparticle on graphene oxide (GO) fabricated carbon electrodes. Acid Red 14 (AR 14) was used as model compound. Graphene oxide nanosheets were synthesized from graphite powder using modified Hummer's method. The nanosheets were characterized with field emission scanning electron microscope (FESEM) images, X-ray diffraction (XRD) and FTIR spectrum. The GO nanoparticles were deposited on carbon electrode (GO-CE) by electrochemical deposition (ECD) method and used as catalyst bed. TiO2 nanoparticles were fixed on the bed (GO-CE- TiO2) with thermal process. Photocatalytic processes were carried out using a 500 ml solution containing dye in batch mode. Each photocatalytic treatment were carried out for 120 min. Effect of dye concentration (mg/L), pH of solution, time (min) and TiO2 content (g/L) on the photocatalytic decolorization was investigated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deep sequencing and proteomic analysis of the microRNA-induced silencing complex in human red blood cells.

PubMed

Azzouzi, Imane; Moest, Hansjoerg; Wollscheid, Bernd; Schmugge, Markus; Eekels, Julia J M; Speer, Oliver

2015-05-01

During maturation, erythropoietic cells extrude their nuclei but retain their ability to respond to oxidant stress by tightly regulating protein translation. Several studies have reported microRNA-mediated regulation of translation during terminal stages of erythropoiesis, even after enucleation. In the present study, we performed a detailed examination of the endogenous microRNA machinery in human red blood cells using a combination of deep sequencing analysis of microRNAs and proteomic analysis of the microRNA-induced silencing complex. Among the 197 different microRNAs detected, miR-451a was the most abundant, representing more than 60% of all read sequences. In addition, miR-451a and its known target, 14-3-3ζ mRNA, were bound to the microRNA-induced silencing complex, implying their direct interaction in red blood cells. The proteomic characterization of endogenous Argonaute 2-associated microRNA-induced silencing complex revealed 26 cofactor candidates. Among these cofactors, we identified several RNA-binding proteins, as well as motor proteins and vesicular trafficking proteins. Our results demonstrate that red blood cells contain complex microRNA machinery, which might enable immature red blood cells to control protein translation independent of de novo nuclei information. Copyright © 2015 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

Sequence analysis of a canine parvovirus isolated from a red panda (Ailurus fulgens) in China.

PubMed

Qin, Qin; Loeffler, I Kati; Li, Ming; Tian, Kegong; Wei, Fuwen

2007-06-01

Canine parvovirus (CPV) was first recognized in the late 1970 s in dogs and has mutated and spread throughout the world in canid and felid species since then. In this study, a novel CPV was isolated from the endangered red panda (Ailurus fulgens) in China. Nucleotide and phylogenetic analysis of the capsid protein VP2 gene classified the red panda parvovirus (RPPV) as a CPV-2a type. Substitution of Val for Gly at the conserved 300 residue in RPPV presents an unusual variation in the CPV-2a amino acid sequence and is further evidence for the continuing evolution of the virus. The 300 residue is important in distinguishing the antigenicity and host range of CPVs. The clinical significance and population impact of RPPV infection in captive red pandas in China is unknown and is an important topic for future research.

Sedimentary environment and tectonic deformations of the Neoproterozoic Iron formation at the Wadi El-Dabbah greenstone sequence, Central Eastern Desert, Egypt

NASA Astrophysics Data System (ADS)

Kiyokawa, S.; Suzuki, T.; Ikehara, M.; Horie, K.; Takehara, M.; Abd-Elmonem, H.; Dawoud, A. D. M.; El-Hasan, M. M.

2017-12-01

El-Dabbah area Central Eastern Desert of the Nubia Shield preserved Neoproterozoic lower green schist faces volcaniclastics greenstone sequence and covered strike-slip deformation related subaerial sedimentary sequence (Hammamat Group). The volcaniclastics greenstone sequence (El-Dabbah Formation) preserved several iron beds bearing well stratified sequence. Four tectonic deformation identified as this area; thrust deformation (D1), strike-slip deformation with transtension normal fault and strong left-lateral shear (D2), subaerial pull apart sediments basin formed strike-slip deformations (D3), and extensional deformation after the Hammamat Group sedimentation (D4). New age data from intrusions identified about 638 Ma white granite and about 660 Ma quartz porphyry. Based on the detail mapping, we reconstruct more than 5000m thick volcano sedimentary succession. At least, 10 iron rich sections were identified within 3500m thick volcano-sedimentary sequence. There are 14 iron formation sequence identified in this greenstone sequence. Each Iron sequences are bedded with greenish-black shales within massive volcaniclastics and lava flow. Iron formation is formed mostly fine grain magnetite deposited within volcanic mudstone and siltstone with gradual distribution. Timing of this iron sediment is identified within Sturtian glaciation (730-700Ma). However, there is no geological direct support evidence in the Snowball earth event at this greenstone sequence. The volcanic activities at this ocean already produced many Fe2+ to ocean water. Repeated iron precipitation occur during volcanic activity interphase period which produced oxidation of iron and produce oxyhydroxide with mud-silt sediment at bottom of ocean.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

PubMed

Smith, Chris R; Smith, Christopher D; Robertson, Hugh M; Helmkampf, Martin; Zimin, Aleksey; Yandell, Mark; Holt, Carson; Hu, Hao; Abouheif, Ehab; Benton, Richard; Cash, Elizabeth; Croset, Vincent; Currie, Cameron R; Elhaik, Eran; Elsik, Christine G; Favé, Marie-Julie; Fernandes, Vilaiwan; Gibson, Joshua D; Graur, Dan; Gronenberg, Wulfila; Grubbs, Kirk J; Hagen, Darren E; Viniegra, Ana Sofia Ibarraran; Johnson, Brian R; Johnson, Reed M; Khila, Abderrahman; Kim, Jay W; Mathis, Kaitlyn A; Munoz-Torres, Monica C; Murphy, Marguerite C; Mustard, Julie A; Nakamura, Rin; Niehuis, Oliver; Nigam, Surabhi; Overson, Rick P; Placek, Jennifer E; Rajakumar, Rajendhran; Reese, Justin T; Suen, Garret; Tao, Shu; Torres, Candice W; Tsutsui, Neil D; Viljakainen, Lumi; Wolschin, Florian; Gadau, Jürgen

2011-04-05

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

PubMed

Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

2018-06-20

The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Serological and molecular epidemiology of canine adenovirus type 1 in red foxes (Vulpes vulpes) in the United Kingdom.

PubMed

Walker, David; Fee, Seán A; Hartley, Gill; Learmount, Jane; O'Hagan, Maria J H; Meredith, Anna L; de C Bronsvoort, Barend M; Porphyre, Thibaud; Sharp, Colin P; Philbey, Adrian W

2016-10-31

Canine adenovirus type 1 (CAV-1) causes infectious canine hepatitis (ICH), a frequently fatal disease which primarily affects canids. In this study, serology (ELISA) and molecular techniques (PCR/qPCR) were utilised to investigate the exposure of free-ranging red foxes (Vulpes vulpes) to CAV-1 in the United Kingdom (UK) and to examine their role as a wildlife reservoir of infection for susceptible species. The role of canine adenovirus type 2 (CAV-2), primarily a respiratory pathogen, was also explored. In foxes with no evidence of ICH on post-mortem examination, 29 of 154 (18.8%) red foxes had inapparent infections with CAV-1, as detected by a nested PCR, in a range of samples, including liver, kidney, spleen, brain, and lung. CAV-1 was detected in the urine of three red foxes with inapparent infections. It was estimated that 302 of 469 (64.4%) red foxes were seropositive for canine adenovirus (CAV) by ELISA. CAV-2 was not detected by PCR in any red foxes examined. Additional sequence data were obtained from CAV-1 positive samples, revealing regional variations in CAV-1 sequences. It is concluded that CAV-1 is endemic in free-ranging red foxes in the UK and that many foxes have inapparent infections in a range of tissues.

Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609.

PubMed

Sambles, Christine; Middelhaufe, Sabine; Soanes, Darren; Kolak, Dagmara; Lux, Thomas; Moore, Karen; Matoušková, Petra; Parker, David; Lee, Rob; Love, John; Aves, Stephen J

2017-09-01

Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula ( Rhodosporidium ) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).

Genome survey sequencing of red swamp crayfish Procambarus clarkii.

PubMed

Shi, Linlin; Yi, Shaokui; Li, Yanhe

2018-06-21

Red swamp crayfish, Procambarus clarkii, presently is an important aquatic commercial species in China. The crayfish is a hot area of research focus, and its genetic improvement is quite urgent for the crayfish aquaculture in China. However, the knowledge of its genomic landscape is limited. In this study, a survey of P. clarkii genome was investigated based on Illumina's Solexa sequencing platform. Meanwhile, its genome size was estimated using flow cytometry. Interestingly, the genome size estimated is about 8.50 Gb by flow cytometry and 1.86 Gb with genome survey sequencing. Based on the assembled genome sequences, total of 136,962 genes and 152,268 exons were predicted, and the predicted genes ranged from 150 to 12,807 bp in length. The survey sequences could help accelerate the progress of gene discovery involved in genetic diversity and evolutionary analysis, even though it could not successfully applied for estimation of P. clarkii genome size.

Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

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

Stackebrandt, Erko; Zeytun, Ahmet; Lapidus, Alla L.

2013-01-01

Coriobacterium glomerans Haas and Ko nig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for whichmore » complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

First report of Enterocytozoon bieneusi from giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens) in China.

PubMed

Tian, Ge-Ru; Zhao, Guang-Hui; Du, Shuai-Zhi; Hu, Xiong-Feng; Wang, Hui-Bao; Zhang, Long-Xian; Yu, San-Ke

2015-08-01

Enterocytozoon bieneusi is an emerging and opportunistic enteric pathogen triggering diarrhea and enteric disease in humans and animals. Despite extensive research on this pathogen, the prevalence and genotypes of E. bieneusi infection in precious wild animals of giant and red pandas have not been reported. In the present study, 82 faecal specimens were collected from 46 giant pandas (Ailuropoda melanoleuca) and 36 red pandas (Ailurus fulgens) in the northwest of China. By PCR and sequencing of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene of E. bieneusi, an overall infection rate of 10.98% (9/82) was observed in pandas, with 8.70% (4/46) for giant pandas, and 13.89% (5/36) for red pandas. Two ITS genotypes were identified: the novel genotype I-like (n=4) and genotype EbpC (n=5). Multilocus sequence typing (MLST) employing three microsatellites (MS1, MS3 and MS7) and one minisatellite (MS4) showed that nine, six, six and nine positive products were amplified and sequenced successfully at four respective loci. A phylogenetic analysis based on a neighbor-joining tree of the ITS gene sequences of E. bieneusi indicated that the genotype EbpC fell into 1d of group 1 of zoonotic potential, and the novel genotype I-like was clustered into group 2. The present study firstly indicated the presence of E. bieneusi in giant and red pandas, and these results suggested that integrated strategies should be implemented to effectively protect pandas and humans from infecting E. bieneusi in China. Copyright © 2015 Elsevier B.V. All rights reserved.

Petrology and geochemistry of samples from bed-contact zones in Tunnel Bed 5, U12g-Tunnel, Nevada Test Site

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

Connolly, J.R.; Keil, K.; Mansker, W.L.

1984-10-01

This report summarizes the detailed geologic characterization of samples of bed-contact zones and surrounding nonwelded bedded tuffs, both within Tunnel Bed 5, that are exposed in the G-Tunnel complex beneath Rainier Mesa on the Nevada Test Site (NTS). Original planning studies treated the bed-contact zones in Tunnel Bed 5 as simple planar surfaces of relatively high permeability. Detailed characterization, however, indicates that these zones have a finite thickness, are depositional in origin, vary considerably over short vertical and horizontal distances, and are internally complex. Fluid flow in a sequence of nonwelded zeolitized ash-flow or bedded tuffs and thin intervening reworkedmore » zones appears to be a porous-medium phenomenon, regardless of the presence of layering. There are no consistent differences in either bulk composition or detailed mineralogy between bedded tuffs and bed-contact zones in Tunnel Bed 5. Although the original bulk composition of Tunnel Bed 5 was probably peralkaline, extensive zeolitization has resulted in a present peraluminous bulk composition of both bedded tuffs and bed-contact zones. The major zeolite present, clinoptilolite, is intermediate (Ca:K:Na = 26:35:39) and effectively uniform in composition. This composition is similar to that of clinoptilolite from the tuffaceous beds of Calico Hills above the static water level in hole USW G-1, but somewhat different from that reported for zeolites from below the static water level in USW G-2. Tunnel Bed 5 also contains abundant hydrous manganese oxides. The similarity in composition of the clinoptilolites from Tunnel Bed 5 and those above the static water level at Yucca Mountain indicates that many of the results of nuclide-migration experiments in Tunnel Bed 5 would be transferrable to zeolitized nonwelded tuffs above the static water level at Yucca Mountain.« less

Identification and genetic characterization of Sarcocystis arctica and Sarcocystis lutrae in red foxes (Vulpes vulpes) from Baltic States and Spain.

PubMed

Kirillova, Viktorija; Prakas, Petras; Calero-Bernal, Rafael; Gavarāne, Inese; Fernández-García, José Luis; Martínez-González, Manuel; Rudaitytė-Lukošienė, Eglė; Martínez-Estéllez, Miguel Ángel Habela; Butkauskas, Dalius; Kirjušina, Muza

2018-03-12

Typically, carnivores serve as definitive hosts for Sarcocystis spp. parasites; currently, their role as intermediate hosts is being elucidated. The present study aimed to identify and molecularly characterize Sarcocystis cysts detected in striated muscle of red foxes from different populations in Latvia, Lithuania and Spain. Muscle samples from 411 red foxes (Vulpes vulpes) and 269 racoon dogs (Nyctereutes procyonoides) from Latvia, 41 red foxes from Lithuania and 22 red foxes from Spain were examined for the presence of Sarcocystis sarcocysts by light microscopy (LM). Sarcocystis spp. were identified by transmission electron microscopy (TEM) and molecular biology techniques. Sarcocystis cysts were detected in 11/411 (2.7%) Latvian, 3/41 (7.3%) Lithuanian, and 6/22 (27.3%) Spanish red foxes, however, cysts were not observed in the muscles of racoon dogs. Based on LM, TEM, 18S rDNA, 28S rDNA, ITS1, cox1 and rpoB sequences, Sarcocystis arctica and Sarcocystis lutrae cysts were identified in red fox muscles from Latvia and Lithuania, whereas only S. arctica was detected in Spain. The 18S rDNA, 28S rDNA and ITS1 sequences from the 21 isolates of S. arctica from Latvia, Lithuania and Spain were identical. By contrast, two and four haplotypes were determined based on mtDNA cox1 and apicoplast rpoB sequences, respectively. Polymorphisms were not detected between the two isolates of S. lutrae from Latvia and Lithuania. Based on phylogenetic results, S. arctica and S. lutrae were most closely related to Sarcocystis spp. using predatory mammals as intermediate hosts and to Sarcocystis species with a bird-bird life-cycle. Based on current knowledge, the red fox and Arctic fox (Vulpes lagopus) could act as intermediate host for the same two Sarcocystis species. Molecular results suggest the existence of two genetic lineages of S. arctica, and such divergence relies on its geographical distribution but not on their intermediate host species.

New Sections and Fossils From the Southern Bighorn Basin, Wyoming Document Faunal Turnover During the PETM

NASA Astrophysics Data System (ADS)

Bloch, J. I.; Boyer, D. M.; Strait, S. G.; Wing, S. L.

2004-12-01

Though earliest Eocene (Wa-0) mammals are known from the southern Bighorn Basin, late Paleocene mammals are not. Recent discovery of latest Paleocene mammals in section with new Wa-0 faunas and floras at Cabin Fork allows for the first studies of terrestrial biotic change across the Paleocene-Eocene boundary interval outside of the northern Bighorn Basin. A differential GPS was used to map the area and provide a framework for high-resolution biostratigraphy. Least squares interpolation of bedding planes from points marking outcrop of beds reveals high r2 coefficients (0.97-0.98). This indicates that small scale folding is minimal and bed traces are smoothly planar. Beds in the study area strike N-NW (355° ) and dip shallowly W-SW (<1.0° ). Smaller scale undulations are present: to the NE beds strike NW and dip to the SW (342° /1.0° ) whereas those to the SW strike NE and dip NW (5° /1.0° ). Shallow dips allow us to approximate stratigraphic thickness with elevation. Paleocene mammals, including diagnostic Clarkforkian land-mammal age indicators, Aletodon gunnelli, Apheliscus nitidus, and Haplomylus simpsoni, were found in a ferruginous, grit-pebble conglomerate at the base of a channel sand at the top of the Fort Union Fm. The fossiliferous horizon is extensive and has produced over 200 specimens from more than 60 sites for which positions have been determined with sub-meter accuracy. Absence of Plesiadapis cookei and Hyracotherium spp., together with high relative abundance of Phenacodus and Ectocion, indicate this fauna is latest Clarkforkian (Phenacodus-Ectocion Range Zone, Cf-3). Earliest Eocene mammals, including diagnostic Wa-0 taxa Arfia junnei, Copecion davisi, Hyracotherium sandrae, and Diacodexis ilicis, are represented by more than 233 specimens from 70 sites at three levels in the lowest Willwood Formation. The lowest fossils come from paleosols and claygall accumulations in stringer sands approximately 3 meters above the top of the channel sand that is the top of the Fort Union Formation, and 8 meters above the Clarkforkian localities. The second level is a fossiliferous paleosol 6-8 meters above the top of the channel sand. The third level is a paleosol fossil accumulation approximately 22 meters above the top of the channel sand and 15 meters below a large and persistent red paleosol informally called ?Big Red.? In the Cabin Fork area, Big Red produces mammal fossils, including Cardiolophus, that have been used to define the succeeding Wa-1 faunal zone (although some Wa-0 taxa have been recovered from Big Red approximately 6 km to the east). The Wa-0 interval in the Cabin Fork area is 38-40 meters thick and bounded by distinct Cf-3 and Wa-1 faunas. Preliminary analyses of fossils from the Cabin Fork section show that the faunal shift marking the PETM was very similar to that seen in the northern Bighorn Basin. This suggests that previously documented differences between Wa-0 mammalian faunas in the southern and northern Bighorn Basin, including the absence of certain diagnostic Wa-0 taxa in the south, may reflect local sampling variation or artifacts rather than regional variation in faunal composition.

Drag reducing polymers improve coronary flow reserve through modulation of capillary resistance.

PubMed

Pacella, John J; Kameneva, Marina V; Villanueva, Flordeliza S

2009-01-01

We have shown that drag-reducing polymers (DRP) reduce microvascular resistance and improve myocardial perfusion during coronary stenosis. We used myocardial contrast echocardiography (MCE) and mathematical modeling to define the DRP microvascular effects. A non-flow-limiting left anterior descending (LAD) stenosis was created in 8 dogs. Intramyocardial blood volume, RBC velocity and flow in the LAD and circumflex (CX) beds were obtained from MCE at baseline, and in hyperemia, stenosis, hyperemia + stenosis, and hyperemia + stenosis + DRP. Microvascular resistances were calculated from a lumped-parameter model. During stenosis + hyperemia, LAD bed microvascular resistance increased (p<0.015), and capillary volume (p<0.002) and red cell velocity (p<0.0004) decreased relative to baseline. With DRP, during stenosis and hyperemia, LAD bed microvascular resistance decreased (p<0.04); there was an increase in capillary volume (p<0.007), RBC velocity (p<0.006), and flow (p<0.05). Decreased model-computed capillary resistance accounted for the reduction in LAD bed resistance after DRP. We conclude that DRP improve flow reserve during coronary stenosis by modulating capillary resistance. Primary modification of the rheological properties of blood to affect capillary resistance is a novel approach for the treatment of acute coronary syndromes.

Thermal Protection Test Bed Pathfinder Development Project

NASA Technical Reports Server (NTRS)

Snapp, Cooper

2015-01-01

In order to increase thermal protection capabilities for future reentry vehicles, a method to obtain relevant test data is required. Although arc jet testing can be used to obtain some data on materials, the best method to obtain these data is to actually expose them to an atmospheric reentry. The overprediction of the Orion EFT-1 flight data is an example of how the ground test to flight traceability is not fully understood. The RED-Data small reentry capsule developed by Terminal Velocity Aerospace is critical to understanding this traceability. In order to begin to utilize this technology, ES3 needs to be ready to build and integrate heat shields onto the RED-Data vehicle. Using a heritage Shuttle tile material for the heat shield will both allow valuable insight into the environment that the RED-Data vehicle can provide and give ES3 the knowledge and capability to build and integrate future heat shields for this vehicle.

Hydrologic environment of the Silurian salt deposits in parts of Michigan, Ohio, and New York

USGS Publications Warehouse

Norris, Stanley E.

1978-01-01

The aggregate thickness of evaporites (salt, gypsum, and anhydrite) in the Silurian Salina sequence in Michigan exceeds 1200 feet in areas near the periphery of the Michigan basin, where the salt beds are less than 3000 feet below land surface. In northeast Ohio the aggregate thickness of salt beds is as much as 200 feet in places, and in western New York it is more than 500 feet, where th beds are less than 3000 feet deep. The salt-bearing rocks dip regionally on the order of 50 feet per mile; those in Michigan dip toward the center of the Michigan basin, and those in Ohio and New York, in the Appalachian basin, dip generally southward. The rocks in both basins thicken downdip. Minor folds and faults occur in the salt-bearing rocks in all three states. Some of this defrmation has been attenuated or absorbed bo the salt beds. Occuring near the middle of thick sedimentary sequences, the salt beds are bounded aboe and below by beds containing water having dissolved-solids concentrations several times that seawter. The brines occur commonly in discrete zones of high permeability at specific places in the stratigraphic sequence. In northeast Ohio two prominent brine zones are recognized by the driller, the Devonian Oriskany Sandstone, or 'first water' zone, above the Salina Formation, and the Newburg or 'second water' zone below the Salina. In each aquifer there is a vertical component of hydraulic head, but little brine probably moves through the salt beds because their permeability is extremely low. Also, ther is little evidence of dissolution of the salt in areas distant from the outcrop, suggesting that if brine does move through the salt, movement is at a slow enough rate so that, in combination with the saturated or near-saturated condition of the water, it precludes significant dissolution. Principal brine movement is probably in the permeable zones in the direction of the hydraulic gradient. Two areas in Michigan and one area each in Ohio and New York appear suitable for additional investigation of salt beds for purposes radioactive waste disposal. One of the Michigan areas is in the northern part of the southern peninsula, in Presque Isle and Alpena Counties; the other is in the southern part of the southern peninsula, in Oakland, Macomb, and St. Clair Counties (fig. 3). In northeast Ohio the area that appears to be suitable for investigation includes most of the eastern half of Lake County and extends eastward into Ashtabula County and southward into Geauga County. In western New York conditions may warrant additional investigation in Schuyler, Tompkins, and western Cortland Counties.

Late Devonian glacial deposits from the eastern United States signal an end of the mid-Paleozoic warm period

USGS Publications Warehouse

Brezinski, D.K.; Cecil, C.B.; Skema, V.W.; Stamm, R.

2008-01-01

A Late Devonian polymictic diamictite extends for more than 400??km from northeastern Pennsylvania across western Maryland and into east-central West Virginia. The matrix-supported, unbedded, locally sheared diamictite contains subangular to rounded clasts up to 2??m in diameter. The mostly rounded clasts are both locally derived and exotic; some exhibit striations, faceting, and polish. The diamictite commonly is overlain by laminated siltstone/mudstone facies associations (laminites). The laminites contain isolated clasts ranging in size from sand and pebbles to boulders, some of which are striated. The diamictite/laminite sequence is capped by massive, coarse-grained, pebbly sandstone that is trough cross-bedded. A stratigraphic change from red, calcic paleo-Vertisols in strata below the diamictite to non-calcic paleo-Spodosols and coal beds at and above the diamictite interval suggests that the climate became much wetter during deposition of the diamictite. The diamictite deposit is contemporaneous with regressive facies that reflect fluvial incision during the Late Devonian of the Appalachian basin. These deposits record a Late Devonian episode of climatic cooling so extreme that it produced glaciation in the Appalachian basin. Evidence for this episode of climatic cooling is preserved as the interpreted glacial deposits of diamictite, overlain by glaciolacustrine varves containing dropstones, and capped by sandstone interpreted as braided stream outwash. The Appalachian glacigenic deposits are contemporaneous with glacial deposits in South America, and suggest that Late Devonian climatic cooling was global. This period of dramatic global cooling may represent the end of the mid-Paleozoic warm interval that began in the Middle Silurian. ?? 2008 Elsevier B.V. All rights reserved.

Sarcocystis spp. Infection in two Red Panda Cubs (Ailurus fulgens).

PubMed

Zoll, W M; Needle, D B; French, S J; Lim, A; Bolin, S; Langohr, I; Agnew, D

2015-01-01

Two neonatal male red panda (Ailurus fulgens) littermates were submitted for necropsy examination. One animal was found dead with no prior signs of illness; the other had a brief history of laboured breathing. Post-mortem examination revealed disseminated protozoal infection. To further characterize the causative agent, transmission electron microscopy (TEM), immunohistochemistry (IHC), polymerase chain reaction (PCR) and amplification and nucleic acid sequencing were performed. IHC was negative for Toxoplasma gondii and Neospora caninum, but was positive for a Sarcocystis spp. TEM of cardiac muscle and lung revealed numerous intracellular apicomplexan protozoa within parasitophorous vacuoles. PCR and nucleic acid sequencing of partial 18S rRNA and the internal transcribed spacer (ITS)-1 region confirmed a Sarcocystis spp. that shared 99% sequence homology to Sarcocystis neurona and Sarcocystis dasypi. This represents the first report of sarcocystosis in red pandas. The histopathological, immunohistochemical, molecular and ultrastructural findings are supportive of vertical transmission resulting in fatal disseminated disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

Blood use in liver transplantation

PubMed Central

Lewis, J. H.; Bontempo, F. A.; Cornell, F.; Ki̋ss, J. E.; Larson, P.; Ragni, M. V.; Rice, E. O.; Spero, J. A.; Starzl, T. E.

2010-01-01

During the first 5 years (1981–1985) of the liver transplantation program in Pittsburgh, a total (preoperative, intraoperative, and postoperative) of 18,668 packed red cell units, 23,627 fresh-frozen plasma units, 20,590 platelet units, and 4241 cryoprecipitate units was transfused for the procedures. This represents 3 to 9 percent of the total of blood products supplied by the Central Blood Bank to its 32 member hospitals. Six hundred thirty-six (636) transplants were performed on 485 patients in two hospitals: the Presbyterian University Hospital (564 beds) and Children’s Hospital of Pittsburgh (236 beds). All of the blood components used in the operations were procured and released by the Central Blood Bank. This report describes some of these findings. PMID:3296340

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

PubMed

Baldwin, Samantha; Revanna, Roopashree; Thomson, Susan; Pither-Joyce, Meeghan; Wright, Kathryn; Crowhurst, Ross; Fiers, Mark; Chen, Leshi; Macknight, Richard; McCallum, John A

2012-11-19

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line 'CUDH2150' and the genetically distant Indian landrace 'Nasik Red', using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of 'Nasik Red' reads onto 'CUDH2150' assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F(2) progeny from a very large F(2) family developed from the 'Nasik Red' x 'CUDH2150' inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

Systemic AA amyloidosis in the red fox (Vulpes vulpes).

PubMed

Rising, Anna; Cederlund, Ella; Palmberg, Carina; Uhlhorn, Henrik; Gaunitz, Stefan; Nordling, Kerstin; Ågren, Erik; Ihse, Elisabet; Westermark, Gunilla T; Tjernberg, Lars; Jörnvall, Hans; Johansson, Jan; Westermark, Per

2017-11-01

Amyloid A (AA) amyloidosis occurs spontaneously in many mammals and birds, but the prevalence varies considerably among different species, and even among subgroups of the same species. The Blue fox and the Gray fox seem to be resistant to the development of AA amyloidosis, while Island foxes have a high prevalence of the disease. Herein, we report on the identification of AA amyloidosis in the Red fox (Vulpes vulpes). Edman degradation and tandem MS analysis of proteolyzed amyloid protein revealed that the amyloid partly was composed of full-length SAA. Its amino acid sequence was determined and found to consist of 111 amino acid residues. Based on inter-species sequence comparisons we found four residue exchanges (Ser31, Lys63, Leu71, Lys72) between the Red and Blue fox SAAs. Lys63 seems unique to the Red fox SAA. We found no obvious explanation to how these exchanges might correlate with the reported differences in SAA amyloidogenicity. Furthermore, in contrast to fibrils from many other mammalian species, the isolated amyloid fibrils from Red fox did not seed AA amyloidosis in a mouse model. © 2017 The Protein Society.

Test Input Generation for Red-Black Trees using Abstraction

NASA Technical Reports Server (NTRS)

Visser, Willem; Pasareanu, Corina S.; Pelanek, Radek

2005-01-01

We consider the problem of test input generation for code that manipulates complex data structures. Test inputs are sequences of method calls from the data structure interface. We describe test input generation techniques that rely on state matching to avoid generation of redundant tests. Exhaustive techniques use explicit state model checking to explore all the possible test sequences up to predefined input sizes. Lossy techniques rely on abstraction mappings to compute and store abstract versions of the concrete states; they explore under-approximations of all the possible test sequences. We have implemented the techniques on top of the Java PathFinder model checker and we evaluate them using a Java implementation of red-black trees.

Changes in markers of bone formation and resorption in a bed rest model of weightlessness

NASA Technical Reports Server (NTRS)

Lueken, S. A.; Arnaud, S. B.; Taylor, A. K.; Baylink, D. J.

1993-01-01

To study the mechanism of bone loss in physical unloading, we examined indices of bone formation and bone resorption in the serum and urine of eight healthy men during a 7 day -6 degrees head-down tilt bed rest. Prompt increases in markers of resorption--pyridinoline (PD), deoxypyridinoline (DPD), and hydroxyproline (Hyp)/g creatinine--during the first few days of inactivity were paralleled by tartrate-resistant acid phosphatase (TRAP) with significant increases in all these markers by day 4 of bed rest. An index of formation, skeletal alkaline phosphatase (SALP), did not change during bed rest and showed a moderate 15% increase 1 week after reambulation. In contrast to SALP, serum osteocalcin (OC) began increasing the day preceding the increase in Hyp, remained elevated for the duration of the bed rest, and returned to pre-bed rest values within 5 days of reambulation. Similarly, DPD increased significantly at the onset of bed rest, remained elevated for the duration of bed rest, and returned to pre-bed rest levels upon reambulation. On the other hand, the other three indices of resorption, Hyp, PD, and TRAP, remained elevated for 2 weeks after reambulation. The most sensitive indices of the levels of physical activity proved to be the noncollagenous protein, OC, and the collagen crosslinker, DPD. The bed rest values of both these markers were significantly elevated compared to both the pre-bed rest values and the post-bed rest values. The sequence of changes in the circulating markers of bone metabolism indicated that increases in serum OC are the earliest responses of bone to head-down tilt bed rest.

TSCA Environmental Release Application (TERA) for Alcaligenes xylosoxidans subspecies denitrificans strain AL6.1

EPA Pesticide Factsheets

TERA submitted by University of California, Riverside and given the tracking designation of R-03-0001. The microorganism has been modified to carry a coding sequence of DsRed for expressing a red fluorescent protein.

Spectroscopic Confirmation of a Massive Red-sequence Selected Galaxy Cluster at Z=1.34 in the SpARCS-South Cluster Survey

NASA Technical Reports Server (NTRS)

Wilson, Gillian; Demarco, Ricardo; Muzzin, Adam; Yee, H.K.C.; Lacy, Mark; Surace, Jason; Gilbank, David; Blindert, Kris; Hoekstra, Henk; Majumdar, Subhabrata;

Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops

PubMed Central

Sun, Xiujun; Liu, Zhihong; Zhou, Liqing; Wu, Biao; Dong, Yinghui; Yang, Aiguo

2016-01-01

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture. PMID:27563719

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

PubMed Central

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B.

2013-01-01

Background The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. Results We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. Conclusions We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo. PMID:24324765

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

PubMed

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

2013-01-01

The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing

PubMed Central

Poojari, Sudarsana; Alabi, Olufemi J.; Fofanov, Viacheslav Y.; Naidu, Rayapati A.

2013-01-01

A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms. PMID:23755117

Isolated thermocouple amplifier system for stirred fixed-bed gasifier

DOEpatents

Fasching, George E.

1992-01-01

A sensing system is provided for determining the bed temperature profile of the bed of a stirred, fixed-bed gasifier including a plurality of temperature sensors for sensing the bed temperature at different levels, a transmitter for transmitting data based on the outputs of the sensors to a remote operator's station, and a battery-based power supply. The system includes an isolation amplifier system comprising a plurality of isolation amplifier circuits for amplifying the outputs of the individual sensors. The isolation amplifier circuits each comprise an isolation operational amplifier connected to a sensor; a first "flying capacitor" circuit for, in operation, controlling the application of power from the power supply to the isolation amplifier; an output sample and hold circuit connected to the transmitter; a second "flying capacitor" circuit for, in operation, controlling the transfer of the output of the isolation amplifier to the sample and hold circuit; and a timing and control circuit for activating the first and second capacitor circuits in a predetermined timed sequence.

PHYSIOLOGICAL AND FOLIAR INJURY RESPONSES OF PRUNUS SEROTINA, FRAXINUS AMERICANA, AND ACER RUBRUM SEEDLINGS TO VARYING SOIL MOISTURE AND OZONE. (R825244)

EPA Science Inventory

Sixteen black cherry (Prunus serotina, Ehrh.), 10 white ash (Fraxinus americana, L.) and 10 red maple (Acer rubrum, L.) 1-year old seedlings were planted per plot in 1997 on a former nursery bed within 12 open-top chambers and six open plots. Seedlings wer...

Spatial distribution of chemical constituents in the Kuskokwim River, Alaska

USGS Publications Warehouse

Wang, Bronwen

1999-01-01

The effects of lithologic changes on the water quality of the Kuskokwim River, Alaska, were evaluated by the U.S. Geological Survey in June 1997. Water, suspended sediments, and bed sediments were sampled from the Kusko-kwim River and from three tributaries, the Holitna River, Red Devil Creek, and Crooked Creek. Dissolved boron, chromium, copper, manganese, zinc, aluminum, lithium, barium, iron, antimony, arsenic, mercury, and strontium were detected. Dissolved manganese and iron concentrations were three and four times higher in the Holitna River than in the Kusko-kwim River. Finely divided ferruginous materials found in the graywacke and shale units of the Kuskokwim Group are the probable source of the iron. The highest concentrations of dissolved strontium and barium were found at McGrath, and the limestone present in the upper basin was the most probable source of strontium. The total mercury concentrations on the Kuskokwim River decreased downstream from McGrath. Dissolved mercury was 24 to 32 percent of the total concentration. The highest concentrations of total mercury, and of dissolved antimony and arsenic were found in Red Devil Creek. The higher concentrations from Red Devil Creek did not affect the main stem mercury transport because the tributary was small relative to the Kuskokwim River. In Red Devil Creek, total mercury exceeded the concentration at which the U.S. Environmental Protection Agency (USEPA) indicates that aquatic life is affected and dissolved arsenic exceeded the USEPA's drinking-water standard. Background mercury and antimony concentrations in bed sediments ranged from 0.09 to 0.15 micrograms per gram for mercury and from 1.6 to 2.1 micrograms per gram for antimony. Background arsenic concentrations were greater than 27 micrograms per gram. Sites near the Red Devil mercury mine had mercury and antimony concentrations greater than background concentrations. These concentrations probably reflect the proximity to the ore body and past mining. Crooked Creek had mercury concentrations greater than the background concentration. The transport of suspended sediment-associated trace elements was lower for all elements in the lower river than in the upper river, indicating storage of sediments and their associated metals within the river system.

Phylogeny of geminivirus coat protein sequences and digital PCR aid in identifying Spissistilus festinus (Say) as a vector of Grapevine red blotch-associated virus

USDA-ARS?s Scientific Manuscript database

Grapevine red blotch-associated virus (GRBaV) is a newly identified virus of grapevines, and a putative member of a new genus within the family Geminiviridae. This virus is associated with red blotch disease that was first reported in California in 2008. It affects the profitability of vineyards by ...

Complete Genome Sequence of a New Ruminococcaceae Bacterium Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Hahnke, Sarah; Abendroth, Christian; Langer, Thomas; Codoñer, Francisco M; Ramm, Patrice; Porcar, Manuel; Luschnig, Olaf; Klocke, Michael

2018-04-05

A new Ruminococcaceae bacterium, strain HV4-5-B5C, participating in the anaerobic digestion of grass, was isolated from a mesophilic two-stage laboratory-scale leach bed biogas system. The draft annotated genome sequence presented in this study and 16S rRNA gene sequence analysis indicated the affiliation of HV4-5-B5C with the family Ruminococcaceae outside recently described genera. Copyright © 2018 Hahnke et al.

The effects of treatment room lighting color on time perception and emotion.

PubMed

Han, Seulki; Lee, Daehee

2017-07-01

[Purpose] The purpose of this study was to investigate the perceived treatment times and emotional reactions under different light colors in the treatment room. [Subjects and Methods] Subjects in this study were 20 healthy young students in their 20s. Under each lighting condition (blue, red, white, and yellow) differentiated by color, each subject laid on a therapeutic bed and underwent ultrasound therapy. Subjects were instructed to press a stopwatch every 1 minute, for a total of 5 times, after therapy started according to their perception of time while the stopwatch's time indicator was blocked. After the experiments, self-administered questionnaires were given to subjects to measure their emotional reactions. [Results] In terms of K-POMS scores, the mood states of depression-dejection, anger-hostility, and confusion-bewilderment were higher scores for blue and red lights compared to yellow light. The mood state of vigor-activity were higher scores for yellow and white lights compared to blue and red lights. [Conclusion] Therefore, it is important to take necessary measures to prevent the negative effects that blue and red light-based therapy can have on patient mood.

Integrated multi-stratigraphic study of the Coll de Terrers late Permian-Early Triassic continental succession from the Catalan Pyrenees (NE Iberian Peninsula): A geologic reference record for equatorial Pangaea

NASA Astrophysics Data System (ADS)

Mujal, Eudald; Fortuny, Josep; Pérez-Cano, Jordi; Dinarès-Turell, Jaume; Ibáñez-Insa, Jordi; Oms, Oriol; Vila, Isabel; Bolet, Arnau; Anadón, Pere

2017-12-01

The most severe biotic crisis on Earth history occurred during the Permian-Triassic (PT) transition around 252 Ma. Whereas in the marine realm such extinction event is well-constrained, in terrestrial settings it is still poorly known, mainly due to the lack of suitable complete sections. This is utterly the case along the Western Tethys region, located at Pangaea's equator, where terrestrial successions are typically build-up of red beds often characterised by a significant erosive gap at the base of the Triassic strata. Henceforth, documenting potentially complete terrestrial successions along the PT transition becomes fundamental. Here, we document the exceptional Coll de Terrers area from the Catalan Pyrenees (NE Iberian Peninsula), for which a multidisciplinary research is conducted along the PT transition. The red-bed succession, located in a long E-W extended narrow rift system known as Pyrenean Basin, resulted from a continuous sedimentary deposition evolving from meandering (lower Upper Red Unit) to playa-lake/ephemeral lacustrine (upper Upper Red Unit) and again to meandering settings (Buntsandstein facies). Sedimentary continuity is suggested by preliminary cyclostratigraphic analysis that warrants further analysis. Our combined sedimentological, mineralogical and geochemical data infer a humid-semiarid-humid climatic trend across the studied succession. The uppermost Permian strata, deposited under an orbitally controlled monsoonal regime, yields a relatively diverse ichnoassemblage mainly composed of tetrapod footprints and arthropod trace fossils. Such fossils indicate appropriate life conditions and water presence in levels that also display desiccation structures. These levels alternate with barren intervals formed under dry conditions, being thus indicative of strong seasonality. All these features are correlated with those reported elsewhere in Gondwana and Laurasia, and suggest that the Permian-Triassic boundary might be recorded somewhere around the Buntsandstein base. Consequently, Coll de Terrers and the whole Catalan Pyrenees become key regions to investigate in detail the Permian extinction event and the Triassic ecosystems recovery.

Paleomagnetic results from Late Pennsylvanian marls and Early Permian red paleosols of the Dunkard group, Ohio and West Virginia, U.S.A.

NASA Astrophysics Data System (ADS)

Abrajevitch, A.; Oliva, B.; Peters, S.; Beehr, A.; van der Voo, R.

2006-12-01

Sediments of the Dunkard Gr. were deposited in the Appalachian foreland basin during the Pennsylvanian and Early Permian, an interval encompassing the long reverse polarity Kiaman chron. Lithofacies in the Dunkard Gr. in eastern Ohio and western West Virginia include lenticular and sheet-form cross-bedded micaceous sandstones, coal, mottled red and purple mudstones, gray laminated mudstones and argillaceous lime mudstones. They are indicative of deposition on a low-gradient, tropical wet-dry fluvial plain. Few lithofacies are laterally persistent over sufficiently long distances, so that correlation schemes are based largely on coal horizons, partly for historical economic reasons and partly because coal beds appear to be more laterally persistent than most other lithofacies. Magnetostratigraphy would therefore provide a powerful additional correlation tool in the Dunkard Gr, A short normal polarity interval has been reported in the Dunkard Gr. (Helsley, 1965), but to date such a change in magnetic field polarity has not been confirmed by later studies. To confirm the presence of the normal polarity subchron and to explore the possibility of using it as a correlation tool in the Dunkard Gr., we sampled 5 sections thought to straddle the Late Pennyslvanian-Early Permian boundary. Sampled lithofacies include red and mottled red-purple paleosols, grey mudstones containing siderite concretions, micaceous sandstones, and dark gray argillaceous limestones. Samples were demagnetized thermally and by AF. The remanent magnetic directions agree with those expected for the Early Permian. A change in polarity was detected in three of the studied sections. Magnetization is carried by several different magnetic minerals, mostly hematite in paleosols and iron sulfides in combination with magnetite in sandstones, marls and limestones. Although we have found good evidence for the normal polarity interval within Kiaman age rocks of the Dunkard Gr., additional magnetostratigraphic data are needed to validate the present lithology-based correlations and to determine the temporal extent of the normal polarity chron.

Cretaceous sedimentation in the outer Eastern Carpathians: Implications for the facies model reconstruction of the Moldavide Basin

NASA Astrophysics Data System (ADS)

Roban, R. D.; Krézsek, C.; Melinte-Dobrinescu, M. C.

2017-06-01

The mid Cretaceous is characterized by high eustatic sea-levels with widespread oxic conditions that made possible the occurrence of globally correlated Oceanic Red Beds. However, very often, these eustatic signals have been overprinted by local tectonics, which in turn resulted in Lower Cretaceous closed and anoxic basins, as in the Eastern Carpathians. There, the black shale to red bed transition occurs in the latest Albian up to the early Cenomanian. Although earlier studies discussed the large-scale basin configuration, no detailed petrography and sedimentology study has been performed in the Eastern Carpathians. This paper describes the Hauterivian to Turonian lithofacies and interprets the depositional settings based on their sedimentological features. The studied sections crop out only in tectonic half windows of the Eastern Carpathians, part of the Vrancea Nappe. The lithofacies comprises black shales interbedded with siderites and sandstones, calcarenites, marls, radiolarites and red shales. The siliciclastic muddy lithofacies in general reflects accumulation by suspension settling of pelagites and hemipelagites in anoxic (black shale) to dysoxic (dark gray and gray to green shales) and oxic (red shales) conditions. The radiolarites alternate with siliceous shales and are considered as evidence of climate changes. The sandstones represent mostly low and high-density turbidite currents in deep-marine lobes, as well as channel/levee systems. The source area is an eastern one, e.g., the Eastern Carpathians Foreland, given the abundance of low grade metamorphic clasts. The Hauterivian - lower Albian sediments are interpreted as deep-marine, linear and multiple sourced mud dominated systems deposited in a mainly anoxic to dysoxic basin. The anoxic conditions existed in the early to late Albian, but sedimentation changed to a higher energy mud/sand-dominated submarine channels and levees. This coarsening upwards tendency is interpreted as the effect of the Aptian to Albian compressional tectonics of the Carpathians. The deepening of the Moldavide Basin from the Cenomanian is most probably linked to a significant sea-level rise.

Depositional conditions for the Kuna Formation, Red Dog Zn-PB-Ag-Barite District, Alaska, inferred from isotopic and chemical proxies

USGS Publications Warehouse

Johnson, Craig A.; Dumoulin, Julie A.; Burruss, Robert A.; Slack, John F.

2015-01-01

Water column redox conditions, degree of restriction of the depositional basin, and other paleoenvironmental parameters have been determined for the Mississippian Kuna Formation of northwestern Alaska from stratigraphic profiles of Mo, Fe/Al, and S isotopes in pyrite, C isotopes in organic matter, and N isotopes in bulk rock. This unit is important because it hosts the Red Dog and Anarraaq Zn-Pb-Ag ± barite deposits, which together constitute one of the largest zinc resources in the world. The isotopic and chemical proxies record a deep basin environment that became isolated from the open ocean, became increasingly reducing, and ultimately became euxinic. The basin was ventilated briefly and then became isolated again just prior to its demise as a discrete depocenter with the transition to the overlying Siksikpuk Formation. Ventilation corresponded approximately to the initiation of bedded barite deposition in the district, whereas the demise of the basin corresponded approximately to the formation of the massive sulfide deposits. The changes in basin circulation during deposition of the upper Kuna Formation may have had multiple immediate causes, but the underlying driver was probably extensional tectonic activity that also facilitated fluid flow beneath the basin floor. Although the formation of sediment-hosted sulfide deposits is generally favored by highly reducing conditions, the Zn-Pb deposits of the Red Dog district are not found in the major euxinic facies of the Kuna basin, nor did they form during the main period of euxinia. Rather, the deposits occur where strata were permeable to migrating fluids and where excess H2S was available beyond what was produced in situ by decomposition of local sedimentary organic matter. The known deposits formed mainly by replacement of calcareous strata that gained H2S from nearby highly carbonaceous beds (Anarraaq deposit) or by fracturing and vein formation in strata that produced excess H2S by reductive dissolution of preexisting barite (Red Dog deposits).

Melanocortin 1 receptor (MC1R) gene sequence variation and melanism in the gray (Sciurus carolinensis), fox (Sciurus niger), and red (Sciurus vulgaris) squirrel.

PubMed

McRobie, Helen R; King, Linda M; Fanutti, Cristina; Coussons, Peter J; Moncrief, Nancy D; Thomas, Alison P M

2014-01-01

Sequence variations in the melanocortin 1 receptor (MC1R) gene are associated with melanism in many different species of mammals, birds, and reptiles. The gray squirrel (Sciurus carolinensis), found in the British Isles, was introduced from North America in the late 19th century. Melanism in the British gray squirrel is associated with a 24-bp deletion in the MC1R. To investigate the origin of this mutation, we sequenced the MC1R of 95 individuals including 44 melanic gray squirrels from both the British Isles and North America. Melanic gray squirrels of both populations had the same 24-bp deletion associated with melanism. Given the significant deletion associated with melanism in the gray squirrel, we sequenced the MC1R of both wild-type and melanic fox squirrels (Sciurus niger) (9 individuals) and red squirrels (Sciurus vulgaris) (39 individuals). Unlike the gray squirrel, no association between sequence variation in the MC1R and melanism was found in these 2 species. We conclude that the melanic gray squirrel found in the British Isles originated from one or more introductions of melanic gray squirrels from North America. We also conclude that variations in the MC1R are not associated with melanism in the fox and red squirrels.

OBSERVATIONAL CONSTRAINTS ON RED AND BLUE HELIUM BURNING SEQUENCES

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

McQuinn, Kristen B. W.; Skillman, Evan D.; Dalcanton, Julianne J.

We derive the optical luminosity, colors, and ratios of the blue and red helium burning (HeB) stellar populations from archival Hubble Space Telescope observations of nineteen starburst dwarf galaxies and compare them with theoretical isochrones from Padova stellar evolution models across metallicities from Z = 0.001 to 0.009. We find that the observational data and the theoretical isochrones for both blue and red HeB populations overlap in optical luminosities and colors and the observed and predicted blue to red HeB ratios agree for stars older than 50 Myr over the time bins studied. These findings confirm the usefulness of applyingmore » isochrones to interpret observations of HeB populations. However, there are significant differences, especially for the red HeB population. Specifically, we find (1) offsets in color between the observations and theoretical isochrones of order 0.15 mag (0.5 mag) for the blue (red) HeB populations brighter than M{sub V} {approx} -4 mag, which cannot be solely due to differential extinction; (2) blue HeB stars fainter than M{sub V} {approx} -3 mag are bluer than predicted; (3) the slope of the red HeB sequence is shallower than predicted by a factor of {approx}3; and (4) the models overpredict the ratio of the most luminous blue to red HeB stars corresponding to ages {approx}< 50 Myr. Additionally, we find that for the more metal-rich galaxies in our sample (Z {approx}> 0.5 Z{sub sun}), the red HeB stars overlap with the red giant branch stars in the color-magnitude diagrams, thus reducing their usefulness as indicators of star formation for ages {approx}> 100 Myr.« less

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan

PubMed Central

CHU, Thi Thanh Huong; MURANO, Takako; UNO, Yukiko; USUI, Tatsufumi; YAMAGUCHI, Tsuyoshi

2015-01-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae. PMID:26074251

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan.

PubMed

Chu, Thi Thanh Huong; Murano, Takako; Uno, Yukiko; Usui, Tatsufumi; Yamaguchi, Tsuyoshi

2015-11-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae.

Structure of the Anayet Permian basin (Axial Zone, Central Pyrenees)

NASA Astrophysics Data System (ADS)

Rodriguez, L.; Cuevas, J.; Tubía, J. M.

2012-04-01

The Anayet Permian basin was generated by strike-slip tectonics that opened subsident basins with pull-apart geometries in the western Spanish Axial Zone (between the Aragon and Tena valleys). A continental succession of Permian age, that represents the first post-variscan deposits in the area, fills the basin and covers discordantly Devonian to Carboniferous limestones, sandstones and slates. Permian deposits have been classically divided in four main detrital groups, with three basic volcanic episodes interbedded (Gisbert, 1984, Bixel, 1987): the Grey Unit (50-120 m, Estefanian to Kungurian) with slates, conglomerates, tobaceous slates, coal and pyroclastic deposits, the Transition Unit (50 m maximum) showing grey and red sandstones and lutites with oolitic limestones intercalated, the Lower Red Unit (250 m) composed of cross-bedded red sandstones and andesitic volcanic rocks at the top, and finally the Upper Red Unit (400 m minimum, top eroded) formed by three fining up megasequences of carbonates, red sandstones and lutites with lacustrine carbonates intercalated and alkali basalts at the top. Increasingly older rocks are found towards the western part of the basin, where its depocenter is located. South-vergent angular folds deform the Permian sedimentary succession. Fold axes are N115 °E-trending, almost horizontal and are characterized by a remarkably constant orientation. Folds exhibit a long limb dipping slightly to the north and a short vertical limb, occasionally reversed. In the Anayet basin four main folds, with a wavelength of 400 m, can be distinguished, two anticlines and two synclines, with minor folds associated. Related to the angular folds an axial plane foliation, E-trending and dipping 40 to 60° to the north, is developed in the lutites. The more competent rocks, conglomerates and breccias, only locally show a spaced fracture cleavage. No main thrusts have been detected in Permian rocks. However, minor scale decollements, usually low angle to bedding-parallel, have been identified along low-dipping limbs of the folds. They can be recognized due to the high colour contrast between the red-coloured Permian beds and the concentration of calcite veins in the decollements. The development of the structures above described has to be linked to the Alpine compressional tectonics. This interpretation is supported by the good correlation in geometry and orientation between the structures observed in the Permian basin and in southernmost areas of the South Pyrenean Zone, where the deformation is imprinted in Cretaceous to Tertiary rocks. In this regard, the southern border of the Anayet basin, at least in the western part, can be interpreted as a normal fault reactivated as a high-angle reverse fault during the positive inversion tectonics induced by the Alpine Orogeny. Bixel, F., 1987. Le volcanisme stephano-permien des Pyrenees petrographie, mineralogie, geochimie. Cuadernos de Geología Ibérica 11, 41-55. Gisbert, J., 1984. Las molasas tardihercínicas del Pirineo, in: Geología de España. Libro Jubilar de J. M. Ríos, Comba, J.A. (Ed.), IGME, Madrid, 168-186.

Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform.

PubMed

Novák, Karel; Pikousová, Jitka; Czerneková, Vladimíra; Mátlová, Věra

2017-07-03

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia.

PubMed

Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

2016-08-11

Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations.

PubMed

Su, B; Fu, Y; Wang, Y; Jin, L; Chakraborty, R

2001-06-01

The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 53 red pandas from two populations in southwestern China. Seventeen polymorphic sites were found, together with a total of 25 haplotypes, indicating a high level of genetic diversity in the red panda. However, no obvious genetic divergence was detected between the Sichuan and Yunnan populations. The consensus phylogenetic tree of the 25 haplotypes was starlike. The pairwise mismatch distribution fitted into a pattern of populations undergoing expansion. Furthermore, Fu's F(S) test of neutrality was significant for the total population (F(S) = -7.573), which also suggests a recent population expansion. Interestingly, the effective population size in the Sichuan population was both larger and more stable than that in the Yunnan population, implying a southward expansion from Sichuan to Yunnan.

Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

USGS Publications Warehouse

Miller, D.N.; Smith, R.L.

2009-01-01

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O2 (> 300????M) and NH4+ (51-800????M). The second site was 2.5??km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O2, NH4+, and NO3- (0-300, 0-500, and 100-200????M with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350??g- 1 and 33 to 35,000??g- 1, respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.

Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

NASA Astrophysics Data System (ADS)

Miller, Daniel N.; Smith, Richard L.

2009-01-01

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O 2 (> 300 µM) and NH 4+ (51-800 µM). The second site was 2.5 km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O 2, NH 4+, and NO 3- (0-300, 0-500, and 100-200 µM with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350 g - 1 and 33 to 35,000 g - 1 , respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH 4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.

Edge Effects Are Important in Supporting Beetle Biodiversity in a Gravel-Bed River Floodplain

PubMed Central

Langhans, Simone D.; Tockner, Klement

2014-01-01

Understanding complex, dynamic, and diverse ecosystems is essential for developing sound management and conservation strategies. Gravel-bed river floodplains are composed of an interlinked mosaic of aquatic and terrestrial habitats hosting a diverse, specialized, and endangered fauna. Therefore, they serve as excellent models to investigate the biodiversity of multiple ecotones and related edge effects. In this study, we investigated the abundance, composition, richness, and conservation status of beetle assemblages at varying sediment depth (0, 0.1, 0.6 and 1.1 m), distance from the channel (1, 5, 20, and 60–100 m, and 5 m within the riparian forest), and time of the year (February–November) across a 200 m-wide gravel bar at the near-natural Tagliamento River (Italy), to detect edge effects in four floodplain ecotones: aquatic-terrestrial, forest-active floodplain, sediment-air, and sediment-groundwater. We used conventional pitfall traps and novel tube traps to sample beetles comparably on the sediment surface and within the unsaturated sediments. We found a total of 308 beetle species (including 87 of conservation concern) that showed multiple, significant positive edge effects across the floodplain ecotones, mainly driven by spatial heterogeneity: Total and red list beetle abundance and richness peaked on the sediment surface, at channel margins, and at the edge of the riparian forest. All ecotones possessed edge/habitat specialists. Most red list species occurred on the sediment surface, including five species previously considered extinct – yet two of these species occurred in higher densities in the unsaturated sediments. Conservation and management efforts along gravel-bed rivers must therefore promote a dynamic flow and sediment regime to create and maintain habitat heterogeneity and ecotone diversity, which support a unique and high biodiversity. PMID:25545280

Edge effects are important in supporting beetle biodiversity in a gravel-bed river floodplain.

PubMed

Langhans, Simone D; Tockner, Klement

2014-01-01

Understanding complex, dynamic, and diverse ecosystems is essential for developing sound management and conservation strategies. Gravel-bed river floodplains are composed of an interlinked mosaic of aquatic and terrestrial habitats hosting a diverse, specialized, and endangered fauna. Therefore, they serve as excellent models to investigate the biodiversity of multiple ecotones and related edge effects. In this study, we investigated the abundance, composition, richness, and conservation status of beetle assemblages at varying sediment depth (0, 0.1, 0.6 and 1.1 m), distance from the channel (1, 5, 20, and 60-100 m, and 5 m within the riparian forest), and time of the year (February-November) across a 200 m-wide gravel bar at the near-natural Tagliamento River (Italy), to detect edge effects in four floodplain ecotones: aquatic-terrestrial, forest-active floodplain, sediment-air, and sediment-groundwater. We used conventional pitfall traps and novel tube traps to sample beetles comparably on the sediment surface and within the unsaturated sediments. We found a total of 308 beetle species (including 87 of conservation concern) that showed multiple, significant positive edge effects across the floodplain ecotones, mainly driven by spatial heterogeneity: Total and red list beetle abundance and richness peaked on the sediment surface, at channel margins, and at the edge of the riparian forest. All ecotones possessed edge/habitat specialists. Most red list species occurred on the sediment surface, including five species previously considered extinct--yet two of these species occurred in higher densities in the unsaturated sediments. Conservation and management efforts along gravel-bed rivers must therefore promote a dynamic flow and sediment regime to create and maintain habitat heterogeneity and ecotone diversity, which support a unique and high biodiversity.

(40)Ar/(39)Ar dating of Bed I, Olduvai Gorge, Tanzania, and the chronology of early Pleistocene climate change.

PubMed

Deino, Alan L

2012-08-01

(40)Ar/(39)Ar dating of tuffs and lavas of the late Pleistocene volcanic and sedimentary sequence of Olduvai Gorge, north-central Tanzania, provides the basis for a revision of Bed I chronostratigraphy. Bed I extends from immediately above the Naabi Ignimbrite at 2.038 ± 0.005 Ma to Tuff IF at 1.803 ± 0.002 Ma. Tuff IB, a prominent widespread marker tuff in the basin and a key to understanding hominin evolutionary chronologies and paleoclimate histories, has an age of 1.848 ± 0.003 Ma. The largest lake expansion event in the closed Olduvai lake basin during Bed I times encompassed the episode of eruption and emplacement of this tuff. This lake event is nearly coincident with the maximum precessional insolation peak of the entire Bed I/Lower Bed II interval, calculated from an astronomical model of the boreal summer orbital insolation time-series. The succeeding precessional peak also apparently coincides with the next youngest expansion of paleo-Lake Olduvai. The extreme wet/dry climate shifts seen in the upper part of Bed I occur during an Earth-orbital eccentricity maximum, similar to episodic lake expansions documented elsewhere in the East African Rift during the Neogene. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Effect of Total Tumor Volume on the Biologically Effective Dose to Tumor and Kidneys for 177Lu-Labeled PSMA Peptides.

PubMed

Begum, Nusrat J; Thieme, Anne; Eberhardt, Nina; Tauber, Robert; D'Alessandria, Calogero; Beer, Ambros J; Glatting, Gerhard; Eiber, Matthias; Kletting, Peter

2018-06-01

The aim of this work was to simulate the effect of prostate-specific membrane antigen (PSMA)-positive total tumor volume (TTV) on the biologically effective doses (BEDs) to tumors and organs at risk in patients with metastatic castration-resistant prostate cancer who are undergoing 177 Lu-PSMA radioligand therapy. Methods: A physiologically based pharmacokinetic model was fitted to the data of 13 patients treated with 177 Lu-PSMA I&T (a PSMA inhibitor for imaging and therapy). The tumor, kidney, and salivary gland BEDs were simulated for TTVs of 0.1-10 L. The activity and peptide amounts leading to an optimal tumor-to-kidneys BED ratio were also investigated. Results: When the TTV was increased from 0.3 to 3 L, the simulated BEDs to tumors, kidneys, parotid glands, and submandibular glands decreased from 22 ± 15 to 11.0 ± 6.0 Gy 1.49 , 6.5 ± 2.3 to 3.7 ± 1.4 Gy 2.5 , 11.0 ± 2.7 to 6.4 ± 1.9 Gy 4.5 , and 10.9 ± 2.7 to 6.3 ± 1.9 Gy 4.5 , respectively (where the subscripts denote that an α/β of 1.49, 2.5, or 4.5 Gy was used to calculate the BED). The BED to the red marrow increased from 0.17 ± 0.05 to 0.32 ± 0.11 Gy 15 For patients with a TTV of more than 0.3 L, the optimal amount of peptide was 273 ± 136 nmol and the optimal activity was 10.4 ± 4.4 GBq. Conclusion: This simulation study suggests that in patients with large PSMA-positive tumor volumes, higher activities and peptide amounts can be safely administered to maximize tumor BEDs without exceeding the tolerable BED to the organs at risk. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Using Wave-Current Observation to Predict Bottom Sediment Processes on Muddy Beaches

DTIC Science & Technology

2011-09-30

as 80% of wave energy over a distance of just a few wave lengths (Gade, 1957; Jiang and Mehta, 1995; deWitt, 1995; Hill and Foda , 1999; Chan and Liu...bed transformation (see Section Figure 1) emerges from the analysis Sheremet et al., 2005; Jaramillo et al., 2008; Robillard, 2009; Sahin et al...Kaihatu et al., 2007; Sheremet et al., 2010). The ongoing work has three directions of research: Data analysis : reconstruct the sequence of bed

A multi-wavelength study of the evolution of early-type galaxies in groups: the ultraviolet view

NASA Astrophysics Data System (ADS)

Rampazzo, R.; Mazzei, P.; Marino, A.; Bianchi, L.; Plana, H.; Trinchieri, G.; Uslenghi, M.; Wolter, A.

2018-04-01

The ultraviolet-optical colour magnitude diagram of rich galaxy groups is characterised by a well developed Red Sequence, a Blue Cloud and the so-called Green Valley. Loose, less evolved groups of galaxies which are probably not virialised yet may lack a well defined Red Sequence. This is actually explained in the framework of galaxy evolution. We are focussing on understanding galaxy migration towards the Red Sequence, checking for signatures of such a transition in their photometric and morphological properties. We report on the ultraviolet properties of a sample of early-type (ellipticals+S0s) galaxies inhabiting the Red Sequence. The analysis of their structures, as derived by fitting a Sérsic law to their ultraviolet luminosity profiles, suggests the presence of an underlying disk. This is the hallmark of dissipation processes that still must have a role to play in the evolution of this class of galaxies. Smooth particle hydrodynamic simulations with chemo-photometric implementations able to match the global properties of our targets are used to derive their evolutionary paths through ultraviolet-optical colour magnitude diagrams, providing some fundamental information such as the crossing time through the Green Valley, which depends on their luminosity. The transition from the Blue Cloud to the Red Sequence takes several Gyrs, being about 3-5 Gyr for the brightest galaxies and longer for fainter ones, if occurring. The photometric study of nearby galaxy structures in the ultraviolet is seriously hampered by either the limited field of view of the cameras (e.g., in Hubble Space Telescope) or by the low spatial resolution of the images (e.g., in the Galaxy Evolution Explorer). Current missions equipped with telescopes and cameras sensitive to ultraviolet wavelengths, such as Swift- UVOT and Astrosat-UVIT, provide a relatively large field of view and a better resolution than the Galaxy Evolution Explorer. More powerful ultraviolet instruments (size, resolution and field of view) are obviously bound to yield fundamental advances in the accuracy and depth of the surface photometry and in the characterisation of the galaxy environment.

Ecology of red swamps in the glaciated northeast: a community profile

USGS Publications Warehouse

Golet, Francis C.; Calhoun, Aram J.K.; DeRagon, William R.

1993-01-01

This report is part of a series of profiles on the ecology of wetland and deepwater habitats. This particular profile addresses red maple swamps in the glaciated northeastern United States. Red maple (Acer rubrum) swamp is a dominant wetland type in most of the region; it reaches its greatest abundance in southern New England and northern New Jersey, where it comprises 60-800/o of all inland wetlands. Red maple swamps occur in a wide variety of hydrogeologic settings, from small, isolated basins in till or glaciofluvial deposits to extensive wetland complexes on glacial lake beds, and from hillside seeps to stream floodplains and lake edges. Individual swamps may be seasonally flooded, temporarily flooded, or seasonally saturated, and soils may be mineral or organic. As many as five distinct vegetation layers may occur in these swamps, including trees, saplings, shrubs, herbs, and ground cover plants such as bryophytes and clubmosses. On a regional scale, red maple swamps support at least 50 species of trees, more than 90 species of shrubs and vines, and more than 300 species of nonwoody plants. These swamps also provide habitat for a rich faunal community, including several wetland-dependent species. In areas that are becoming urbanized, these wetlands often constitute critical habitat for facultative species as well. Red maple swamps also are important sites for flood storage, water quality improvement, recreation, scenic beauty, and open space.

Extraction of dye from aqueous solution in rotating packed bed.

PubMed

Modak, Jayant B; Bhowal, Avijit; Datta, Siddhartha

2016-03-05

The influence of centrifugal acceleration on mass transfer rates in liquid-liquid extraction was investigated experimentally in rotating packed bed (RPB) contactor. The extraction of methyl red using xylene was studied in the equipment. The effect of rotational speed (300-900rpm), flow rate of the aqueous (4.17-20.8×10(-6)m(3)/s), and organic phase (0.83-2.5×10(-6)m(3)/s) on the mass transfer performance was examined. The maximum stage efficiency attained was ∼0.98 at aqueous to organic flow rate ratio of 10. The results suggest that contactor volume required to carry out a given separation can be reduced by an order of magnitude with RPB in comparison to conventional extractors. Copyright © 2015 Elsevier B.V. All rights reserved.

Experiment to evaluate feasibility of utilizing Skylab-EREP remote sensing data for tectonic analysis of the Bighorn Mountains region, Wyoming-Montana

NASA Technical Reports Server (NTRS)

Hoppin, R. A. (Principal Investigator)

1974-01-01

The author has identified the following significant results. S-190A color transparencies from SL-2 of the Big Horn basin region provide the best format to date for geologic study of that region; red beds are quite mappable and resistant key beds sharply outlined. An S-190B color frame from SL-3 of the Pryor-Bighorn mountains provides no indication that the Nye-Bowler lineament extends east of East Pryor Mountain. This has important implications regarding the role of this and other lineaments (which also appear to be of restricted length) in the tectonics of the region. Extensions of these lineaments for great distances does not seem warranted on the basis of surface evidence.

Diversity changes of microbial communities into hospital surface environments.

PubMed

Yano, Rika; Shimoda, Tomoko; Watanabe, Reina; Kuroki, Yasutoshi; Okubo, Torahiko; Nakamura, Shinji; Matsuo, Junji; Yoshimura, Sadako; Yamaguchi, Hiroyuki

2017-07-01

Previous works have demonstrated considerable variability in hospital cleanliness in Japan, suggesting that contamination is driven by factors that are currently poorly controlled. We undertook 16S rRNA sequence analysis to study population structures of hospital environmental microbiomes to see which factor(s) impacted contamination. One hundred forty-four samples were collected from surfaces of three hospitals with distinct sizes ("A": >500 beds, "B": 100-500 beds, "C": <100 beds). Sample locations of two ward types (Surgical and Internal) included patient room bed table (multiple) (4BT), patient overbed table (multiple) (4OT), patient room sink (multiple) (4S), patient room bed table (single) (SBT), patient overbed table (single) (SOT), patient room sink (single) (SS), nurse desk (ND), and nurse wagon (NW). Total DNA was extracted from each sample, and the 50 samples that yielded sufficient DNA were used for further 16S rRNA sequencing of hospital microbiome populations with cluster analysis. The number of assigned bacterial OTU populations was significantly decreased in hospital "C" compared to the other hospitals. Cluster analysis of sampling locations revealed that the population structure in almost all locations of hospital "C" and some locations in the other hospitals was very similar and unusually skewed with a family, Enterobacteriaceae. Interestingly, locations included patient area (4OT, 4BT, SBT) and nurse area (ND), with a device (NW) bridging the two and a place (4S and SS) shared between patients or visitors. We demonstrated diversity changes of hospital environmental microbiomes with a skewed population, presumably by medical staff pushing NWs or sinks shared by patients or visitors. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

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

Depositional environment and sedimentary of the basinal sediments in the Eibiswalder Bucht (Radl Formation and Lower Eibiswald Beds), Miocene Western Styrian Basin, Austria

NASA Astrophysics Data System (ADS)

Stingl, K.

1994-12-01

The Eibiswald Bucht is a small subbasin of the Western Styrian Basin exposing sediments of Lower Miocene age. In the past the entire sequence exposed in the Eibiswalder Bucht has been interpreted as being of fluvial/lacustrine origin; here, results are presented of detailed sedimentological investigations that lead to a revision of this concept. The lowermost siliciclastic sedimentary unit of the Eibiswalder Bucht sequence is the Radl Formation. It is overlain by the Eibiswald Beds, which are subdivided into the Lower, Middle and Upper Eibiswald Beds. The Radl Formation and the Lower Eibiswald Beds are interpreted as a fan delta complex deposited along NNW-SSE striking faults. Based on the sedimentary facies this fan delta can be subdivided into a subaerial alluvial fan facies group, a proximal delta facies group and a distal delta/prodelta facies group. The Radl Formation comprises the alluvial fan and proximal delta facies groups, the Lower Eibiswald Beds the distal delta/prodelta facies group. The alluvial fan and the proximal delta consist of diverse deposits of gravelly flows. The distal delta/prodelta consists of wave-reworked, bioturbated, low density turbidites intercalated with minor gravelly mass flows. The prodelta can be regarded as as the basin facies of the small and shallow Eibiswalder Bucht, where marine conditions prevailed. The basin was probably in part connected with the Eastern Styrian Basin, the contemporary depositional environment of the Styrian Schlier (mainly turbiditic marine offshore sediments in the Eastern Styrian Basin). Analysis of the clast composition, in conjunction with the paleotransport direction of the coarse delta mass flows of the Radl Formation, shows that the source rocks were exclusively crystalline rocks ranging from greenschists to eclogites.

The importance of satellite quenching for the build-up of the red sequence of present-day galaxies

NASA Astrophysics Data System (ADS)

van den Bosch, Frank C.; Aquino, Daniel; Yang, Xiaohu; Mo, H. J.; Pasquali, Anna; McIntosh, Daniel H.; Weinmann, Simone M.; Kang, Xi

2008-06-01

According to the current paradigm, galaxies initially form as disc galaxies at the centres of their own dark matter haloes. During their subsequent evolution, they may undergo a transformation to a red, early-type galaxy, thus giving rise to the build-up of the red sequence. Two important, outstanding questions are (i) which transformation mechanisms are most important and (ii) in what environment do they occur. In this paper, we study the impact of transformation mechanisms that operate only on satellite galaxies, such as strangulation, ram-pressure stripping and galaxy harassment. Using a large galaxy group catalogue constructed from the Sloan Digital Sky Survey, we compare the colours and concentrations of satellites galaxies to those of central galaxies of the same stellar mass, adopting the hypothesis that the latter are the progenitors of the former. On average, satellite galaxies are redder and more concentrated than central galaxies of the same stellar mass, indicating that satellite-specific transformation processes do indeed operate. Central-satellite pairs that are matched in both stellar mass and colour, however, show no average concentration difference, indicating that the transformation mechanisms operating on satellites affect colour more than morphology. We also find that the colour and concentration differences of matched central-satellite pairs are completely independent of the mass of the host halo (not to be confused with the subhalo) of the satellite galaxy, indicating that satellite-specific transformation mechanisms are equally efficient in host haloes of all masses. This strongly rules against mechanisms that are thought to operate only in very massive haloes, such as ram-pressure stripping or harassment. Instead, we argue that strangulation is the main transformation mechanism for satellite galaxies. Finally, we determine the relative importance of satellite quenching for the build-up of the red sequence. We find that roughly 70 per cent of red-sequence satellite galaxies with M* ~ 109h-2Msolar had their star formation quenched as satellites. This drops rapidly with increasing stellar mass, reaching virtually zero at M* ~ 1011h-2Msolar. Therefore, a very significant fraction of red satellite galaxies were already quenched before they became a satellite.

Record of complex scoria cone eruptive activity at Red Mountain, Arizona, USA, and implications for monogenetic mafic volcanoes

NASA Astrophysics Data System (ADS)

Riggs, N. R.; Duffield, W. A.

2008-12-01

Scoria cone eruptions are generally modeled as a simple succession from explosive eruption to form the cone to passive effusion of lava, generally from the base of the cone. Sector collapse of scoria cones, wherein parts of the cone are rafted on a lava flow, is increasingly recognized as common, but the reasons that a cone may not be rebuilt are poorly understood. Red Mountain volcano is a Pleistocene scoria cone in the San Francisco Volcanic Field of northern Arizona, USA. The cone lies along the trace of a major steeply dipping normal fault that originated during Proterozoic tectonism and was reactivated in Tertiary time. The earliest phase of eruption at Red Mountain was typical "Strombolian", forming a cone that was followed by or possibly synchronous with lava effusion, toward the west from the base of the cone. Rafting then ensued as the west side of the cone collapsed; approximately 15% of the cone is preserved in mounds as much as 30 m high. Rafting was extensive enough to remove most of the cone over the vent area, which effectively reduced the pressure cap on the magma conduit. Resultant low fountaining fed clastogenic lava flows and minor scoria fallback. Clastogenic flows traveled as far as 4 km and now form a cliff 30-40 m high at the edge of the lava platform. Although several possibilities explain the change in vent dynamics and eruptive style, we favor the interpretation that an increase in magma-rise rate caused collapse of the cone. The abrupt removal of 300 m of material over the vent removed a conduit "cork" and low fountaining began. Magma that had erupted effusively suddenly became explosive. This aspect of scoria cone rafting at Red Mountain is broadly similar to sector collapse followed by explosive eruption in larger systems. A steep-walled, 150-m-high amphitheatre on the northeast side of Red Mountain exposes weakly to strongly altered scoria cemented by calcite, iron, and zeolites. We suggest that vapor-phase alteration was responsible for sealing fine-grained ash beds in the cone, and a pressurized system developed. Residual heat from a dike that was emplaced as part of the magmatic activity provided heat that drove groundwater along the regional fault up into the cone. Eventually the overpressurized system exploded in a phreatic eruption that created the amphitheatre, which has subsequently been enlarged by water and wind erosion. The combined sequence of events at Red Mountain illustrates some of the complexities in monogenetic scoria cone eruptions that have received little attention to date.

Measurement of the temporal progression of scour in a pool-riffle sequence in a gravel bed stream using an electronic scour monitor

NASA Astrophysics Data System (ADS)

Devries, Paul; Burges, Stephen J.; Daigneau, Julie; Stearns, Daniel

2001-11-01

A relatively inexpensive prototype monitor was designed and developed to record temporal variation in scour depth and was field-tested in a gravel bed stream. The device consists of plastic practice golf balls that are fitted internally with ring magnets and strung on a two-conductor cable enclosing a small reed switch. The balls are installed and oriented near-vertically in the streambed. As each ball is disturbed and released, it slides along the cable past the reed switch, and the time of circuit closure caused by passage of the magnet is recorded by a data logger. The device can be applied in arrays that span large areas of the streambed, including in wide channels that are inaccessible during a flood. Data obtained from 19 devices installed in an aggrading site described scouring processes in a pool-riffle interface during a bed load transport event. Substantial bed excavation occurred in the region of the pool edge during the rising stage, indicating existence of a local, temporally varying imbalance in bed load transport rate. Bed disturbance in the rest of the site prior to aggradation was limited to the surface and immediate subpavement layer.

Variations in Grain-Scale Sediment Structure in a Gravel-Bed Channel as a Function of Fine Sediment Content and Morphological Location

NASA Astrophysics Data System (ADS)

Voepel, H.; Ahmed, S. I.; Hodge, R. A.; Leyland, J.; Sear, D. A.

2016-12-01

One of the major causes of uncertainty in estimates of bedload transport rates in gravel bed rivers is a lack of understanding of grain-scale sediment structure, and the impact that this structure has on bed stability. Furthermore, grain-scale structure varies throughout a channel and over time in ways that have not been fully quantified. Our research aims to quantify variations in sediment structure caused by two key variables; morphological location within a riffle-pool sequence (reflecting variation in hydraulic conditions), and the fine sediment content of the gravel bed (sand and clay). We report results from a series of flume experiments in which we water-worked a gravel bed with a riffle-pool morphology. The fine sediment content of the bed was incrementally increased over a series of runs from gravel only, to coarse sand, fine sand and two concentrations of clay. After each experimental run intact samples of the bed at different locations were extracted and the internal structure of the bed was measured using non-destructive, micro-focus X-ray computed tomography (CT) imaging. The CT images were processed to measure the properties of individual grains, including volume, center of mass, dimension, and contact points. From these data we were able to quantify the sediment structure through metrics including measurement of grain pivot angles, grain exposure and protrusion, and vertical variation in bed porosity and fine sediment content. Metrics derived from the CT data were verified using data from grain counts and tilt-table measurements on co-located samples. Comparison of the metrics across different morphological locations and fine sediment content demonstrates how these factors affect the bed structure. These results have implications for the development of sediment entrainment models for gravel bed rivers.

Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family

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

Sharrock, R.A.; Quail, P.H.

1989-01-01

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. The authors have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that theymore » have low sequence identity with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far red light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.« less

RNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.

PubMed

Hyun, Tae Kyung; Lee, Sarah; Kumar, Dhinesh; Rim, Yeonggil; Kumar, Ritesh; Lee, Sang Yeol; Lee, Choong Hwan; Kim, Jae-Yean

2014-10-01

Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data containing abundant information on genes involved in the metabolic pathways in R. idaeus cv. Nova fruits. Rubus idaeus (Red raspberry) is one of the important economical crops that possess numerous nutrients, micronutrients and phytochemicals with essential health benefits to human. The molecular mechanism underlying the ripening process and phytochemical biosynthesis in red raspberry is attributed to the changes in gene expression, but very limited transcriptomic and genomic information in public databases is available. To address this issue, we generated more than 51 million sequencing reads from R. idaeus cv. Nova fruit using Illumina RNA-Seq technology. After de novo assembly, we obtained 42,604 unigenes with an average length of 812 bp. At the protein level, Nova fruit transcriptome showed 77 and 68 % sequence similarities with Rubus coreanus and Fragaria versa, respectively, indicating the evolutionary relationship between them. In addition, 69 % of assembled unigenes were annotated using public databases including NCBI non-redundant, Cluster of Orthologous Groups and Gene ontology database, suggesting that our transcriptome dataset provides a valuable resource for investigating metabolic processes in red raspberry. To analyze the relationship between several novel transcripts and the amounts of metabolites such as γ-aminobutyric acid and anthocyanins, real-time PCR and target metabolite analysis were performed on two different ripening stages of Nova. This is the first attempt using Illumina sequencing platform for RNA sequencing and de novo assembly of Nova fruit without reference genome. Our data provide the most comprehensive transcriptome resource available for Rubus fruits, and will be useful for understanding the ripening process and for breeding R. idaeus cultivars with improved fruit quality.

Retrodeformable cross sections and Oak Ridge fault, Ventura basin, California

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

Yeats, R.S.; Huftile, G.F.

1988-03-01

A retrodeformable (balanced) cross section is constructed such that stratified rocks are restored to their undeformed state without loss or gain of bed length or bed thickness. Ductile strata may be area-balanced if original thickness is known. Near Ventura, folds in Pliocene-Pleistocene turbidites and Miocene-early Pliocene shales (Rincon, Monterey, Sisquoc) overlie an unfolded competent Paleogene sequence. The basal decollement of the foldbelt is in the ductile Rincon Formation (lower Miocene). The overlying Sulphur Mountain, Ventura Avenue, San Miguelito, and Rincon anticlines are fault-propagation folds developing from south-dipping, largely late Quaternary frontal ramp thrusts (Sisar-Big Canyon-Lion fault set, Barnard fault set,more » padre Juan fault, and C-3 fault, respectively) that rise from the decollement. Cross-section balancing shows that the overlying fold-thrust belt has shortened 2.5-6 km more than subjacent Paleogene competent strata. This excess bed length is taken up in the Paleogene sequence on the Oak Ridge fault as a ramp from the brittle-plastic transition zone through the upper crust. This implies that the basal decollement is the frontal active thrust of the Oak Ridge fault. The decollement dies out southeast of a line between Timber Canyon oil field and the west end of Oak Ridge, possibly because of decreased ductility in the Miocene decollement sequence due to appearance of sandstone interbeds. Farther southeast, late Quaternary displacement concentrated on the Oak Ridge fault itself at rates greater than 10 mm/year.« less

Amdoparvovirus Infection in Red Pandas ( Ailurus fulgens).

PubMed

Alex, Charles E; Kubiski, Steven V; Li, Linlin; Sadeghi, Mohammadreza; Wack, Raymund F; McCarthy, Megan A; Pesavento, Joseph B; Delwart, Eric; Pesavento, Patricia A

2018-01-01

Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda ( Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.

Molecular Survey of Hepatozoon canis in Red Foxes (Vulpes vulpes) from Romania.

PubMed

Imre, Mirela; Dudu, Andreea; Ilie, Marius S; Morariu, Sorin; Imre, Kálmán; Dărăbuş, Gheorghe

2015-08-01

Blood samples of 119 red foxes, originating from 44 hunting grounds of 3 western counties (Arad, Hunedoara, and Timiş) of Romania, have been examined for the presence of Hepatozoon canis infection using the conventional polymerase chain reaction (PCR) of the fragment of 18S rRNA gene. Overall, 15 (12.6%) samples were found to be PCR-positive. Of the sampled hunting grounds, 29.5% (13/44) were found positive. Positive samples were recorded in all screened counties with the prevalence of 14.8% (9/61) in Arad, 9.8% (5/51) in Timiş, and 14.3% (1/7) in Hunedoara, respectively. No correlation was found (P > 0.05) between H. canis positivity and gender or territorial distribution of the infection. To confirm PCR results, 9 randomly selected amplicons were sequenced. The obtained sequences were identical to each other, confirmed the results of the conventional PCR, and showed 98-100% homology to other H. canis sequences. The results of the current survey support the role of red foxes as sylvatic reservoirs of H. canis in Romania.

Radio Emission from Red-Giant Hot Jupiters

NASA Technical Reports Server (NTRS)

Fujii, Yuka; Spiegel, David S.; Mroczkowski, Tony; Nordhaus, Jason; Zimmerman, Neil T.; Parsons, Aaron R.; Mirbabayi, Mehrdad; Madhusudhan, Nikku

2016-01-01

When planet-hosting stars evolve off the main sequence and go through the red-giant branch, the stars become orders of magnitudes more luminous and, at the same time, lose mass at much higher rates than their main sequence counterparts. Accordingly, if planetary companions exist around these stars at orbital distances of a few au, they will be heated up to the level of canonical hot Jupiters and also be subjected to a dense stellar wind. Given that magnetized planets interacting with stellar winds emit radio waves, such "Red-Giant Hot Jupiters" (RGHJs) may also be candidate radio emitters. We estimate the spectral auroral radio intensity of RGHJs based on the empirical relation with the stellar wind as well as a proposed scaling for planetary magnetic fields. RGHJs might be intrinsically as bright as or brighter than canonical hot Jupiters and about 100 times brighter than equivalent objects around main-sequence stars. We examine the capabilities of low-frequency radio observatories to detect this emission and find that the signal from an RGHJ may be detectable at distances up to a few hundred parsecs with the Square Kilometer Array.

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.

PubMed

Al-Rshaidat, Mamoon M D; Snider, Allison; Rosebraugh, Sydney; Devine, Amanda M; Devine, Thomas D; Plaisance, Laetitia; Knowlton, Nancy; Leray, Matthieu

2016-09-01

High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp.

PubMed

Deng, Peng; Tan, Xiaoqing; Wu, Ying; Bai, Qunhua; Jia, Yan; Xiao, Hong

2015-03-01

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica , which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function.

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp

PubMed Central

DENG, PENG; TAN, XIAOQING; WU, YING; BAI, QUNHUA; JIA, YAN; XIAO, HONG

2015-01-01

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica, which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function. PMID:25667630

Origin of red pelagic carbonates as an interplay of global climate and local basin factors: Insight from the Lower Devonian of the Prague Basin, Czech Republic

NASA Astrophysics Data System (ADS)

Bábek, Ondřej; Faměra, Martin; Hladil, Jindřich; Kapusta, Jaroslav; Weinerová, Hedvika; Šimíček, Daniel; Slavík, Ladislav; Ďurišová, Jana

2018-02-01

Red pelagic sediments are relatively common in the Phanerozoic. They are often interpreted as products of sea-bottom oxidation during greenhouse climate showing a conspicuous alternation with black shales and thus carrying important palaeoceanographic information. The Lower Devonian (Pragian) carbonate strata of the Prague Basin, Czech Republic (Praha Formation) contain a marked band of red pelagic carbonate, up to 15 m thick, which can be correlated for several tens of km. We investigated seven sections (17 to 255 m thick) of the Prague Basin using the methods of facies analysis, outcrop gamma-ray logging, diffuse reflectance spectroscopy, optical microscopy, element geochemistry, magneto-mineralogy and electron microprobe analysis. The aim was to find the mineral carriers of the red colour, investigate the stratigraphic context of the red carbonates and evaluate the local and global prerequisites for their formation. The red pigmentation represents enrichment by hematite with respect to goethite. Approximately 31% of the total reflectance falling in the red colour band represents a threshold for red coloration. The red pigmentation is carried by submicronic hematite dispersed in argillaceous pelagic calcilutite and/or inside skeletal allochems. Gamma-ray log correlation indicates that the red carbonate band developed in stratigraphic levels with low sedimentation rates, typically from 1 to 7.1 mm/kyr, which are comparable to the Mesozoic Rosso Ammonitico facies. The red beds and the whole Praha Formation (Pragian to early Emsian) are characterized by low TOC values (< 0.05%) and low U/Th, Mo/Al, V/Al, Zn/Al, Cu/Al and P/Al ratios indicating oligotrophic, highly oxic sea-bottom conditions. This period was characterized by global cooling, a drop in silicate weathering rates and in atmospheric pCO2 levels. The lower Devonian successions of the Prague Basin indicate that switching between two greenhouse climatic modes, colder oligotropic and warmer mesotrophic, may have been responsible for the alternation of red and grey carbonate strata, respectively.

Testing the age calibration of the Newark-Hartford APTS by magnetostratigraphic correlation of U-Pb zircon-dated tuffaceous beds in the Late Traissic Chinle Formation in core PFNP-1A from the Petrified Forest National Park (Arizona, USA)

NASA Astrophysics Data System (ADS)

Kent, D. V.; Olsen, P. E.; Mundil, R.; Lepre, C. J.

2017-12-01

The Newark-Hartford APTS extends over 27 Myr according to cycle stratigraphy of the Norian and Rhaetian of the Late Triassic and Hettangian and Sinemurian of the Early Jurassic and an additional 6 Myr by extrapolation into the Carnian; the entire sequence is anchored by U-Pb zircon dating of CAMP activity that provides a calibration date of 201.6 Ma for Chron E23r just below the end-Triassic extinction and the earliest CAMP basalts in the Newark basin (Blackburn+2013 Science; Kent+2017 ESR). The developing APTS has been successfully used for global correlations in marine and non-marine facies but there have been ongoing suggestions that millions of years of Rhaetian time are missing in a cryptic unconformity that supposedly occurs just above E23r in the Newark Supergroup basins. Testing the continuity of the APTS by magnetostratigraphic correlation of U-Pb zircon-dated tuffaceous beds in the Chinle Formation was a prime scientific objective for core PFNP-1A. Paleomagnetic results were obtained using stepwise thermal demagnetization to 680°C from >150 samples of finer-grained red lithologies from the upper 250 m of the cored section of the Chinle (upper Sonsela, Petrified Forest including the Black Forest Bed, and lower Owl Rock Members). Characteristic directions isolated in 2/3 of the samples showed antipodal directions that were shallow with respect to reference directions (flattening factor 0.5), consistent with early acquisition of remanence. Seven polarity magnetozones produce a distinctive pattern correlated to Chrons E17r to E14r of the APTS. The Black Forest Bed at 209.93±0.26 Ma (Ramezani+2011 GSAB), confirmed by our new U-Pb dates from core PFNP-1A, occurs in a reverse polarity magnetozone correlated to E16r (209.95-210.25 Ma), which puts the U-Pb zircon date(s) in excellent agreement with the inferred APTS age. Rather than a 'missing Rhaetian', the apparent regional differences in appearances and disappearances of palynoflora, conchostracans, and other endemic taxa in continental deposits are more likely a reflection of demonstrated continental drift across climate belts and the misinterpretation of ecostratigraphy as chronostratigraphy. A suite of new U-Pb dates in conjunction with paleomagnetic analyses in PFNP-1A is expected to calibrate much of Triassic succession of the Colorado Plateau.

Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily

PubMed Central

2010-01-01

Background The extended light-harvesting complex (LHC) protein superfamily is a centerpiece of eukaryotic photosynthesis, comprising the LHC family and several families involved in photoprotection, like the LHC-like and the photosystem II subunit S (PSBS). The evolution of this complex superfamily has long remained elusive, partially due to previously missing families. Results In this study we present a meticulous search for LHC-like sequences in public genome and expressed sequence tag databases covering twelve representative photosynthetic eukaryotes from the three primary lineages of plants (Plantae): glaucophytes, red algae and green plants (Viridiplantae). By introducing a coherent classification of the different protein families based on both, hidden Markov model analyses and structural predictions, numerous new LHC-like sequences were identified and several new families were described, including the red lineage chlorophyll a/b-binding-like protein (RedCAP) family from red algae and diatoms. The test of alternative topologies of sequences of the highly conserved chlorophyll-binding core structure of LHC and PSBS proteins significantly supports the independent origins of LHC and PSBS families via two unrelated internal gene duplication events. This result was confirmed by the application of cluster likelihood mapping. Conclusions The independent evolution of LHC and PSBS families is supported by strong phylogenetic evidence. In addition, a possible origin of LHC and PSBS families from different homologous members of the stress-enhanced protein subfamily, a diverse and anciently paralogous group of two-helix proteins, seems likely. The new hypothesis for the evolution of the extended LHC protein superfamily proposed here is in agreement with the character evolution analysis that incorporates the distribution of families and subfamilies across taxonomic lineages. Intriguingly, stress-enhanced proteins, which are universally found in the genomes of green plants, red algae, glaucophytes and in diatoms with complex plastids, could represent an important and previously missing link in the evolution of the extended LHC protein superfamily. PMID:20673336

Do genes lie? Mitochondrial capture masks the Red Sea collector urchin's true identity (Echinodermata: Echinoidea: Tripneustes).

PubMed

Bronstein, Omri; Kroh, Andreas; Haring, Elisabeth

2016-11-01

Novel COI and bindin sequences of the Red Sea collector echinoid Tripneustes gratilla elatensis are used to show that (1) discordance between mitochondrial and nuclear loci exists in this echinoid genus, (2) Tripneustes gratilla as currently defined possibly comprises a complex of cryptic species, and (3) Red Sea Tripneustes form a genetically distinct clade in the bindin tree, which diverged from other Tripneustes clades at least 2-4million years ago. Morphological reassessment of T. gratilla elatensis shows perfect congruence between identification based on skeletal features and genetic data based on a nuclear marker sequence. Hence the Red Sea Tripneustes subspecies established by Dafni in 1983 is a distinct biological unit. All T. g. elatensis samples analyzed are highly similar to or share mtDNA haplotypes with Philippine T. g. gratilla, as do representatives from other edge-of-range occurrences. This lack of genetic structure in Indo-Pacific Tripneustes is interpreted as a result of wide-spread mitochondrial introgression. New fossil specimens from the Red Sea area confirm the sympatric occurrence of T. g. elatensis and T. g. gratilla in the northern Red Sea during Late Pleistocene, identifying a possible timing for the introgression. In addition, present-day distribution shows a contact zone in the Southern Red Sea (in the Dahlak Archipelago). T. g. elatensis, is yet another example of a Red Sea taxon historically identified as conspecific with its Indo-Pacific relatives, but which turned out to be a morphologically and genetically distinct endemic taxon, suggesting that the level of endemism in the Red Sea may still be underestimated. Copyright © 2016 Elsevier Inc. All rights reserved.

The use of enzymopathic human red cells in the study of malarial parasite glucose metabolism.

PubMed

Roth, E; Joulin, V; Miwa, S; Yoshida, A; Akatsuka, J; Cohen-Solal, M; Rosa, R

1988-05-01

The in vitro growth of Plasmodium falciparum malaria parasites was assayed in mutant red cells deficient in either diphosphoglycerate mutase (DPGM) or phosphoglycerate kinase (PGK). In addition, cDNA probes developed for human DNA sequences coding for these enzymes were used to examine the parasite genome by means of restriction endonuclease digestion and Southern blot analysis of parasite DNA. In both types of enzymopathic red cells, parasite growth was normal. In infected DPGM deficient red cells, no DPGM activity could be detected, and in normal red cells, DPGM activity declined slightly in a manner suggestive of parasite catabolism of host protein. However, in infected PGK deficient red cells, there was a 100-fold increase in PGK activity, and in normal red cells, a threefold increase in PGK activity was observed. Parasite PGK could be recovered from isolated parasites, and a marked increase in heat instability of parasite PGK as compared with the host cell enzyme was noted. Neither cDNA probe was found to cross-react with DNA sequences in the parasite genome. It is concluded that the parasite has no requirement for DPGM, and probably has no gene for this enzyme. On the other hand, the parasite does require PGK, (an adenosine triphosphate [ATP] generating enzyme) and synthesizes its own enzyme, which must have been encoded in the parasite genome. The parasite PGK gene most likely lacks sufficient homology to be detected by a human cDNA probe. Enzymopathic red cells are useful tools for elucidating the glycolytic enzymology of parasites and their co-evolution with their human hosts.

Sedimentology of paleochannels on foreland coastal plain, Judith River Formation (upper Cretaceous), southeast Alberta

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

Koster, E.H.

1984-04-01

The upper 90 m (295 ft) of the sub-Bearpaw Judith River Formation, continuously exposed in the badlands along the Red Deer River 185 km (115 mi) east of Calgary, is famous for the unrivaled assemblage of dinosaur fossils. Dinosaur Provincial Park presents are a rare opportunity to view the architecture of a foreland coastal-plain sequence as well as to clarify the origin and distribution of subbituminous coal zones and gas reservoirs associated with this formation across southeast Alberta. The distal reaches of paleodrainage from the developing Cordillera to the Western Interior seaway are being examined by north-south traversed across themore » badlands. Sharp-based paleochannel units, enclosed by rooted, olive-gray mudstone sequences that are commonly 4-6 m (13-20 ft) thick, vary between 2 end members. The first contains laterally accreted sand-mud couplets with abundant macrofloral debris, and represents cyclical, low-energy growth of point bars, possible with an estuarine influence. The second, mainly comprising cosets of large trough cross-beds with mudstone intraclasts, was formed by episodic aggradation of high-energy systems. An intermediate composite type displays evidence for an energy increase as channel sinuosity decreased. This variation in paleochannel type is attributed to alternating alluviation/rejuvenation associated with an unstable base level. Coal zones and potential reservoirs appear to be associated with the transgressive and regressive phases, respectively, of the Bearpaw coast. Amalgamation of paleochannels - marked by laterally extensive horizons of bone fragments, lithic and intraclastic gravel - is more common seaward over the axial region of the Sweetgrass arch.« less

Rapid identification of pathogenic streptococci isolated from moribund red tilapia (Oreochromis spp.).

PubMed

Abdelsalam, Mohamed; Elgendy, Mamdouh Y; Shaalan, Mohamed; Moustafa, Mohamed; Fujino, Masayuki

2017-03-01

Accurate and rapid identification of bacterial pathogens of fish is essential for the effective treatment and speedy control of infections. Massive mortalities in market-sized red tilapia (Oreochromis spp.) were noticed in mariculture concrete ponds in northern Egypt. Histopathological examination revealed marked congestion in the central vein of the liver with the presence of bacterial aggregates inside the lumen and in the vicinity of the central vein. A total of 12 isolates of streptococci were obtained from the moribund fish. This study documented the ability of the MicroSeq 500 16S bacterial sequencing method to accurately identify Streptococcus agalactiae and S. dysgalactiae mixed infections from moribund red tilapia that were difficult to be recognised by the commercial biochemical systems. The continuously decreasing cost of the sequencing technique should encourage its application in routine diagnostic procedures.

Interaction of healthcare worker hands and portable medical equipment: a sequence analysis to show potential transmission opportunities.

PubMed

Jinadatha, Chetan; Villamaria, Frank C; Coppin, John D; Dale, Charles R; Williams, Marjory D; Whitworth, Ryan; Stibich, Mark

2017-12-28

While research has demonstrated the importance of a clean health care environment, there is a lack of research on the role portable medical equipment (PME) play in the transmission cycle of healthcare-acquired infections (HAIs). This study investigated the patterns and sequence of contact events among health care workers, patients, surfaces, and medical equipment in a hospital environment. Research staff observed patient care events over six different 24 h periods on six different hospital units. Each encounter was recorded as a sequence of events and analyzed using sequence analysis and visually represented by network plots. In addition, a point prevalence microbial sample was taken from the computer on wheels (COW). The most touched items during patient care was the individual patient (850), bedrail (375), bed-surface (302), and bed side Table (223). Three of the top ten most common subsequences included touching PME and the patient: computer on wheels ➔ patient (62 of 274 total sequences, 22.6%, contained this sequence), patient ➔ COW (20.4%), and patient ➔ IV pump (16.1%). The network plots revealed large interconnectedness among objects in the room, the patient, PME, and the healthcare worker. Our results demonstrated that PME such as COW and IV pump were two of the most highly-touched items during patient care. Even with proper hand sanitization and personal protective equipment, this sequence analysis reveals the potential for contamination from the patient and environment, to a vector such as portable medical equipment, and ultimately to another patient in the hospital.

The Odorant Receptor Co-Receptor from the Bed Bug, Cimex lectularius L

PubMed Central

Hansen, Immo A.; Rodriguez, Stacy D.; Drake, Lisa L.; Price, David P.; Blakely, Brittny N.; Hammond, John I.; Tsujimoto, Hitoshi; Monroy, Erika Y.; Maio, William A.; Romero, Alvaro

2014-01-01

Recently, the bed bug, Cimex lectularius L. has re-emerged as a serious and growing problem in many parts of the world. Presence of resistant bed bugs and the difficulty to eliminate them has renewed interest in alternative control tactics. Similar to other haematophagous arthropods, bed bugs rely on their olfactory system to detect semiochemicals in the environment. Previous studies have morphologically characterized olfactory organs of bed bugs’ antenna and have physiologically evaluated the responses of olfactory receptor neurons (ORNs) to host-derived chemicals. To date, odorant binding proteins (OBPs) and odorant receptors (ORs) associated with these olfaction processes have not been studied in bed bugs. Chemoreception in insects requires formation of heteromeric complexes of ORs and a universal OR coreceptor (Orco). Orco is the constant chain of every odorant receptor in insects and is critical for insect olfaction but does not directly bind to odorants. Orco agonists and antagonists have been suggested as high-value targets for the development of novel insect repellents. In this study, we have performed RNAseq of bed bug sensory organs and identified several odorant receptors as well as Orco. We characterized Orco expression and investigated the effect of chemicals targeting Orco on bed bug behavior and reproduction. We have identified partial cDNAs of six C. lectularius OBPs and 16 ORs. Full length bed bug Orco was cloned and sequenced. Orco is widely expressed in different parts of the bed bug including OR neurons and spermatozoa. Treatment of bed bugs with the agonist VUAA1 changed bed bug pheromone-induced aggregation behavior and inactivated spermatozoa. We have described and characterized for the first time OBPs, ORs and Orco in bed bugs. Given the importance of these molecules in chemoreception of this insect they are interesting targets for the development of novel insect behavior modifiers. PMID:25411789

The odorant receptor co-receptor from the bed bug, Cimex lectularius L.

PubMed

Hansen, Immo A; Rodriguez, Stacy D; Drake, Lisa L; Price, David P; Blakely, Brittny N; Hammond, John I; Tsujimoto, Hitoshi; Monroy, Erika Y; Maio, William A; Romero, Alvaro

2014-01-01

Recently, the bed bug, Cimex lectularius L. has re-emerged as a serious and growing problem in many parts of the world. Presence of resistant bed bugs and the difficulty to eliminate them has renewed interest in alternative control tactics. Similar to other haematophagous arthropods, bed bugs rely on their olfactory system to detect semiochemicals in the environment. Previous studies have morphologically characterized olfactory organs of bed bugs' antenna and have physiologically evaluated the responses of olfactory receptor neurons (ORNs) to host-derived chemicals. To date, odorant binding proteins (OBPs) and odorant receptors (ORs) associated with these olfaction processes have not been studied in bed bugs. Chemoreception in insects requires formation of heteromeric complexes of ORs and a universal OR coreceptor (Orco). Orco is the constant chain of every odorant receptor in insects and is critical for insect olfaction but does not directly bind to odorants. Orco agonists and antagonists have been suggested as high-value targets for the development of novel insect repellents. In this study, we have performed RNAseq of bed bug sensory organs and identified several odorant receptors as well as Orco. We characterized Orco expression and investigated the effect of chemicals targeting Orco on bed bug behavior and reproduction. We have identified partial cDNAs of six C. lectularius OBPs and 16 ORs. Full length bed bug Orco was cloned and sequenced. Orco is widely expressed in different parts of the bed bug including OR neurons and spermatozoa. Treatment of bed bugs with the agonist VUAA1 changed bed bug pheromone-induced aggregation behavior and inactivated spermatozoa. We have described and characterized for the first time OBPs, ORs and Orco in bed bugs. Given the importance of these molecules in chemoreception of this insect they are interesting targets for the development of novel insect behavior modifiers.

The late Barremian Halimedides horizon of the Dolomites (Southern Alps, Italy).

PubMed

Lukeneder, Alexander; Uchman, Alfred; Gaillard, Christian; Olivero, Davide

2012-06-01

A new trace fossil marker level, the Halimedides horizon, is proposed for the Lower Cretaceous pelagic to hemipelagic succession of the Puez area (Southern Alps, Italy). The horizon occurs in the middle part of the late Barremian Gerhardtia sartousiana Zone ( Gerhardtia sartousiana Subzone). It is approximately 20 cm thick and restricted to the uppermost part of the Puez Limestone Member (marly limestones; Hauterivian-Barremian; Puez Formation). It is fixed to the top 20 cm of bed P1/204. The grey-whitish limestone bed of the G. sartousiana Zone is penetrated by Aptian red marls-siltstones of the Redbed Member. The horizon is documented for the first time from the Southern Alps, including the Dolomites, and can be correlated with other Mediterranean localities. The trace fossil assemblage of this marker bed with the co-occurrence of Halimedides , Spongeliomorpha and Zoophycos sheds light on the Lower Cretaceous sedimentological history and current system of the Puez area within the Dolomites. It also highlights the palaeoenvironmental evolution of basins and plateaus and provides insights into the late Barremian interval.

The late Barremian Halimedides horizon of the Dolomites (Southern Alps, Italy)

PubMed Central

Lukeneder, Alexander; Uchman, Alfred; Gaillard, Christian; Olivero, Davide

2012-01-01

A new trace fossil marker level, the Halimedides horizon, is proposed for the Lower Cretaceous pelagic to hemipelagic succession of the Puez area (Southern Alps, Italy). The horizon occurs in the middle part of the late Barremian Gerhardtia sartousiana Zone (Gerhardtia sartousiana Subzone). It is approximately 20 cm thick and restricted to the uppermost part of the Puez Limestone Member (marly limestones; Hauterivian–Barremian; Puez Formation). It is fixed to the top 20 cm of bed P1/204. The grey–whitish limestone bed of the G. sartousiana Zone is penetrated by Aptian red marls–siltstones of the Redbed Member. The horizon is documented for the first time from the Southern Alps, including the Dolomites, and can be correlated with other Mediterranean localities. The trace fossil assemblage of this marker bed with the co-occurrence of Halimedides, Spongeliomorpha and Zoophycos sheds light on the Lower Cretaceous sedimentological history and current system of the Puez area within the Dolomites. It also highlights the palaeoenvironmental evolution of basins and plateaus and provides insights into the late Barremian interval. PMID:27087717

Factors influencing humanitarian care and the treatment of local patients within the deployed military medical system: casualty referral limitations.

PubMed

Causey, Marlin; Rush, Robert M; Kjorstad, Randy J; Sebesta, James A

2012-05-01

Humanitarian medical care is an essential task of the deployed military health care system. The purpose of this study was to analyze referral acceptance in treating injured local national patients during Operation Enduring Freedom. A prospective observation study of local nationals who were referred for humanitarian trauma care in Afghanistan from March through August 2009. Sixty-six patients were referred for evacuation for suspected non-coalition-caused injuries. The bed status at the receiving hospital was defined as green (able to accept patients), amber (nearing capacity), and red (at capacity). The only factor associated with acceptance was the accepting hospital bed status (odds ratio = 1.57%, 95% confidence interval, 1.11-2.22; P = .009). Factors not significant were age, the province of origin, the type of referring facility, a prior operation before the request, patient status/affiliation, or the mechanism of injury. Humanitarian medical care is directly related to the capacity for high-acuity care because bed availability is the predominate reason for acceptance or rejection. Published by Elsevier Inc.

Tsunami recurrence in the eastern Alaska-Aleutian arc: A Holocene stratigraphic record from Chirikof Island, Alaska

USGS Publications Warehouse

Nelson, Alan R.; Briggs, Richard; Dura, Tina; Engelhart, Simon E.; Gelfenbaum, Guy; Bradley, Lee-Ann; Forman, S.L.; Vane, Christopher H.; Kelley, K.A.

2015-01-01

Despite the role of the Alaska-Aleutian megathrust as the source of some of the largest earthquakes and tsunamis, the history of its pre–twentieth century tsunamis is largely unknown west of the rupture zone of the great (magnitude, M 9.2) 1964 earthquake. Stratigraphy in core transects at two boggy lowland sites on Chirikof Island’s southwest coast preserves tsunami deposits dating from the postglacial to the twentieth century. In a 500-m-long basin 13–15 m above sea level and 400 m from the sea, 4 of 10 sandy to silty beds in a 3–5-m-thick sequence of freshwater peat were probably deposited by tsunamis. The freshwater peat sequence beneath a gently sloping alluvial fan 2 km to the east, 5–15 m above sea level and 550 m from the sea, contains 20 sandy to silty beds deposited since 3.5 ka; at least 13 were probably deposited by tsunamis. Although most of the sandy beds have consistent thicknesses (over distances of 10–265 m), sharp lower contacts, good sorting, and/or upward fining typical of tsunami deposits, the beds contain abundant freshwater diatoms, very few brackish-water diatoms, and no marine diatoms. Apparently, tsunamis traveling inland over low dunes and boggy lowland entrained largely freshwater diatoms. Abundant fragmented diatoms, and lake species in some sandy beds not found in host peat, were probably transported by tsunamis to elevations of >10 m at the eastern site. Single-aliquot regeneration optically stimulated luminescence dating of the third youngest bed is consistent with its having been deposited by the tsunami recorded at Russian hunting outposts in 1788, and with the second youngest bed being deposited by a tsunami during an upper plate earthquake in 1880. We infer from stratigraphy, 14C-dated peat deposition rates, and unpublished analyses of the island’s history that the 1938 tsunami may locally have reached an elevation of >10 m. As this is the first record of Aleutian tsunamis extending throughout the Holocene, we cannot estimate source earthquake locations or magnitudes for most tsunami-deposited beds. We infer that no more than 3 of the 23 possible tsunamis beds at both sites were deposited following upper plate faulting or submarine landslides independent of megathrust earthquakes. If so, the Semidi segment of the Alaska-Aleutian megathrust near Chirikof Island probably sent high tsunamis southward every 180–270 yr for at least the past 3500 yr.                   

A study on the use of the BioBall® as a biofilm carrier in a sequencing batch reactor.

PubMed

Masłoń, Adam; Tomaszek, Janusz A

2015-11-01

Described in this study are experiments conducted to evaluate the removal of organics and nutrients from synthetic wastewater by a moving bed sequencing batch biofilm reactor using BioBall® carriers as biofilm media. The work involving a 15L-laboratory scale MBSBBR (moving bed sequencing batch biofilm reactor) model showed that the wastewater treatment system was based on biochemical processes taking place with activated sludge and biofilm microorganisms developing on the surface of the BioBall® carriers. Classical nitrification and denitrification and the typical enhanced biological phosphorus removal process were achieved in the reactor analyzed, which operated with a volumetric organic loading of 0.84-0.978gCODL(-1)d(-1). The average removal efficiencies for COD, total nitrogen and total phosphorus were found to be 97.7±0.5%, 87.8±2.6% and 94.3±1.3%, respectively. Nitrification efficiency reached levels in the range 96.5-99.7%. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sediment concentrations, loads, and particle-size distributions in the Red River of the North and selected tributaries near Fargo, North Dakota, during the 2011 spring high-flow event

USGS Publications Warehouse

Galloway, Joel M.; Blanchard, Robert A.; Ellison, Christopher A.

2011-01-01

Most of the bedload samples had particle sizes in the 0.5 to 1 millimeter and 0.25 to 0.5 millimeter ranges from the Maple River, Wild Rice River, Rush River, Buffalo River, and Red River sites. The Rush and Lower Branch Rush Rivers also had a greater portion of larger particle sizes in the 1 to 2 millimeter range. The Sheyenne River sites had a greater portion of smaller particle sizes in the bedload in the 0.125 to 0.5 millimeter range compared to the other sites. The bed material in samples collected during the 2011 spring high-flow event demonstrated a wider distribution of particle sizes than were observed in the bedload; the coarsest material was found at the Red River near Christine and the Lower Branch Rush River and the finest material at the Sheyenne River sites.

Column performance of carbon nanotube packed bed for methylene blue and orange red dye removal from waste water

NASA Astrophysics Data System (ADS)

Gill, G. K.; Mubarak, N. M.; Nizamuddin, S.; Al-Salim, H. S.; Sahu, J. N.

2017-06-01

Environmental issues have always been a major issue among human kind for the past decades. As the time passes by, the technology field has grown and has helped a lot in order to reduce these environmental issues. Industries such as metal plating facilities, mining operations and batteries production are a few examples that involves in the environmental issues. Carbon nanotube is proven to possess excellent adsorption capacity for the removal of methylene blue and orange red dyes. The effect of process parameters such as pH and contact time was investigated The results revealed that optimized conditions for the highest removal for methylene blue (MB) (97%) and orange red (94%) are at pH 10, CNTs dosage of 1 grams, and 15 minutes for each dyes removal respectively. The equilibrium adsorption data obtained was best fit to Freundlich model, while kinetic data can be characterized by the pseudo second-order rate kinetics.

Reconnaissance for trace metals in bed sediment, Wright Patman Lake, near Texarkana, Texas

USGS Publications Warehouse

McKee, Paul W.

2001-01-01

Many contaminants can be introduced into the environment by urban and industrial activities. The drainage area of Wright Patman Lake is influenced by these activities. Among the contaminants associated with urban and industrial activities are trace metals such as arsenic, lead, mercury, and zinc. These contaminants are relatively insoluble in water and commonly are found in stream, lake, and reservoir bottom sediment, especially the clays and silts within the sediment.Wright Patman Lake serves as the major potable water supply for the city of Texarkana and surrounding communities. Texarkana, located in the northeastern corner of Texas and the southwestern corner of Arkansas, had a population of about 56,000 in 1998, which reflects an increase of about 3.4 percent from the 1990 census (Ramos, 1999). Texarkana Water Utilities, which manages the water-treatment facilities for Texarkana, proposes to dredge the lake bed near the water intake in the Elliot Creek arm of Wright Patman Lake. It is possible that arsenic, lead, mercury, and other trace metals might be released into the water if the bed sediment is disturbed. Bed sediment in the Elliot Creek arm of the lake, in particular, could contain trace metals because of its proximity to Red River Army Depot and because industrial land use is prevalent in the headwaters of Elliot Creek.The U.S. Geological Survey (USGS), in cooperation with Reconnaissance for Trace Metals in Bed Sediment, Wright Patman Lake, Near Texarkana, Texas In cooperation with the Texarkana Water Utilities conducted a reconnaissance of Wright Patman Lake to collect bed-sediment samples for analysis of trace metals. This report presents trace metal concentrations in bed-sediment samples collected at six sites along the Elliot Creek arm of the lake, one site each in two adjacent arms, and one site near the dam on June 16, 1999 (fig. 1). One bed-sediment sample was collected at each of the nine sites, and one sediment core was collected at each of two of the sites. Trace metal concentrations are compared to sediment-quality guidelines for the protection of aquatic life and to screening levels based on historical trace metal concentrations in bed sediment of Texas reservoirs.

TOF-SIMS Analysis of Red Color Inks of Writing and Printing Tools on Questioned Documents.

PubMed

Lee, Jihye; Nam, Yun Sik; Min, Jisook; Lee, Kang-Bong; Lee, Yeonhee

2016-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established surface technique that provides both elemental and molecular information from several monolayers of a sample surface while also allowing depth profiling or image mapping to be performed. Static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric, biological, archaeological, and forensic materials. In forensic investigation, the use of a minimal sample for the analysis is preferable. Although the TOF-SIMS technique is destructive, the probing beams have microsized diameters so that only small portion of the questioned sample is necessary for the analysis, leaving the rest available for other analyses. In this study, TOF-SIMS and attenuated total reflectance Fourier transform infrared (ATR-FTIR) were applied to the analysis of several different pen inks, red sealing inks, and printed patterns on paper. The overlapping areas of ballpoint pen writing, red seal stamping, and laser printing in a document were investigated to identify the sequence of recording. The sequence relations for various cases were determined from the TOF-SIMS mapping image and the depth profile. TOF-SIMS images were also used to investigate numbers or characters altered with two different red pens. TOF-SIMS was successfully used to determine the sequence of intersecting lines and the forged numbers on the paper. © 2016 American Academy of Forensic Sciences.

Development of a codon optimization strategy using the efor RED reporter gene as a test case

NASA Astrophysics Data System (ADS)

Yip, Chee-Hoo; Yarkoni, Orr; Ajioka, James; Wan, Kiew-Lian; Nathan, Sheila

2018-04-01

Synthetic biology is a platform that enables high-level synthesis of useful products such as pharmaceutically related drugs, bioplastics and green fuels from synthetic DNA constructs. Large-scale expression of these products can be achieved in an industrial compliant host such as Escherichia coli. To maximise the production of recombinant proteins in a heterologous host, the genes of interest are usually codon optimized based on the codon usage of the host. However, the bioinformatics freeware available for standard codon optimization might not be ideal in determining the best sequence for the synthesis of synthetic DNA. Synthesis of incorrect sequences can prove to be a costly error and to avoid this, a codon optimization strategy was developed based on the E. coli codon usage using the efor RED reporter gene as a test case. This strategy replaces codons encoding for serine, leucine, proline and threonine with the most frequently used codons in E. coli. Furthermore, codons encoding for valine and glycine are substituted with the second highly used codons in E. coli. Both the optimized and original efor RED genes were ligated to the pJS209 plasmid backbone using Gibson Assembly and the recombinant DNAs were transformed into E. coli E. cloni 10G strain. The fluorescence intensity per cell density of the optimized sequence was improved by 20% compared to the original sequence. Hence, the developed codon optimization strategy is proposed when designing an optimal sequence for heterologous protein production in E. coli.

Early Archean spherule beds of possible impact origin from Barberton, South Africa: A detailed mineralogical and geochemical study

NASA Technical Reports Server (NTRS)

Koeberl, Christian; Reimold, Wolf Uwe; Boer, Rudolf H.

1992-01-01

The Barberton Greenstone belt is a 3.5- to 3.2-Ga-old formation situated in the Swaziland Supergroup near Barberton, northeast Transvaal, South Africa. The belt includes a lower, predominantly volcanic sequence, and an upper sedimentary sequence (e.g., the Fig Tree Group). Within this upper sedimentary sequence, Lowe and Byerly identified a series of different beds of spherules with diameters of around 0.5-2 mm. Lowe and Byerly and Lowe et al. have interpreted these spherules to be condensates of rock vapor produced by large meteorite impacts in the early Archean. We have collected a series of samples from drill cores from the Mt. Morgan and Princeton sections near Barberton, as well as samples taken from underground exposures in the Sheba and Agnes mines. These samples seem much better preserved than the surface samples described by Lowe and Byerly and Lowe et al. Over a scale of just under 30 cm, several well-defined spherule beds are visible, interspaced with shales and/or layers of banded iron formation. Some spherules have clearly been deposited on top of a sedimentary unit because the shale layer shows indentions from the overlying spherules. Although fresher than the surface samples (e.g., spherule bed S-2), there is abundant evidence for extensive alteration, presumably by hydrothermal processes. In some sections of the cores sulfide mineralization is common. For our mineralogical and petrographical studies we have prepared detailed thin sections of all core and underground samples (as well as some surface samples from the S-2 layer for comparison). For geochemical work, layers with thicknesses in the order of 1-5 mm were separated from selected core and underground samples. The chemical analyses are being performed using neutron activation analysis in order to obtain data for about 35 trace elements in each sample. Major elements are being determined by XRF and plasma spectrometry. To clarify the history of the sulfide mineralization, sulfur isotopic compositions are being determined.

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.

Anisotropic and heterogeneous mechanical properties of a stratified shale/limestone sequence at Nash Point, South Wales: A case study for hydraulic fracture propagation through a layered medium

NASA Astrophysics Data System (ADS)

Forbes Inskip, Nathaniel; Meredith, Philip; Gudmundsson, Agust

2016-04-01

While considerable effort has been expended on the study of fracture propagation in rocks in recent years, our understanding of how fractures propagate through layered sedimentary rocks with different mechanical and elastic properties remains poorly constrained. Yet this is a key issue controlling the propagation of both natural and anthropogenic hydraulic fractures in layered sequences. Here we report measurements of the contrasting mechanical and elastic properties of the Lower Lias at Nash Point, South Wales, which comprises an interbedded sequence of shale and limestone layers, and how those properties may influence fracture propagation. Elastic properties of both materials have been characterised via ultrasonic wave velocity measurements as a function of azimuth on samples cored both normal and parallel to bedding. The shale is highly anisotropic, with P-wave velocities varying from 2231 to 3890 m s-1, giving an anisotropy of ~55%. By contrast, the limestone is essentially isotropic, with a mean P-wave velocity of 5828 m s-1 and an anisotropy of ~2%. The dynamic Young's modulus of the shale, calculated from P- and S-wave velocity data, is also anisotropic with a value of 36 GPa parallel to bedding and 12 GPa normal to bedding. The modulus of the limestone is again isotropic with a value of 80 GPa. It follows that for a vertical fracture propagating (i.e. normal to bedding) the modulus contrast is 6.6. This is important because the contrast in elastic properties is a key factor in controlling whether fractures arrest, deflect, or propagate across interfaces between layers in a sequence. There are three principal mechanisms by which a fracture may deflect across or along an interface, namely: Cook-Gordon debonding, stress barrier, and elastic mismatch. Preliminary numerical modelling results (using a Finite Element Modelling software) of induced fractures at Nash Point suggest that all three are important. The results demonstrate a rotation of the maximum principal compressive stress across an interface but also a confinement of tensile stress within the host layer. Mechanical properties have been characterised by indirect measurement of the tensile strength using the Brazil-Disk technique. Measurements were made in the three principal orientations relative to bedding, Arrester, Divider, and Short-Transverse, and also at 15° intervals between these planes. Values for the shale again showed a high degree of anisotropy; with similar values in the Arrester and Divider orientations, but with much lower values in the Short-Transverse (bedding parallel) orientation. The tensile strength of the limestone is considerably higher than that of the shale and exhibits no significant anisotropy. Current work is underway to characterise the fracture propagation properties by measuring the fracture toughness and fracture ductility of both rocks using a combination of the Semi-Circular Bend and Short-Rod techniques.

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.

Effects of acute exercise on attenuated vagal baroreflex function during bed rest

NASA Technical Reports Server (NTRS)

Convertino, Victor A.; Doerr, Donald F.; Guell, Antonio; Marini, J.-F.

1992-01-01

We measured carotid baroreceptor-cardiac reflex responses in six healthy men, 24 h before and 24 h after a bout of leg exercise during 6 deg head-down bed rest to determine if depressed vagal baroreflex function associated with exposure to microgravity environments could be reversed by a single exposure to acute intense exercise. Baroreflex responses were measured before bed rest and on day 7 of bed rest. An exercise bout consisting of dynamic and isometric actions of the quadriceps at graded speeds and resistances was performed on day 8 of bed rest and measurements of baroreflex response were repeated 24 h later. Vagally-mediated cardiac responses were provoked with ramped neck pressure-suction sequences comprising pressure elevations to +40 mm Hg, followed by serial, R-wave triggered 15 mm Hg reductions, to -65 mm Hg. Baroreceptor stimulus-cardiac response relationships were derived by plotting each R-R interval as a function of systolic pressure less the neck chamber pressure applied during the interval. Compared with pre-bed rest baseline measurements, 7 d of bed rest decreased the gain (maximum slope) of the baroreflex stimulus-response relationship by 16.8 +/- 3.4 percent (p less than 0.05). On day 9 of bed rest, 24 h after exercise, the maximum slope of the baroreflex stimulus-response relationship was increased (p less than 0.05) by 10.7 +/- 3.7 percent above pre-bed rest levels and 34.3 +/- 7.9 percent above bed rest day 7. Our data verify that vagally-mediated baroreflex function is depressed by exposure to simulated microgravity and demonstrate that this effect can be acutely reversed by exposure to a single bout of intense exercise.

The star forming universe after z=1

NASA Astrophysics Data System (ADS)

Harker, Justin J.

This dissertation explores three projects in the field of galaxy formation and evolution: the formation of the red sequence via quenching, the detection, characterization, and frequency of starbursts in the DEEP2 sample, and the behavior of a main sequence of star forming galaxies whose behavior is determined by baryonic mass, referred to as staged star formation. The first section, in Chapter 2, presents a breakdown of several population synthesis models designed to probe the history of the red sequence. Known from measurements at low redshift to be composed of objects with a large range of ages, the red sequence is not well-modeled as being the result of a single monolithic event in the distant past. By combining information on restframe color, Balmer absorption line strengths, and the number density of L* galaxies as a function of redshift, we find evidence that the red sequence is built up over time. The second section, in Chapter 3 and 4, presents a novel method for determining simultaneously the absorption line and emission line contributions to the total measured equivalent width of Balmer lines. Relying on the predictable behavior of both absorption lines, which are to first order equivalent to one another, and emission lines, which follow a predictable decrement toward shorter wavelengths, a single measurement of total line strength for Hb and Hd yield uncoupled emission and absorption line components. Using the measurement of Hd in absorption against D n 4000 and Hb in emission, we isolate a population of potential starbursts in the DEEP2 sample. The final section, in Chapter 5, explores the regularity of star formation as a function of redshift, using the staged star formation prescription of Noeske et al. (2007a). We compute a set of t-models using the prescription, and compare them to the data in a number of parameters in addition to mass and star formation. While the staged star formation model is a good match in a number of parameters, we find several irregularities.

A molecular survey of Babesia spp. and Theileria spp. in red foxes (Vulpes vulpes) and their ticks from Thuringia, Germany.

PubMed

Najm, Nour-Addeen; Meyer-Kayser, Elisabeth; Hoffmann, Lothar; Herb, Ingrid; Fensterer, Veronika; Pfister, Kurt; Silaghi, Cornelia

2014-06-01

Wild canines which are closely related to dogs constitute a potential reservoir for haemoparasites by both hosting tick species that infest dogs and harbouring tick-transmitted canine haemoparasites. In this study, the prevalence of Babesia spp. and Theileria spp. was investigated in German red foxes (Vulpes vulpes) and their ticks. DNA extracts of 261 spleen samples and 1953 ticks included 4 tick species: Ixodes ricinus (n=870), I. canisuga (n=585), I. hexagonus (n=485), and Dermacentor reticulatus (n=13) were examined for the presence of Babesia/Theileria spp. by a conventional PCR targeting the 18S rRNA gene. One hundred twenty-one out of 261 foxes (46.4%) were PCR-positive. Out of them, 44 samples were sequenced, and all sequences had 100% similarity to Theileria annae. Similarly, sequencing was carried out for 65 out of 118 PCR-positive ticks. Theileria annae DNA was detected in 61.5% of the sequenced samples, Babesia microti DNA was found in 9.2%, and Babesia venatorum in 7.6% of the sequenced samples. The foxes were most positive in June and October, whereas the peak of tick positivity was in October. Furthermore, the positivity of the ticks was higher for I. canisuga in comparison to the other tick species and for nymphs in comparison to adults. The high prevalence of T. annae DNA in red foxes in this study suggests a reservoir function of those animals for T. annae. To our knowledge, this is the first report of T. annae in foxes from Germany as well as the first detection of T. annae and B. microti in the fox tick I. canisuga. Detection of DNA of T. annae and B. microti in three tick species collected from foxes adds new potential vectors for these two pathogens and suggests a potential role of the red fox in their natural endemic cycles. Copyright © 2014 Elsevier GmbH. All rights reserved.

Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis.

PubMed

Abendroth, Christian; Hahnke, Sarah; Codoñer, Francisco M; Klocke, Michael; Luschnig, Olaf; Porcar, Manuel

2017-10-05

A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism. Copyright © 2017 Abendroth et al.

Training with the International Space Station interim resistive exercise device

NASA Technical Reports Server (NTRS)

Schneider, Suzanne M.; Amonette, William E.; Blazine, Kristi; Bentley, Jason; Lee, Stuart M C.; Loehr, James A.; Moore, Alan D Jr; Rapley, Michael; Mulder, Edwin R.; Smith, Scott M.

2003-01-01

A unique, interim elastomer-based resistive exercise device (iRED) is being used on the International Space Station. PURPOSE: This study characterized iRED training responses in a 1-g environment by: 1) determining whether 16 wk of high-intensity training with iRED produces increases in muscle strength and volume and bone mineral density (BMD), 2) comparing training responses with iRED to free weights, and 3) comparing iRED training responses at two training volumes. METHODS: Twenty-eight untrained men were assigned to four groups of seven subjects each: a no exercise control group (CON), an iRED group who trained with three sets/exercise (iRED3), a free-weight group (FW) who trained with three sets/exercise, and an iRED group who trained with six sets/exercise (iRED6). Training exercises included squat (SQ), heel raise (HR), and dead lift (DL) exercises, 3 d.wk(-1) for 16 wk. RESULTS: For CON, no changes occurred pre- to posttraining. For iRED3, increases (P< or =0.05) in one-repetition maximum (1-RM) strength (SQ 21 +/- 4%, HR 17 +/- 4%, DL 29 +/- 5%), leg lean mass (3.1 +/- 0.5%) by dual energy x-ray absorptiometry (DXA), and thigh (4.5 +/- 0.9%) and calf (5.9 +/- 0.7%) muscle volume (by magnetic resonance imaging) occurred after training with no changes in BMD (DXA). For FW, increases in 1-RM strength (SQ 22 +/- 5%, HR 24 +/- 3%, DL 41 +/- 7%), whole body (3.0 +/- 1.1%) and leg lean mass (5.4 +/- 1.2%), thigh (9.2 +/- 1.3%) and calf (4.2 +/- 1.0%) muscle volumes, and lumbar BMD (4.2 +/- 0.7%) occurred after training. For iRED6, all responses were similar to iRED3. CONCLUSION: High-intensity training with the iRED produced muscle responses similar to FW but was not effective in stimulating bone. Bed rest and spaceflight studies are needed to evaluate the effectiveness of the iRED to prevent microgravity deconditioning.

The Mid-infrared View of Red Sequence Galaxies in Abell 2218 with AKARI

NASA Astrophysics Data System (ADS)

Ko, Jongwan; Im, Myungshin; Lee, Hyung Mok; Lee, Myung Gyoon; Hopwood, Ros H.; Serjeant, Stephen; Smail, Ian; Hwang, Ho Seong; Hwang, Narae; Shim, Hyunjin; Kim, Seong Jin; Lee, Jong Chul; Lim, Sungsoon; Seo, Hyunjong; Goto, Tomotsugu; Hanami, Hitoshi; Matsuhara, Hideo; Takagi, Toshinobu; Wada, Takehiko

2009-04-01

We present the AKARI Infrared Camera (IRC) imaging observation of early-type galaxies (ETGs) in A2218 at zsime 0.175. Mid-infrared (MIR) emission from ETGs traces circumstellar dust emission from asymptotic giant branch (AGB) stars or/and residual star formation. Including the unique imaging capability at 11 and 15 μm, our AKARI data provide an effective way to investigate MIR properties of ETGs in the cluster environment. Among our flux-limited sample of 22 red sequence ETGs with precise dynamical and line strength measurements (less than 18 mag at 3 μm), we find that at least 41% have MIR-excess emission. The N3 - S11 versus N3 (3 and 11 μm) color-magnitude relation shows the expected blue sequence, but the MIR-excess galaxies add a red wing to the relation especially at the fainter end. A spectral energy distribution analysis reveals that the dust emission from AGB stars is the most likely cause of the MIR excess, with a low level of star formation being the next possible explanation. The MIR-excess galaxies show a wide spread of N3 - S11 colors, implying a significant spread (2-11 Gyr) in the estimated mean ages of stellar populations. We study the environmental dependence of MIR-excess ETGs over an area out to a half virial radius (~1 Mpc). We find that the MIR-excess ETGs are preferentially located in the outer region. From this evidence, we suggest that the fainter, MIR-excess ETGs have just joined the red sequence, possibly due to the infall and subsequent morphological/spectral transformation induced by the cluster environment.

Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants.

PubMed

Iso-Touru, T; Sahana, G; Guldbrandtsen, B; Lund, M S; Vilkki, J

2016-03-22

The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health traits offers a great opportunity to study production traits and identify causal variants behind them. In this study, we used whole genome sequence level data from 4280 progeny tested Nordic Red Cattle bulls to scan the genome for loci affecting milk, fat and protein yields. Using a genome-wise significance threshold, regions on Bos taurus chromosomes 5, 14, 23, 25 and 26 were associated with fat yield. Regions on chromosomes 5, 14, 16, 19, 20 and 25 were associated with milk yield and chromosomes 5, 14 and 25 had regions associated with protein yield. Significantly associated variations were found in 227 genes for fat yield, 72 genes for milk yield and 30 genes for protein yield. Ingenuity Pathway Analysis was used to identify networks connecting these genes displaying significant hits. When compared to previously mapped genomic regions associated with fertility, significantly associated variations were found in 5 genes common for fat yield and fertility, thus linking these two traits via biological networks. This is the first time when whole genome sequence data is utilized to study genomic regions affecting milk production in the Nordic Red Cattle population. Sequence level data offers the possibility to study quantitative traits in detail but still cannot unambiguously reveal which of the associated variations is causative. Linkage disequilibrium creates difficulties to pinpoint the causative genes and variations. One solution to overcome these difficulties is the identification of the functional gene networks and pathways to reveal important interacting genes as candidates for the observed effects. This information on target genomic regions may be exploited to improve genomic prediction.

Initiation and Along-Axis Segmentation of Seaward-Dipping Volcanic Sequences Captured in Afar

NASA Astrophysics Data System (ADS)

Ebinger, C.; Wolfenden, E.; Yirgu, G.; Keir, D.

2003-12-01

The Afar triple junction zone provides a unique opportunity to examine the early development of magmatic margins, as respective limbs of the triple junction capture different stages of the breakup process. Initial rifting in the southernmost Red Sea occurred concurrent with, or soon after flood basaltic magmatism at ~31 Ma in the Ethiopia-Yemen plume province, whereas the northern part of the Main Ethiopian rift initiated after 12 Ma. Both rift systems initiated with the development of high-angle border fault systems bounding broad basins, but 8-10 My after rifting we see riftward migration of strain from the western border fault to narrow zones of increasingly more basaltic magmatism. These localised zones of faulting and volcanism (magmatic segments) show a segmentation independent of the border fault segmentation. The much older, more evolved magmatic segments in the southern Red Sea, where not onlapped by Pliocene-Recent sedimentary strata, dip steeply riftward and define a regional eastward flexure into transitional oceanic crust, as indicated by gravity models constrained by seismic refraction and receiver function data. The southern Red Sea magmatic segments have been abandoned in Pliocene-Recent triple junction reorganisations, whereas the process of seaward-dipping volcanic sequence emplacement is ongoing in the seismically and volcanically active Main Ethiopian rift. Field, remote sensing, gravity, and seismicity data from the Main Ethiopian and southern Red Sea rifts indicate that seaward-dipping volcanic sequences initiate in moderately stretched continental crust above a narrow zone of dike-intrusion. Our comparison of active and ancient magmatic segments show that they are the precursors to seaward-dipping volcanic sequences analogous to those seen on passive continental margins, and provides insights into the initiation of along-axis segmentation of seafloor-spreading centers.

Color-magnitude distribution of face-on nearby galaxies in Sloan digital sky survey DR7

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

Jin, Shuo-Wen; Feng, Long-Long; Gu, Qiusheng

2014-05-20

We have analyzed the distributions in the color-magnitude diagram (CMD) of a large sample of face-on galaxies to minimize the effect of dust extinctions on galaxy color. About 300,000 galaxies with log (a/b) < 0.2 and redshift z < 0.2 are selected from the Sloan Digital Sky Survey DR7 catalog. Two methods are employed to investigate the distributions of galaxies in the CMD, including one-dimensional (1D) Gaussian fitting to the distributions in individual magnitude bins and two-dimensional (2D) Gaussian mixture model (GMM) fitting to galaxies as a whole. We find that in the 1D fitting, two Gaussians are not enoughmore » to fit galaxies with the excess present between the blue cloud and the red sequence. The fitting to this excess defines the center of the green valley in the local universe to be (u – r){sub 0.1} = –0.121M {sub r,} 0{sub .1} – 0.061. The fraction of blue cloud and red sequence galaxies turns over around M {sub r,} {sub 0.1} ∼ –20.1 mag, corresponding to stellar mass of 3 × 10{sup 10} M {sub ☉}. For the 2D GMM fitting, a total of four Gaussians are required, one for the blue cloud, one for the red sequence, and the additional two for the green valley. The fact that two Gaussians are needed to describe the distributions of galaxies in the green valley is consistent with some models that argue for two different evolutionary paths from the blue cloud to the red sequence.« less

Co-infection and cross-species transmission of divergent Hepatocystis lineages in a wild African primate community.

PubMed

Thurber, Mary I; Ghai, Ria R; Hyeroba, David; Weny, Geoffrey; Tumukunde, Alex; Chapman, Colin A; Wiseman, Roger W; Dinis, Jorge; Steeil, James; Greiner, Ellis C; Friedrich, Thomas C; O'Connor, David H; Goldberg, Tony L

2013-07-01

Hemoparasites of the apicomplexan family Plasmodiidae include the etiological agents of malaria, as well as a suite of non-human primate parasites from which the human malaria agents evolved. Despite the significance of these parasites for global health, little information is available about their ecology in multi-host communities. Primates were investigated in Kibale National Park, Uganda, where ecological relationships among host species are well characterized. Blood samples were examined for parasites of the genera Plasmodium and Hepatocystis using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene, followed by Sanger sequencing. To assess co-infection, "deep sequencing" of a variable region within cytochrome b was performed. Out of nine black-and-white colobus (Colobus guereza), one blue guenon (Cercopithecus mitis), five grey-cheeked mangabeys (Lophocebus albigena), 23 olive baboons (Papio anubis), 52 red colobus (Procolobus rufomitratus) and 12 red-tailed guenons (Cercopithecus ascanius), 79 infections (77.5%) were found, all of which were Hepatocystis spp. Sanger sequencing revealed 25 different parasite haplotypes that sorted phylogenetically into six species-specific but morphologically similar lineages. "Deep sequencing" revealed mixed-lineage co-infections in baboons and red colobus (41.7% and 64.7% of individuals, respectively) but not in other host species. One lineage infecting red colobus also infected baboons, but always as the minor variant, suggesting directional cross-species transmission. Hepatocystis parasites in this primate community are a diverse assemblage of cryptic lineages, some of which co-infect hosts and at least one of which can cross primate species barriers. Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Signatures of adaptation in the weedy rice genome

USDA-ARS?s Scientific Manuscript database

Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

The Fate of Exoplanets and the Red Giant Rapid Rotator Connection

NASA Astrophysics Data System (ADS)

Carlberg, Joleen K.; Majewski, Steven R.; Arras, Phil; Smith, Verne V.; Cunha, Katia; Bizyaev, Dmitry

2011-03-01

We have computed the fate of exoplanet companions around main sequence stars to explore the frequency of planet ingestion by their host stars during the red giant branch evolution. Using published properties of exoplanetary systems combined with stellar evolution models and Zahn's theory of tidal friction, we modeled the tidal decay of the planets' orbits as their host stars evolve. Most planets currently orbiting within 2 AU of their star are expected to be ingested by the end of their stars' red giant branch ascent. Our models confirm that many transiting planets are sufficiently close to their parent star that they will be accreted during the main sequence lifetime of the star. We also find that planet accretion may play an important role in explaining the mysterious red giant rapid rotators, although appropriate planetary systems do not seem to be plentiful enough to account for all such rapid rotators. We compare our modeled rapid rotators and surviving planetary systems to their real-life counterparts and discuss the implications of this work to the broader field of exoplanets.

Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon

PubMed Central

Ahuka-Mundeke, Steve; Liegeois, Florian; Ayouba, Ahidjo; Foupouapouognini, Yacouba; Nerrienet, Eric; Delaporte, Eric; Peeters, Martine

2010-01-01

Simian immunodeficiency viruses (SIVs) are lentiviruses that infect an extensive number of wild African primate species. Here we describe for the first time SIV infection in a captive agile mangabey (Cercocebus agilis) from Cameroon. Phylogenetic analysis of the full-length genome sequence of SIVagi-00CM312 showed that this novel virus fell into the SIVrcm lineage and was most closely related to a newly characterized SIVrcm strain (SIVrcm-02CM8081) from a wild-caught red-capped mangabey (Cercocebus torquatus) from Cameroon. In contrast to red-capped mangabeys, no 24 bp deletion in CCR5 has been observed in the agile mangabey. Further studies on wild agile mangabeys are needed to determine whether agile and red-capped mangabeys are naturally infected with the same SIV lineage, or whether this agile mangabey became infected with an SIVrcm strain in captivity. However, our study shows that agile mangabeys are susceptible to SIV infection. PMID:20797968

Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon.

PubMed

Ahuka-Mundeke, Steve; Liegeois, Florian; Ayouba, Ahidjo; Foupouapouognini, Yacouba; Nerrienet, Eric; Delaporte, Eric; Peeters, Martine

2010-12-01

Simian immunodeficiency viruses (SIVs) are lentiviruses that infect an extensive number of wild African primate species. Here we describe for the first time SIV infection in a captive agile mangabey (Cercocebus agilis) from Cameroon. Phylogenetic analysis of the full-length genome sequence of SIVagi-00CM312 showed that this novel virus fell into the SIVrcm lineage and was most closely related to a newly characterized SIVrcm strain (SIVrcm-02CM8081) from a wild-caught red-capped mangabey (Cercocebus torquatus) from Cameroon. In contrast to red-capped mangabeys, no 24 bp deletion in CCR5 has been observed in the agile mangabey. Further studies on wild agile mangabeys are needed to determine whether agile and red-capped mangabeys are naturally infected with the same SIV lineage, or whether this agile mangabey became infected with an SIVrcm strain in captivity. However, our study shows that agile mangabeys are susceptible to SIV infection.

Nitrogen removal in moving bed sequencing batch reactor using polyurethane foam cubes of various sizes as carrier materials.

PubMed

Lim, Jun-Wei; Seng, Chye-Eng; Lim, Poh-Eng; Ng, Si-Ling; Sujari, Amat-Ngilmi Ahmad

2011-11-01

The performance of moving bed sequencing batch reactors (MBSBRs) added with 8 % (v/v) of polyurethane (PU) foam cubes as carrier media in nitrogen removal was investigated in treating low COD/N wastewater. The results indicate that MBSBR with 8-mL cubes achieved the highest total nitrogen (TN) removal efficiency of 37% during the aeration period, followed by 31%, 24% and 19 % for MBSBRs with 27-, 64- and 125-mL cubes, respectively. The increased TN removal in MBSBRs was mainly due to simultaneous nitrification and denitrification (SND) process which was verified by batch studies. The relatively lower TN removal in MBSBR with larger PU foam cubes was attributed to the observation that larger PU foam cubes were not fully attached by biomass. Higher concentrations of 8-mL PU foam cubes in batch reactors yielded higher TN removal. Copyright © 2011 Elsevier Ltd. All rights reserved.

Alternative marine and fluvial models for the non-fossiliferous quartzitic sandstones of the Early Proterozoic Daspoort Formation, Transvaal Sequence of southern Africa

NASA Astrophysics Data System (ADS)

Eriksson, P. G.; Schreiber, U. M.; van der Neut, M.; Labuschagne, H.; Van Der Schyff, W.; Potgieter, G.

1993-04-01

This paper discusses some of the problems related to the palaeoenvironmental interpretation of non-fossiliferous, early Precambrian, recrystallised quartzitic sandstones, using the Early Proterozoic Daspoort Formation, Transvaal Sequence of southern Africa as a case study. These cross-bedded and planar stratified rocks have been interpreted previously as shallow marine deposits, based on limited studies of areas with well-exposed, relatively undeformed outcrops. This postulate rests largely on the apparently mature nature of the recrystallised sandstones and their thin bedding. Examination of outcrops throughout the preserved basin, including those which have been deformed and metamorphosed, reveals the presence of subordinate immature sandstones. Lateral facies relationships permit an alternative distal fan-fluvial braidplain model to be proposed. This is compatible with collected palaeocurrent data, thicknes trends and results of thin section petrography.

Contrasting environmental memories by ancient soils on different parent rocks in the South-western Italian Alps

NASA Astrophysics Data System (ADS)

D'Amico, Michele; Catoni, Marcella; Bonifacio, Eleonora; Zanini, Ermanno

2014-05-01

Ancient soils (pre-Holocenic paleosols and vetusols) are uncommon on the Alps, because of the extensive Pleistocenic glaciations which erased most of the previously existing soils, the slope steepness and climatic conditions favoring soil erosion. However, in few sites, particularly in the outermost sections of the Alpine range, Pleistocene glaciers covered only small and scattered surfaces because of the low altitude reached in the basins, and ancient soils could be preserved for long periods of time on particularly stable surfaces. We described and sampled soils on 11 stable surfaces in the Upper Tanaro valley, Ligurian Alps (Southwestern Piemonte, Italy). The sampling sites were characterized by low steepness and elevation between 600 to 1600 m, under present day lower montane Castanea sativa/Ostrya carpinifolia forests, montane Fagus sylvatica and Pinus uncinata forests or montane heath/grazed grassland, on different substrata. In particular, we sampled soils developed on dolomite, limestone, quartzite, gneiss and shales. The soils were always well representative of the pedogenic trends active on the respective parent materials, i.e. the skeletal fraction in each soil was always composed of just one rock type, despite the proximity of lithological boundaries and the small dimensions of the different outcrops, often coexisting on the same stable surface. All the considered profiles showed signs of extremely long pedogenesis and/or different phases of intense pedogenesis interrupted by the deposition of periglacial cover beds in the steepest sites. Up to four phases of intense pedogenesis were recognized where cover beds were developed, presumably during cold Pleistocene phases, as present-day climate is not cold enough to create such periglacial morphologies. In such cases, each cover bed underwent similar pedogenesis, strongly dependent on the parent material: on quartzite, podzols with thick E horizons and well developed placic ones were formed in all phases except the most superficial one (i.e., Holocene phase), where non cemented spodic horizons or weakly cemented ortstein were formed; placic horizons were never found in Holocene soils. On limestone, each cover bed separated soils with extremely hard petrocalcic horizons overlaid by argillic ones. Where no cover beds were observed, podzols with extremely thick E horizons (up to more than 2 m thick) and a very hard, very thick ortstein were formed on quartzite. Red Nitisols-like or reddish brown Luvisols were formed on limestone and dolomite, while red, extremely acidic Alisols, with or without fragipan horizons were formed on shales. Very large stone circles and other large patterned ground features, which can be interpreted as evidence of past permafrost conditions, were preserved on coarse quartzitic conglomerate. These soils represent excellent pedo-signatures of different specific past climatic or environmental conditions, as a response of different lithologies to specific soil-forming environments, which range from warm and humid climates typical of red Luvisols and Nitisols, to cool and wet climates leading to the formation of Podzols with placic or ortstein horizons, to extremely cold and dry ones characterizing permafrost sites and often associated with fragipan formation, to warm and dry leading to the cementation of petrocalcic horizons. The precise dating and interpretation of these soils are intriguing.

Performance Study of Fluidized Bed Dryer with Immersed Heater for Paddy Drying

NASA Astrophysics Data System (ADS)

Suherman, S.; Azaria, N. F.; Karami, S.

2018-03-01

This paper investigated the performance of fluidized bed dryer with immersed heater for paddy drying. The influence of drying temperature and the temperature of immersed heater on drying curve, thermal efficiency, and quality of paddy was investigated. The fixed operating conditions are drying time of 60 minutes, paddy weight of 200 grams and the air velocity of 0.4 m/s. The variables are drying temperature and the temperature immersed heater namely 50, 60, 70, 80, 90 (°C). The results show addition immersed heater will increase drying rates. No constant drying rate was found. Increasing the temperature will decrease the utilized energy. The thermal efficiency decreases with increasing temperature. The increasing temperature and use immersed heater will decrease the residual moisture content, increase damaged and yellow paddy grain, and increase red paddy grain.

Laser Beam Melting of Alumina: Effect of Absorber Additions

NASA Astrophysics Data System (ADS)

Moniz, Liliana; Colin, Christophe; Bartout, Jean-Dominique; Terki, Karim; Berger, Marie-Hélène

2018-03-01

Ceramic laser beam melting offers new manufacturing possibilities for complex refractory structures. Poor absorptivity in near infra-red wavelengths of oxide ceramics is overcome with absorber addition to ceramic powders. Absorbers affect powder bed densities and geometrical stability of melted tracks. Optimum absorber content is defined for Al2O3 by minimizing powder bed porosity, maximizing melting pool geometrical stability and limiting shrinkage. Widest stability fields are obtained with addition of 0.1 wt.% C and 0.5 wt.% β-SiC. Absorption coefficient values of Beer-Lambert law follow stability trends: they increase with C additions, whereas with β-SiC, a maximum is reached for 0.5 wt.%. Powder particle ejections are also identified. Compared to metallic materials, this ejection phenomenon can no longer be neglected when establishing a three-dimensional manufacturing strategy.

Palaeomagnetism of the Late Neoproterozoic of Ella O, North-East Greenland

NASA Astrophysics Data System (ADS)

Kilner, B.; Mac Niocaill, C.; Stouge, S.; Harper, D.

2004-12-01

Neoproterozoic to lower Ordovician sediments outcrop in a N-S trending band in the fjord region of North-East Greenland. The sequence comprises, in ascending order, the Eleonore Bay Group, the Tillite Group and the Canyon and Spiral Creek Formations. The Eleonore Bay Group is thought to be Upper Riphean in age and consists of cherty limestone and dolomite capped by red siltstone. The overlying Tillite Group contains two tillite packages separated by an intertillite which comprises marine siltstone and sandstone. The Canyon and Spiral Creek Formation consist of evaporitic red siltstone, with chert-rich horizons and some dolomite. The Spiral Creek Formation is overlain by a basal Cambrian quartzite. 500 samples were collected from the late Precambrian succession on the island of Ella O in Kong Oscars Fjord. Sampling was aimed in particular at red beds and other likely magnetic targets. The specimens were demagnetised using progressive alternating frequency and thermal techniques and typically revealed a multi-component remanence structure. A majority of the specimens carry a low stability (generally < 20mt, < 250° ) component, directed north and steeply down. This closely resembles present Earth's field. Demagnetisation of the Eleonore Bay Group reveals a high stability component directed south and shallow down, with an opposing component north and up. After tilt correction the mean direction yields a palaeolatitude of 4° . This component passes field tests, and is interpreted as primary. Magnetic characteristics in the Tillite Group are distinct from those of the Eleonore Bay Group. The Lower Tillite Formation carries an east directed shallow down component. The palaeolatitude derived from this direction indicates low latitude deposition for the glacial rocks above the Eleonore Bay Group. The Upper Tillite Formation carries a high stability component directed steeply upwards. Specimens from a limited pilot study pass reversal and fold tests, but further experiments are required to verify the result. If confirmed, this would indicate a hiatus between the lower and upper tillites. It also suggests that the Upper Tillite, which potentially correlates with the 630Ma 'snowball' Earth event, was deposited at high latitude. This would be the first confirmation that the late Neoproterozoic Marinoan glaciation extended over a broad range of latitudes.

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

Erosion Resistance Index (ERI) to Assess Surface Stability in Desert Environments

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

Hamada, Yuki; Grippo, Mark A.

2015-11-01

A new spectral index—erosion resistance index (ERI)—was developed to assess erosion risks in desert landscapes. The index was developed by applying trigonometry to the combination of the green/red band-ratio and the red/near infrared band-ratio from very high spatial resolution imagery. The resultant ERI maps showed spatially cohesive distributions of high and low index values across the study areas. High index values were observed over areas that were resistant to erosion (such as desert pavement and dense vegetation), while low index values overlapped with areas likely dominated by loose sandy soils, such as stream beds and access roads. Although further investigationmore » is warranted, this new index, ERI, shows promise for the assessment of erosion risks in desert regions.« less

Potential nitrification and denitrification and the corresponding composition of the bacterial communities in a compact constructed wetland treating landfill leachates.

PubMed

Sundberg, C; Tonderski, K; Lindgren, P E

2007-01-01

Constructed wetlands can be used to decrease the high ammonium concentrations in landfill leachates. We investigated nitrification/denitrification activity and the corresponding bacterial communities in landfill leachate that was treated in a compact constructed wetland, Tveta Recycling Facility, Sweden. Samples were collected at three depths in a filter bed and the sediment from a connected open pond in July, September and November 2004. Potential ammonia oxidation was measured by short-term incubation method and potential denitrification by the acetylene inhibition technique. The ammonia-oxidising and the denitrifying bacterial communities were investigated using group-specific PCR primers targeting 16S rRNA genes and the functional gene nosZ, respectively. PCR products were analysed by denaturing gradient gel electrophoresis and nucleotide sequencing. The same degree of nitrification activity was observed in the pond sediment and at all levels in the filter bed, whereas the denitrification activity decreased with filter bed depth. Denitrification rates were higher in the open pond, even though the denitrifying bacterial community was more diverse in the filter bed. The ammonia-oxidising community was also more varied in the filter bed. In the filter bed and the open pond, there was no obvious relationship between the nitrification/denitrification activities and the composition of the corresponding bacterial communities.

Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes.

PubMed

Kumar, Vikas; Kutschera, Verena E; Nilsson, Maria A; Janke, Axel

2015-08-07

The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method

PubMed Central

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the ‘Mantianhong’ and ‘Hongxiangsu’ red-skinned cultivars. The ‘Dangshansuli’ cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit. PMID:29118994

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

PubMed

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars. The 'Dangshansuli' cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit.

In search of Nemesis

NASA Technical Reports Server (NTRS)

Carlson, S.; Culler, T.; Muller, R. A.; Tetreault, M.; Perlmutter, S.

1994-01-01

The parallax of all stars of visual magnitude greater than about 6.5 has already been measured. If Nemesis is a main-sequence star 1 parsec away, this requires Nemesis's mass to be less than about 0.4 solar masses. If it were less than about 0.05 solar masses its gravity would be too weak to trigger a comet storm. If Nemesis is on the main sequence, this mass range requires it to be a red dwarf. A red dwarf companion would probably have been missed by standard astronomical surveys. Nearby stars are usually found because they are bright or have high proper motion. However, Nemesis's proper motion would now be 0.01 arcsec/yr, and if it is a red dwarf its magnitude is about 10 - too dim to attract attention. Unfortunately, standard four-color photometry does not distinguish between red dwarfs and giants. So although surveys such as the Dearborn Red Star Catalog list stars by magnitude and spectral type, they do not identify the dwarfs. Every star of the correct spectral type and magnitude must be scrutinized. Our candidate list is a hybrid; candidate red stars are identified in the astrometrically poor Dearborn Red Star Catalog and their positions are corrected using the Hubble Guide Star Catalog. When errors in the Dearborn catalog make it impossible to identify the corresponding Hubble star, the fields are split so that we have one centering on each possible candidate. We are currently scrutinizing 3098 fields, which we believe contain all possible red dwarf candidates in the northern hemisphere. Since our last report the analysis and database software has been completely rebuilt to take advantage of updated hardware, to make the data more accessible, and to implement improved methods of data analysis. The software is now completed and we are eliminating stars every clear night.

Bedload transport over run-of-river dams, Delaware, U.S.A.

NASA Astrophysics Data System (ADS)

Pearson, Adam J.; Pizzuto, Jim

2015-11-01

We document the detailed morphology and bed sediment size distribution of a stream channel upstream and downstream of a 200-year-old run-of-river dam on the Red Clay Creek, a fifth order stream in the Piedmont of northern Delaware, and combine these data with HEC-RAS modeling and bedload transport computations. We hypothesize that coarse bed material can be carried through run-of-river impoundments before they completely fill with sediment, and we explore mechanisms to facilitate this transport. Only 25% of the accommodation space in our study site is filled with sediment, and maximum water depths are approximately equal to the dam height. All grain-size fractions present upstream of the impoundment are also present throughout the impoundment. A characteristic coarse-grained sloping ramp leads from the floor of the impoundment to the crest of the dam. A 2.3-m-deep plunge pool has been excavated below the dam, followed immediately downstream by a mid-channel bar composed of coarse bed material similar in size distribution to the bed material of the impoundment. The mid-channel bar stores 1472 m3 of sediment, exceeding the volume excavated from the plunge pool by a factor of 2.8. These field observations are typical of five other sites nearby and suggest that all bed material grain-size fractions supplied from upstream can be transported through the impoundment, up the sloping ramp, and over the top of the dam. Sediment transport computations suggest that all grain sizes are in transport upstream and within the impoundment at all discharges with return periods from 1 to 50 years. Our computations suggest that transport of coarse bed material through the impoundment is facilitated by its smooth, sandy bed. Model results suggest that the impoundment is currently aggrading at 0.26 m/year, but bed elevations may be recovering after recent scour from a series of large floods during water year 2011-2012. We propose that impoundments upstream of these run-of-river dams behave as long pools that adjust their bed elevation and texture to transport the load supplied by the watershed, rather than as impounded reservoirs with little bed material transport capacity. Scour may only occur during episodic high flows, followed by aggradation during periods of low flow.

Identification of Multiple Novel Viruses, Including a Parvovirus and a Hepevirus, in Feces of Red Foxes

PubMed Central

van der Giessen, Joke; Haagmans, Bart L.; Osterhaus, Albert D. M. E.; Smits, Saskia L.

2013-01-01

Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified. PMID:23616657

Characterization of Novel Simian Immunodeficiency Viruses from Red-Capped Mangabeys from Nigeria (SIVrcmNG409 and -NG411)

PubMed Central

Beer, Brigitte E.; Foley, Brian T.; Kuiken, Carla L.; Tooze, Zena; Goeken, Robert M.; Brown, Charles R.; Hu, Jinjie; Claire, Marisa St.; Korber, Bette T.; Hirsch, Vanessa M.

2001-01-01

Two novel simian immunodeficiency virus (SIV) strains from wild-caught red-capped mangabeys (Cercocebus torquatus torquatus) from Nigeria were characterized. Sequence analysis of the fully sequenced SIV strain rcmNG411 (SIVrcmNG411) and gag and pol sequence of SIVrcmNG409 revealed that they were genetically most closely related to the recently characterized SIVrcm from Gabon (SIVrcmGB1). Thus, red-capped mangabeys from distant geographic locations harbor a common lineage of SIV. SIVrcmNG411 carried a vpx gene in addition to vpr, suggesting a common evolutionary ancestor with SIVsm (from sooty mangabeys). However, SIVrcm was only marginally closer to SIVsm in that region than to any of the other lentiviruses. SIVrcm showed the highest similarity in pol with SIVdrl, isolated from a drill, a primate that is phylogenetically distinct from mangabey monkeys, and clustered with other primate lentiviruses (primarily SIVcpz [from chimpanzees] and SIVagmSab [from African green monkeys]) discordantly in different regions of the genome, suggesting a history of recombination. Despite the genetic relationship to SIVcpz in the pol gene, SIVrcmNG411 did not replicate in chimpanzee peripheral blood mononuclear cells (PBMC), although two other viruses unrelated to SIVcpz, SIVmndGB1 (from mandrills) and SIVlhoest (from L'Hoest monkeys), were able to grow in chimpanzee PBMC. The CCR5 24-bp deletion previously described in red-capped mangabeys from Gabon was also observed in Nigerian red-capped mangabeys, and SIVrcmNG411, like SIVrcmGB1, used CCR2B and STRL33 as coreceptors for virus entry. SIVrcm, SIVsm, SIVmndGB1, and all four SIVlhoest isolates but not SIVsun (from sun-tailed monkeys) replicated efficiently in human PBMC, suggesting that the ability to infect the human host can vary within one lineage. PMID:11711592

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.

Light regulation of the abundance of mRNA encoding a nucleolin-like protein localized in the nucleoli of pea nuclei.

PubMed Central

Tong, C G; Reichler, S; Blumenthal, S; Balk, J; Hsieh, H L; Roux, S J

1997-01-01

A cDNA encoding a nucleolar protein was selected from a pea (Pisum sativum) plumule library, cloned, and sequenced. The translated sequence of the cDNA has significant percent identity to Xenopus laevis nucleolin (31%), the alfalfa (Medicago sativa) nucleolin homolog (66%), and the yeast (Saccharomyces cerevisiae) nucleolin homolog (NSR1) (28%). It also has sequence patterns in its primary structure that are characteristic of all nucleolins, including an N-terminal acidic motif, RNA recognition motifs, and a C-terminal Gly- and Arg-rich domain. By immunoblot analysis, the polyclonal antibodies used to select the cDNA bind selectively to a 90-kD protein in purified pea nuclei and nucleoli and to an 88-kD protein in extracts of Escherichia coli expressing the cDNA. In immunolocalization assays of pea plumule cells, the antibodies stained primarily a region surrounding the fibrillar center of nucleoli, where animal nucleolins are typically found. Southern analysis indicated that the pea nucleolin-like protein is encoded by a single gene, and northern analysis showed that the labeled cDNA binds to a single band of RNA, approximately the same size and the cDNA. After irradiation of etiolated pea seedlings by red light, the mRNA level in plumules decreased during the 1st hour and then increased to a peak of six times the 0-h level at 12 h. Far-red light reversed this effect of red light, and the mRNA accumulation from red/far-red light irradiation was equal to that found in the dark control. This indicates that phytochrome may regulate the expression of this gene. PMID:9193096

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

Stochastic environmental fluctuations drive epidemiology in experimental host–parasite metapopulations

PubMed Central

Duncan, Alison B.; Gonzalez, Andrew; Kaltz, Oliver

2013-01-01

Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5°C) and permissive (23°C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645

The Red Spiral Galaxy UGC11680: Clues for the Inside-Out Quenching.

NASA Astrophysics Data System (ADS)

Bárcenas, J.; Sanchez, S. F.

2016-06-01

Broadly, galaxies can be divided in two groups, thanks to the Color-Magnitude Diagram: the lively star formation ones, ``The blue Cloud'' and galaxies which halted their star formation, ``The Red Sequence''. It is a currently accepted that the galaxies start their lifespan as a blue objects, turning red when they stop to assembly more mass and thus more stars. Nevertheless, This change need to be quick (˜ 1 Gyr), due to the dearth of galaxies between this two populations (the so called ``green valley'').Previous works have found two distinct stellar mass assembly modes, they are termed as ``the inside-out'' and ``the outside-in'' growth scenarios in the literature. In the ``inside-out'' scenario, mass assembly is finished in the galactic central region. In some cases, the inflow gas can fuel the central SuperMassive BlackHole. The subsequent AGN feedback will then shut-off the central star formation. One possible case of this scenario is the galaxy UGC11680, an unusual face-on red spiral galaxy with an AGN type 2, at the red sequence belonging to the CALIFA survey. We used the so called fossil method to study its star formation history and try to understand what happened to its stellar populations.

Outbreak and genotyping of canine distemper virus in captive Siberian tigers and red pandas.

PubMed

Zhang, He; Shan, Fen; Zhou, Xia; Li, Bing; Zhai, Jun-Qiong; Zou, Shu-Zhan; Wu, Meng-Fan; Chen, Wu; Zhai, Shao-Lun; Luo, Man-Lin

2017-08-15

In this study, four canine distemper virus (CDV) strains were isolated from captive Siberian tigers (Panthera tigris altaica) and red pandas (Ailurus fulgens) during two separate CDV outbreaks in a zoo in Guangdong province, China. Sequence alignment and phylogenetic analyses based on the full-length hemagglutinin (H) and fusion (F) genes showed that they were closely identical to genotype Asia-1. Prior to confirmation of CDV in Siberian tigers, to control spread of the disease, a live attenuated combination CDV vaccine was used among almost all carnivore animals except for red pandas in which another recombinant combination CDV vaccine was used. However, about two months later, CDV re-emerged and caused the death among red pandas. Based on the vaccination records, the live combination vaccine could be considered an ideal weapon against CDV in zoo carnivore animals. Although the recombinant combination CDV vaccine was safe for red pandas, its protection effectiveness remains to be further investigated. Moreover, according to the outbreak interval time and sequence characterization, we suspected that stray cats circulating in the zoo were the intermediate host, which contributed to CDV spread from stray dogs to zoo animals. This study revealed the importance of vaccination and biosecurity for zoo animals.

[Correlation between adenylosuccinate lyase (ADSL) gene polymorphism and inosine monophosphate acid (IMP) content in domestic fowl and genetic relationship between red jungle fowl and domestic fowl].

PubMed

Shu, Jing-Ting; Bao, Wen-Bin; Zhang, Hong-Xia; Zhang, Xue-Yu; Ji, Cong-Liang; Chen, Guo-Hong

2007-03-01

This study investigates single nucleotide polymorphism (SNP) of the adenylosuccinate lyase(ADSL) gene in variety chicken breeds, including Recessive White chickens, Silkies chickens, Baier chickens, Tibetan chickens and two red jungle fowls. Primers for exon 2 in ADSL gene were designed based on the chicken genomic sequence and a SNP(C/T at 3484) was detected by PCR-SSCP and DNA sequencing. Three genotypes within all breeds were found and least square analysis showed that TT genotype birds had a significant higher inosine monophosphate acid (IMP) content than TC (P < 0.01) and CC (P < 0.05) genotype birds, TC genotype birds had a little higher IMP content than CC genotype birds, but the difference was not significant. We proposed this SNP site correlated with IMP content in chickens. A neighbour-joining dendrogram was constructed based on the Nei's genentic distance. The genetic relationship between Chinese red jungle fowl and Tibetan chickens was the nearest, whereas Baier chickens were more closer to Silkies chickens. The Chinese red jungle fowls were relatively closer to the domestic fowls, whereas Thailand red jungle fowls were relatively diverging to the Chinese native breeds. These results supported the theory concerning the independent origins of Chinese native fowl breeds.

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.

PubMed

Al-Amoudi, Soha; Essack, Magbubah; Simões, Marta F; Bougouffa, Salim; Soloviev, Irina; Archer, John A C; Lafi, Feras F; Bajic, Vladimir B

2016-09-10

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

Permo Triassic unconformity-related Au-Pd mineralisation, South Devon, UK: new insights and the European perspective

NASA Astrophysics Data System (ADS)

Shepherd, Tom J.; Bouch, Jon E.; Gunn, Andrew G.; McKervey, John A.; Naden, Jonathan; Scrivener, Richard C.; Styles, Michael T.; Large, Duncan E.

2005-07-01

An integrated mineralogical-geochemical study of unconformity-related Au-Pd occurrences within and around the Permo Triassic basins of southwest England, UK, has confirmed the importance of low temperature (86±13°C), hydrothermal carbonate veins as hosts for the mineralisation. Fluid inclusion data for the carbonate gangue, supported by stable isotope (13C and 18O) and radiogenic (87Sr/86Sr) data, have identified three principal fluids: (1) a reducing calcic brine [>25 wt% salinity, <0.5 NaCl/(NaCl+CaCl2)] originating in the sub-unconformity basement and an expression of advanced mineral fluid interaction; (2) an oxidising sodic brine [~16 wt% salinity, >0.9 NaCl/(NaCl+CaCl2)] originating in the post-unconformity red beds under evaporitic conditions, and (3) an oxygenated, low salinity groundwater (<3 wt% salinity). The sodic brine is reasoned to be the parent metalliferous fluid and to have acquired its enrichment in Au and Pd by the leaching of immature sediments and intra-rift volcanic rocks within the local Permo Triassic basins. Metal precipitation is linked to the destabilisation of Au and Pd chloride complexes by either mixing with calcic brines, dilution by groundwaters or interaction with reduced lithologies. This explains the diversity of mineralised settings below and above the unconformity and their affinity with red bed brines. The paucity of sulphide minerals, the development of selenides (as ore minerals and as mineral inclusion in gold grains), the presence of rhodochrosite and manganoan calcites (up to 2.5 wt% Mn in calcite) and the co-precipitation of hematite and manganese oxides are consistent with the overall high oxidation state of the ore fluids. A genetic model is proposed linking Permo Triassic red beds, the mixing of oxidising and reducing brines, and the development of unconformity-related precious metal mineralisation. Comparison with other European Permo Triassic basins reveals striking similarities in geological setting, mineralogy and geochemistry with Au, Au-Pd and selenide occurrences in Germany (Tilkerode, Korbach-Goldhausen), Poland (Lubin) and the Czech Republic (Svoboda nad Úpou and Stupná). Though the known Au-Pd occurrences are sub-economic, several predictive criteria are proposed for further exploration.

Red Misfits in the Sloan Digital Sky Survey: properties of star-forming red galaxies

NASA Astrophysics Data System (ADS)

Evans, Fraser A.; Parker, Laura C.; Roberts, Ian D.

2018-06-01

We study Red Misfits, a population of red, star-forming galaxies in the local Universe. We classify galaxies based on inclination-corrected optical colours and specific star formation rates derived from the Sloan Digital Sky Survey Data Release 7. Although the majority of blue galaxies are star-forming and most red galaxies exhibit little to no ongoing star formation, a small but significant population of galaxies (˜11 per cent at all stellar masses) are classified as red in colour yet actively star-forming. We explore a number of properties of these galaxies and demonstrate that Red Misfits are not simply dusty or highly inclined blue cloud galaxies or quiescent red galaxies with poorly constrained star formation. The proportion of Red Misfits is nearly independent of environment, and this population exhibits both intermediate morphologies and an enhanced likelihood of hosting an active galactic nucleus. We conclude that Red Misfits are a transition population, gradually quenching on their way to the red sequence and this quenching is dominated by internal processes rather than environmentally driven processes. We discuss the connection between Red Misfits and other transition galaxy populations, namely S0s, red spirals, and green valley galaxies.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

PubMed

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Linear Test Bed. Volume 2: Test Bed No. 2. [linear aerospike test bed for thrust vector control

NASA Technical Reports Server (NTRS)

1974-01-01

Test bed No. 2 consists of 10 combustors welded in banks of 5 to 2 symmetrical tubular nozzle assemblies, an upper stationary thrust frame, a lower thrust frame which can be hinged, a power package, a triaxial combustion wave ignition system, a pneumatic control system, pneumatically actuated propellant valves, a purge and drain system, and an electrical control system. The power package consists of the Mark 29-F fuel turbopump, the Mark 29-0 oxidizer turbopump, a gas generator assembly, and propellant ducting. The system, designated as a linear aerospike system, was designed to demonstrate the feasibility of the concept and to explore technology related to thrust vector control, thrust vector optimization, improved sequencing and control, and advanced ignition systems. The propellants are liquid oxygen/liquid hydrogen. The system was designed to operate at 1200-psia chamber pressure at an engine mixture ratio of 5.5. With 10 combustors, the sea level thrust is 95,000 pounds.

Eukaryotic algal phytochromes span the visible spectrum

PubMed Central

Rockwell, Nathan C.; Duanmu, Deqiang; Martin, Shelley S.; Bachy, Charles; Price, Dana C.; Bhattacharya, Debashish; Worden, Alexandra Z.; Lagarias, J. Clark

2014-01-01

Plant phytochromes are photoswitchable red/far-red photoreceptors that allow competition with neighboring plants for photosynthetically active red light. In aquatic environments, red and far-red light are rapidly attenuated with depth; therefore, photosynthetic species must use shorter wavelengths of light. Nevertheless, phytochrome-related proteins are found in recently sequenced genomes of many eukaryotic algae from aquatic environments. We examined the photosensory properties of seven phytochromes from diverse algae: four prasinophyte (green algal) species, the heterokont (brown algal) Ectocarpus siliculosus, and two glaucophyte species. We demonstrate that algal phytochromes are not limited to red and far-red responses. Instead, different algal phytochromes can sense orange, green, and even blue light. Characterization of these previously undescribed photosensors using CD spectroscopy supports a structurally heterogeneous chromophore in the far-red–absorbing photostate. Our study thus demonstrates that extensive spectral tuning of phytochromes has evolved in phylogenetically distinct lineages of aquatic photosynthetic eukaryotes. PMID:24567382

M dwarf spectra from 0.6 to 1.5 micron - A spectral sequence, model atmosphere fitting, and the temperature scale

NASA Technical Reports Server (NTRS)

Kirkpatrick, J. D.; Kelly, Douglas M.; Rieke, George H.; Liebert, James; Allard, France; Wehrse, Rainer

1993-01-01

Red/infrared (0.6-1.5 micron) spectra are presented for a sequence of well-studied M dwarfs ranging from M2 through M9. A variety of temperature-sensitive features useful for spectral classification are identified. Using these features, the spectral data are compared to recent theoretical models, from which a temperature scale is assigned. The red portion of the model spectra provide reasonably good fits for dwarfs earlier than M6. For layer types, the infrared region provides a more reliable fit to the observations. In each case, the wavelength region used includes the broad peak of the energy distribution. For a given spectral type, the derived temperature sequence assigns higher temperatures than have earlier studies - the difference becoming more pronounced at lower luminosities. The positions of M dwarfs on the H-R diagram are, as a result, in closer agreement with theoretical tracks of the lower main sequence.

Characterization of short interspersed elements (SINEs) in a red alga, Porphyra yezoensis.

PubMed

Zhang, Wenbo; Lin, Xiaofei; Peddigari, Suresh; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

2007-02-01

Short interspersed element (SINE)-like sequences referred to as PySN1 and PySN2 were identified in a red alga, Porphyra yezoensis. Both elements contained an internal promoter with motifs (A box and B box) recognized by RNA polymerase III, and target site duplications at both ends. Genomic Southern blot analysis revealed that both elements were widely and abundantly distributed on the genome. 3' and 5' RACE suggested that PySN1 was expressed as a chimera transcript with flanking SINE-unrelated sequences and possessed the poly-A tail at the same position near the 3' end of PySN1.

SN 1987A - The evolution from red to blue

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

Tuchman, Y.; Wheeler, J.C.

1989-11-01

Envelope models in thermal and dynamic equilibrium are used to explore the nature of the transition of SK -69 deg 202, the progenitor of SN 1987A, from the Hayashi track to its final blue position in the H-R diagram. Loci of possible thermal equilibrium solutions are presented as a function of Teff and M(C/O), the mass of the carbon/oxygen core interior to the helium burning shell. It is found that uniform helium enrichment of the envelope results in red-blue evolution but that the resulting blue solution is much hotter than SK -69 deg 202. Solutions in which the only changemore » is to redistribute the portion of the envelope enriched in helium during main-sequence convective core contraction into a step function with Y of about 0.5 at a mass cut of about 10 solar masses give a natural transition from red to blue and a final value of Teff in agreement with observations. It is argued that SK -69 deg 202 probably fell on a post-Hayashi track sequence at moderate Teff. The possible connection of this sequence to the step distribution in the H-R diagram of the LMC. 19 refs.« less

QUENCHING STAR FORMATION AT INTERMEDIATE REDSHIFTS: DOWNSIZING OF THE MASS FLUX DENSITY IN THE GREEN VALLEY

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

Goncalves, Thiago S.; Menendez-Delmestre, Karin; Martin, D. Christopher

2012-11-01

The bimodality in galaxy properties has been observed at low and high redshifts, with a clear distinction between star-forming galaxies in the blue cloud and passively evolving objects in the red sequence; the absence of galaxies with intermediate properties indicates that the quenching of star formation and subsequent transition between populations must happen rapidly. In this paper, we present a study of over 100 transiting galaxies in the so-called green valley at intermediate redshifts (z {approx} 0.8). By using very deep spectroscopy with the DEIMOS instrument at the Keck telescope we are able to infer the star formation histories ofmore » these objects and measure the stellar mass flux density transiting from the blue cloud to the red sequence when the universe was half its current age. Our results indicate that the process happened more rapidly and for more massive galaxies in the past, suggesting a top-down scenario in which the massive end of the red sequence is forming first. This represents another aspect of downsizing, with the mass flux density moving toward smaller galaxies in recent times.« less

RADIO EMISSION FROM RED-GIANT HOT JUPITERS

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

Fujii, Yuka; Spiegel, David S.; Mroczkowski, Tony

2016-04-01

When planet-hosting stars evolve off the main sequence and go through the red-giant branch, the stars become orders of magnitudes more luminous and, at the same time, lose mass at much higher rates than their main-sequence counterparts. Accordingly, if planetary companions exist around these stars at orbital distances of a few au, they will be heated up to the level of canonical hot Jupiters and also be subjected to a dense stellar wind. Given that magnetized planets interacting with stellar winds emit radio waves, such “Red-Giant Hot Jupiters” (RGHJs) may also be candidate radio emitters. We estimate the spectral auroralmore » radio intensity of RGHJs based on the empirical relation with the stellar wind as well as a proposed scaling for planetary magnetic fields. RGHJs might be intrinsically as bright as or brighter than canonical hot Jupiters and about 100 times brighter than equivalent objects around main-sequence stars. We examine the capabilities of low-frequency radio observatories to detect this emission and find that the signal from an RGHJ may be detectable at distances up to a few hundred parsecs with the Square Kilometer Array.« less

Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.

PubMed

Speth, Daan R; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei-Yuan; Dutilh, Bas E; Jetten, Mike S M

2017-07-01

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp.

PubMed

Ye, Lihai; Zhang, Chun; Tang, Xiaojun; Chen, Yiyi; Liu, Shaojun

2017-08-08

The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs). The CDSs of the 5S rDNAs in both parental fishes were conserved, while their NTS units seemed to have been subjected to rapid evolution. The diploid hybrid 2nF 1 inherited all the types of 5S rDNAs in both progenitors and there were no signs of homeologous recombination in the 5S rDNAs of 2nF 1 by sequencing of PCR products. We obtained two segments of 5S rDNA with a total length of 16,457 bp from allotetraploid offspring 4nAT through bacterial artificial chromosome (BAC) sequencing. Using this sequence together with the 5S rDNA sequences amplified from the genomic DNA of 4nAT, we deduced that the 5S rDNAs of 4nAT might be inherited from the maternal progenitor red crucian carp. Additionally, the IPRs in the 5S rDNAs of 4nAT contained A-repeats and TA-repeats, which was not the case for the IPRs in the 5S rDNAs of 2nF 1 . We also detected two signals of a 200-bp fragment of 5S rDNA in the chromosomes of parental progenitors and hybrid progenies by fluorescence in situ hybridization (FISH). We deduced that during the evolution of 5S rDNAs in different ploidy hybrid fishes, interlocus gene conversion events and tandem repeat insertion events might occurred in the process of polyploidization. This study provided new insights into the relationship among the evolution of 5S rDNAs, hybridization and polyploidization, which were significant in clarifying the genome evolution of polyploid fish.

Geology of the Jewel Cave SW Quadrangle, Custer County, South Dakota

USGS Publications Warehouse

Braddock, William A.

1963-01-01

The Jewel Cave SW quadrangle is in the southwestern part of the Black Hills in Custer County, S. Dak., about midway between Edgemont, S. Dak., and Newcastle, Wyo. All the rocks that crop out within the quadrangle are of sedimentary origin and range in age from Pennsylvanian to Early Cretaceous. The Minnesota Formation of Pennsylvania and Permian age, which is about 1,000 feet thick, was studied in outcrop and from two diamond-drill cores. In the subsurface the upper part of the formation consists of gray sandstone, very fine grained dolomite, and anhydrite. The anhydrite has been leached from the formation near the outcrop, perhaps in the early part of the Cenozoic Era, and the resulting subsidence has produced collapse breccias in the Minnelusa and milder deformation in the overlying units. In the collapse breccias the rocks have been oxidized and are red, whereas in the subsurface they are gray. The anhydrite cement of the subsurface sandstone has been replaced by calcite, and the dolomite beds have been partially converted to limestone. The Opeche Formation of Permian age consists of 75 to 115 feet of red siltstone and shale and two thin gypsum beds. The Minnekahta Limestone of Permian age is about 40 feet thick. The Spearfish Formation of Permian and Triassic age is about 550 feet thick and consists of red siltstone red sandstone, dolomite, and gypsum. The dolomite and gypsum beds are restricted to the lower half of the formation. In the northeast corner of the quadrangle the gypsum beds have been dissolved by ground water. The Sundance Formation of Late Jurassic age is divided into five members that have a total thickness of about 360 feet. The Morrison Formation of Late Jurassic age ranges in thickness from 60 to 120 feet. It consists of blocky weathering noncarbonaceous mudstone and subordinate beds of limestone and sandstone. The Inyan Kara Group of Early Cretaceous age has been subdivided into the Lakota Formation and the Fall River Formation. The Lakota Formation consists of 200 to 300 feet of carbonaceous siltstone blocky-weathering claystone, and fine-grained to conglomeratic sandstone. These rocks were deposited in stream channels, flood plains, and ponds. The Fall River Formation is about 110 to 130 feet thick. Along the northeast side of the outcrop the formation consists of fine- to medium-grained sandstone, which forms an elongate body at least 1-1/2 miles wide and more than 25 miles long. To the southwest the formation consists of thinly stratified interbedded sandstone, carbonaceous siltstone, and varicolored mudstone. The Skull Creek and Mowry Shales of Early Cretaceous age consist of black fissile shale. The Mowry contains abundant fish scales and weathers to a silver gray. Alluvium fills the bottom of many intermittent streams, and small gravel-covered terraces mark the former high levels of these streams. Gravel, which caps hills at altitudes of 4,460 to 4,620 feet, is believed to have been deposited by a Pleistocene stream that drained southeastward toward the town of Minnekahta. Many landslides are present along the northward- and eastward-facing scarp of the Inyan Kara hogback. The Dewey fault, trending N. 75 deg E., crosses the quadrangle. It is probably a vertical dip-slip fault, and has an apparent displacement of 250 to 440 feet. Two northwest-trending anticlines are in the quadrangle - one extends from the Edgemont NE quadrangle to near the center of the Jewel Cave SW quadrangle, and the other is limited to the center of the Jewel Cave SW quadrangle. Collapse structures, which were produced by the solution of anhydrite, are (a) breccias in the Minnelusa Formation, (b) limestone-dolomite breccias in the Spearfish Formation, (c) undulations and normal faults in the formations overlying the Minnelusa and (d) breccia pipes that extend upward from the Minnelusa to at least as high as the Lakota Formation. The leaching probably occurred in early Cenozoic time. Minor deformationa

Transcriptomics of the Bed Bug (Cimex lectularius)

PubMed Central

Rajarapu, Swapna P.; Jones, Susan C.; Mittapalli, Omprakash

2011-01-01

Background Bed bugs (Cimex lectularius) are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its high-impact status, scant knowledge exists at the genomic level for C. lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance. Methodology and Principal Findings Using 454 pyrosequencing, we obtained a total of 216,419 reads with 79,596,412 bp, which were assembled into 35,646 expressed sequence tags (3902 contigs and 31744 singletons). Nearly 85.9% of the C. lectularius sequences showed similarity to insect sequences, but 44.8% of the deduced proteins of C. lectularius did not show similarity with sequences in the GenBank non-redundant database. KEGG analysis revealed putative members of several detoxification pathways involved in pesticide resistance. Lamprin domains, Protein Kinase domains, Protein Tyrosine Kinase domains and cytochrome P450 domains were among the top Pfam domains predicted for the C. lectularius sequences. An initial assessment of putative defense genes, including a cytochrome P450 and a glutathione-S-transferase (GST), revealed high transcript levels for the cytochrome P450 (CYP9) in pesticide-exposed versus pesticide-susceptible C. lectularius populations. A significant number of single nucleotide polymorphisms (296) and microsatellite loci (370) were predicted in the C. lectularius sequences. Furthermore, 59 putative sequences of Wolbachia were retrieved from the database. Conclusions To our knowledge this is the first study to elucidate the genetic makeup of C. lectularius. This pyrosequencing effort provides clues to the identification of potential detoxification genes involved in pesticide resistance of C. lectularius and lays the foundation for future functional genomics studies. PMID:21283830

Petroleum geology and resources of the Volga-Ural province, U.S.S.R.

USGS Publications Warehouse

Peterson, James A.; Clarke, James W.

1983-01-01

The Volga-Ural petroleum province is, in general, coincident with the Volga-Ural regional high, a broad upwarp of the east-central part of the Russian (East European) Platform. The central part of the province is occupied by the Tatar arch, which contains the major share of the oilfields of the province. The Komi-Perm arch forms the northeastern part of the regional high, and the Zhigulevsko-Pugachev and Orenburg arches make up the southern part. These arches are separated from one another by elongate downwarps. The platform cover overlies an Archean crystalline basement and consists of seven main sedimentation cycles. (1) Riphean (lower Bavly) continental sandstone, shale, and conglomerate beds, from 500 to 5,000 m thick, were deposited in aulacogens. (2) Vendian (upper Bavly) continental and marine shale and sandstone are up to 3,000 m thick. (3) Middle Devonian-Tournaisian transgressive deposits, which are sandstone, siltstone, and shale in the lower part and carbonates and abundant reefs in the upper part, range from 300 to 1,000 m in thickness. The upper carbonate part includes the Kamsko-Kinel trough system, which consists of narrow, interconnected, deepwater troughs. (4) The Visean-Namurian-Bashkirian cycle began with deposition of Visean clastic deposits, which draped over reefs of the previous cycle and filled in an erosional relief that had formed in some places on the sediments of the previous cycle. The Visean clastic deposits are overlain by marine carbonate beds. The cycle is from 50 to 800 m thick. (5) The lower Moscovian-Lower Permian cycle consists of 1,000 to 3,000 m of terrigenous clastic deposits and marine carbonate beds. (6) The upper Lower Permian-Upper Permian cycle reflects the maximum growth of the Ural Mountains and the associated Ural foredeep. Evaporite deposits were first laid down, followed by marine limestones and dolomites, which intertongue eastward with clastic sediments from the Ural Mountains. (7) Continental red beds of Triassic age and mixed continental and marine clastic beds of Jurassic and Cretaceous age were deposited on the western, southwestern, and northern margins of the Russian Platform; they are generally absent in the Volga-Ural province, however. Approximately 600 oilfields and gasfields and 2,000 pools have been found in the Volga-Ural province. Nine productive sequences are recognized; these are, in general, the same as the sedimentation cycles, although some subdivisions have been added. The clastic section of Middle and early Late Devonian age contains the major recoverable oil accumulations, including the supergiant Romashkino field. Cumulative production to 1980 is estimated at 30 to 35 billion barrels of oil equivalent, identified reserves at about 10 billion barrels of oil equivalent, and undiscovered resources at about 7 billion barrels of oil equivalent. Identified reserves of natural gas are estimated at 100 trillion cubic feet and undiscovered resources at 63 trillion cubic feet.

Study of Upper Miocene Oysters(Plecypoda) From the Mishan Formation in south west of Firuzabad, Fars, Iran(Zagros mountain)

NASA Astrophysics Data System (ADS)

Dehbozorgi, Mehdi; Sabouhi, Mostafa; Nabavi, Hamid

2010-05-01

The out crapes of Mishan Formation located in Aghar area(Firuzabad city) south west of Fars and 70km south west of Firuzabad. this Formation mostly consist of limestone, marly limestone and marlstone with 800m thickness. 6key beds distinctive from limestone beds are recognized in this area. this key beds are useful for local and regional correlation in Zagros mountains. the key beds from base to top are: Red algae, Bryozoa, Gastropoda and Plecypoda, Crabs and Oysters. Mishan Formation in this area is between Gachsaran F.M(Under Formation), Conformable and Aghajari F.M(Upper Formation), Conformable. With due attention to rang and distribution of the Macrofossils, 5 local assmblage biozone were recognized, that is confirming time limit from Early- Upper Miocene. this research cheked and controled a biostrom Plecypoda(Oysters) level by thickness 3- 4m. this biostrom located around 550m the base of section. Ofcurse more of this Plecypoda be assinged to order pterriodia and Genus Oyster. Along with Oysters, Pecten and Venus can be see. This biostrom made up a bioclastic shoal shallow deep in the margin of sea Miocene. This Oysters report from Mishan Formation of Firuzabad, Fars, Zagros, Iran: Ostrea virleti var. crassicostat, Ostrea virleti Desh var. persica, Ostrea digitatai Echiwald var. rohlfsi, Ostrea lamellose. Ostrea cf. biowwondeli. Master of science in Geology (Paleontology), University of Isfahan, Iran.

Comparison of Structural and Functional Ocular Outcomes Between 14- and 70 Day Bed Rest

NASA Technical Reports Server (NTRS)

Cromwell, R. L.; Taibbi, G.; Zanello, S. B.; Yarbough, P. O.; Ploutz-Snyder, R. J.; Vizzeri, G.

2016-01-01

Purpose: To compare structural and functional ocular outcomes in healthy human subjects undergoing 14- and/or 70-day head-down-tilt bed rest (HDTBR). We hypothesized the amount of HDTBR-induced ocular changes be affected by the HDTBR duration. Methods: The studies were conducted at the NASA Flight Analogs Research Unit, The University of Texas Medical Branch at Galveston, Galveston, TX. Participants were selected using NASA standard screening procedures. Standardized NASA screening procedures and bed rest conditions (e.g., strict sleep-wake cycle, standardized diet, continuous video monitoring) were implemented in both studies. Participants maintained a 6deg HDTBR position for 14 and/or 70 consecutive days and did not engage in exercise. Weekly ophthalmological examinations were conducted in the sitting (pre/post-bed rest only) and HDT positions. Ocular outcomes of interest included: near best-corrected visual acuity (BCVA); spherical equivalent, as determined by cycloplegic autorefraction; Goldmann applanation tonometry and iCare (Icare Finland Oy, Espoo, Finland) intraocular pressure (IOP) measurement; color vision; red dot test; modified Amsler grid test; confrontational visual field; stereoscopic color fundus photography; Spectralis OCT (Heidelberg Engineering, GmbH, Heidelberg, Germany) retinal nerve fiber layer thickness (RNFLT), peripapillary and macular retinal thicknesses. Mixed-effects linear models were used to compare pre- and post-HDTBR observations between 14- and 70-day HDTBR for our continuously scaled outcomes.

Evaluating De-centralised and Distributional Options for the Distributed Electronic Warfare Situation Awareness and Response Test Bed

DTIC Science & Technology

2013-12-01

effectors (deployed on ground based or aerial platforms) to detect , identify, locate, track or suppress stationary or slow moving surface based RF...ground based or aerial platforms) to detect , identify, locate, track or suppress stationary or slow moving surface based RF emitting targets. In the...Electronic Support EO Electro-Optic FPGAs Field Programmable Gate Arrays IR Infra-red LADAR Laser Detection and Ranging OSX Mac OS X; the apple

Remote sensing and extractable biological resources

NASA Technical Reports Server (NTRS)

Cronin, L. E.

1972-01-01

The nature and quantity of extractable biological resources available in the Chesapeake Bay are discussed. The application of miniaturized radio sensors to track the movement of fish and birds is described. The specific uses of remote sensors for detecting and mapping areas of algae, red tide, thermal pollution, and vegetation beds are presented. The necessity for obtaining information on the physical, chemical, and meteorological features of the entire bay in order to provide improved resources management is emphasized.

Simulation of geochemical processes responsible for the formation of the Zhezqazghan deposit

NASA Astrophysics Data System (ADS)

Ryzhenko, B. N.; Cherkasova, E. V.

2014-05-01

Physicochemical computer simulation of water-rock systems at a temperature of 25-150°C and under a pressure of up to 600 bar has been carried out for quantitative description of the mineralization formation conditions at sandstone- and shale-hosted copper deposits. The simulation is based on geological and geochemical information concerning the Zhezqazghan deposit and considers (i) a source of ore matter, (ii) composition of the fluid that transfers ore matter to the ore formation zone, and (iii) factors of ore concentration. It has been shown that extraction of copper from minerals of rocks and its accumulation in aqueous solution are optimal at a high mass ratio of rock to water (R/W > 10), Eh of +200 to -100 mV, and an obligatory content of chloride ions in the aqueous phase. The averaged ore-bearing fluid Cl95SO44//Ca50(Na + K)30Mg19 (eq %), pH ˜ 4, mineralization of up to 400 g/L, is formed by the interaction of red sandstone beds with a sedimentogenic brine (a product of metamorphism of seawater in carbonate rocks enriched in organic matter). The ore concentration proceeds in the course of cooling from 150 to 50°C during filtration of ore-bearing fluid through red sandstone beds in the rock-water system thermodynamically opened with respect to the reductive components.

The mesoproterozoic midcontinent rift system, Lake Superior region, USA

USGS Publications Warehouse

Ojakangas, R.W.; Morey, G.B.; Green, J.C.

2001-01-01

Exposures in the Lake Superior region, and associated geophysical evidence, show that a 2000 km-long rift system developed within the North American craton ??? 1109-1087 Ma, the age span of the most of the volcanic rocks. This system is characterized by immense volumes of mafic igneous rocks, mostly subaerial plateau basalts, generated in two major pulses largely by a hot mantle plume. A new ocean basin was nearly formed before rifting ceased, perhaps due to the remote effect of the Grenville continental collision to the east. Broad sagging/subsidence, combined with a system of axial half-grabens separated along the length of the rift by accommodation zones, provided conditions for the accumulation of as much as 20 km of volcanic rocks and as much as 10 km of post-rift clastic sediments, both along the rift axis and in basins flanking a central, post-volcanic horst. Pre-rift mature, quartzose sandstones imply little or no uplift prior to the onset of rift volcanism. Early post-rift red-bed sediments consist almost entirely of intrabasinally derived volcanic sediment deposited in alluvial fan to fluvial settings; the exception is one gray to black carbon-bearing lacustrine(?) unit. This early sedimentation phase was followed by broad crustal sagging and deposition of progressively more mature red-bed, fluvial sediments with an extra-basinal provenance. ?? 2001 Elsevier Science B.V. All rights reserved.

Paleo-environmental interpretation of Paleocene Sepultura Formation in type locality, Mesa La sepultura, Baja California, Mexico

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

Arzate-Hernandez, L.; Tellezduarte, M.

1988-03-01

The Sepultura Formation in its type locality consists of two major lithostratigraphic units. The basal A unit overlies the Cretaceous Rosario Formation. It consists predominantly of fine-grained, poorly consolidated sandstones; some conglomerates; and thin beds of well-consolidated lenticular fossiliferous sandstones, which show some cyclic sedimentation. The poorly consolidated sandstones contain glauconitic layers; abundant shark teeth, benthic forams, and ostracods; and sparse mollusks, brachiopods, and Ophiomorpha-like trace fossils. These faunas indicate deposition in nearshore shallow waters. The interbedded consolidated lenticular sandstones probably indicate storm-induced deposition below wave base. This mechanism is assumed to be responsible for the high concentration of fossilsmore » consisting predominantly of unworn molluscan shells, scaphopods, echinoid spines, corals, and forams. In places, the elongated shells of Turritella pachecoensis show a preferential orientation to the southwest. At the top of the unit, a poorly fossiliferous red conglomerate indicates deltaic conditions. Overlying the conglomerate is unit B which shows a change in the sedimentary environment. It consists of a calcareous shallowing upward sequence of nodular to massive algal limestone with caliche at top. The microfossils of this unit show glauconitization in places, and consist, in addition to algal fragments, of forams, microscopic mollusks, and some ostracods and calcispherules from shallow waters (less than 30 m deep).« less

Sequence stratigraphy of the lower Upper Cretaceous Elbtal Group (Saxony, Germany): new data from Middle Cenomanian-Upper Turonian outcrops and boreholes

NASA Astrophysics Data System (ADS)

Richardt, Nadine; Wilmsen, Markus

2013-04-01

The formations of the Saxonian Cretaceous have been combined in the so-called Elbtal Group. Their sedimentation took place in a terrestrial to neritic environment palaeogeographically located between the Mid-European Island (MEI) in the SW and the Lusatian Massif in the NE. The through extended from the narrow marine strait of Saxony into the broad Bohemian Cretaceous Basin (Czech Republic) further to the SE. Deposition has been dominated by marine siliciclastics that accumulated on a graded shelf with basically three main facies zones: the coarse-grained nearshore zone ("Küstensandsteinzone"), the transitional zone ("Faziesübergangszone") and the fine-grained marly offshore facies zone ("Plänerfazies"). In general, transgression proceeded in late Early Cenomanian times from the N. Relictic remains of these marine bioclastic conglomerates (Meißen Formation) only occur in the northwesternmost area of the basin around Meißen and are related to the highstand of the depositional sequence Cenomanian 3 (DS Ce 3). After a short stratigraphic gap, onlap continued in the Middle Cenomanian with the following Niederschöna Formation consisting of coarse-grained braided river deposits at the base grading via carbonaceous point-bar cycles of a meandering river system into bioturbated, partly cross-bedded estuarine sediments toward the top. These sediments record DS Ce 4 and are capped by a paleosol. Sedimentation of DS Ce 5 started with a renewed transgressional pulse initiating the Late Cenomanian. The strata consist of bioturbated, cross-bedded predominantly fine- to medium-grained quartz sandstones with some shell-rich horizons corresponding to the Oberhäslich Formation. The unconformably overlying DS Tu 1 comprises the uppermost Cenomanian Dölzschen Formation and the Lower Turonian part of the Schmilka Formation. The onset of this depositional sequence is marked by a major transgression ("plenus Transgression) drowning the remaining pre-transgression topography (onlap of Dölzschen Formation onto basement highs). The lowermost Turonian "Lohmgrund Marl" defines the base of the Schmilka Formation changing gradually into strongly bioturbated, silty Pläner and coarsening upward into moderately bioturbated, thick-bedded-massive, mainly fine-grained quartz sandstones with occasional clayey or silty layers, shell-rich horizons and sparse wood remains. After an interruption in sedimentation indicated by a root horizon or a conspicuous erosional surface, the Schmilka Formation continues with similar lithology into the early Middle Turonian. It is replaced up-section by the overlying Middle-Upper Turonian Postelwitz Formation, characterized by decreasing thickness of bedding and stronger sedimentary variability (grain size, bioturbation, glauconite and fossil content), including the intercalation of thick units of silty Pläner. The lithological variations of sandy and Pläner intervals nicely reflect the Middle-Late Turonian sea-level changes of DS Tu 2 (early Middle Turonian), DS Tu 3 (late Middle-earliest Late Turonian) and DS Tu 4 (early Late-mid-Late Turonian): Pläner units represent transgressive and highstand conditions, sand packages late highstand as well as falling and lowstand systems tracts. A major mid-Late Turonian sea-level fall is indicated in the upper Postelwitz Formation, initiating DS Tu 5 (Late Turonian) with a strongly basin-ward prograding unit of coarse-grained sandstone. The following transgression culminated in a prominent maximum flooding interval represented by the intercalation of a clayey-fine-grained regional marker bed, forming the base of the Schrammstein Formation (thick-bedded, unfossiliferous medium- to coarse-grained quartz sandstones). In conclusion, all depositional sequences of Middle Cenomanian-Late Turonian age and their bounding unconformities (sequence boundaries SB Ce 4 and 5, SB Tu 1-4) reported from coeval sections around the MEI (e. g., Münsterland Creatceous Basin, Lower Saxonian and Danubian Cretaceous) and other Cretaceous basins in the Tethyan region (e. g., Egypt) are also developed in the Saxonian Cretaceous, supporting eustatic sea-level changes as main triggers for the sequence stratigraphic architecture of the Elbtal Group.

Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

Treesearch

Preston R. Aldrich; Charles H. Michler; Weilin Sun; Jeanne Romero-Severson

2002-01-01

We provide primer sequences for 14 (GA)n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent-offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus....

Middle Pleistocene interglacial Thames--Medway deposits at Clacton-on-Sea, England: Reconsideration of the biostratigraphical and environmental context of the type Clactonian Palaeolithic industry

NASA Astrophysics Data System (ADS)

Bridgland, David R.; Field, Michael H.; Holmes, Jonathan A.; McNabb, John; Preece, Richard C.; Selby, Ian; Wymer, John J.; Boreham, Steve; Irving, Brian G.; Parfitt, Simon A.; Stuart, Anthony J.

In 1987 an archaeological investigation was undertaken during redevelopment of the erstwhile Butlin's holiday camp at Clacton-on-Sea, on the grounds that the Middle Pleistocene Clacton Channel Deposits, containing the type-Clactonian Palaeolithic industry, were known to extend beneath the site. Excavations for a storm-drain allowed sampling at points along a longitudinal traverse of the main Clacton Channel. Analysis of these samples has provided new palaeontological information, including data pertaining to the rise in relative sea level during the interglacial represented. Systematic studies of molluscs and ostracods, the latter undertaken at Clacton for the first time, have been particularly valuable. Information from the Butlin's site supplements evidence previously gathered from the West Cliff section and from other localities at Clacton. The calcareous clay ('marl') that underlies the Clacton golf course extends beneath Butlin's, where it was found to be part of the Freshwater Beds, not the Estuarine Beds, as hitherto supposed. The Clacton Estuarine Beds, restricted to the eastern end of the site, have their base just below 2 m O.D., implying that their superposition upon the Clacton Freshwater Beds occurred when relative sea level in this area was close to present ordnance datum. Correlation of the Clacton Channel Deposits with the interglacial immediately following the Anglian/Elsterian Stage appears secure; equivalence with Oxygen Isotope Stage 11 of the oceanic sequence is most probable. A borehole survey and subsequent excavation revealed a Holocene sequence of unlithified tufa and organic sediments beneath part of the site.

Red-light excitation of protoporphyrin IX fluorescence for subsurface tumor detection.

PubMed

Roberts, David W; Olson, Jonathan D; Evans, Linton T; Kolste, Kolbein K; Kanick, Stephen C; Fan, Xiaoyao; Bravo, Jaime J; Wilson, Brian C; Leblond, Frederic; Marois, Mikael; Paulsen, Keith D

2018-06-01

OBJECTIVE The objective of this study was to detect 5-aminolevulinic acid (ALA)-induced tumor fluorescence from glioma below the surface of the surgical field by using red-light illumination. METHODS To overcome the shallow tissue penetration of blue light, which maximally excites the ALA-induced fluorophore protoporphyrin IX (PpIX) but is also strongly absorbed by hemoglobin and oxyhemoglobin, a system was developed to illuminate the surgical field with red light (620-640 nm) matching a secondary, smaller absorption peak of PpIX and detecting the fluorescence emission through a 650-nm longpass filter. This wide-field spectroscopic imaging system was used in conjunction with conventional blue-light fluorescence for comparison in 29 patients undergoing craniotomy for resection of high-grade glioma, low-grade glioma, meningioma, or metastasis. RESULTS Although, as expected, red-light excitation is less sensitive to PpIX in exposed tumor, it did reveal tumor at a depth up to 5 mm below the resection bed in 22 of 24 patients who also exhibited PpIX fluorescence under blue-light excitation during the course of surgery. CONCLUSIONS Red-light excitation of tumor-associated PpIX fluorescence below the surface of the surgical field can be achieved intraoperatively and enables detection of subsurface tumor that is not visualized under conventional blue-light excitation. Clinical trial registration no.: NCT02191488 (clinicaltrials.gov).

Lower Cretaceous paleo-Vertisols and sedimentary interrelationships in stacked alluvial sequences, Utah, USA

NASA Astrophysics Data System (ADS)

Joeckel, R. M.; Ludvigson, G. A.; Kirkland, J. I.

2017-11-01

The Yellow Cat Member of the Cedar Mountain Formation in Poison Strip, Utah, USA, consists of stacked, erosionally bounded alluvial sequences dominated by massive mudstones (lithofacies Fm) with paleo-Vertisols. Sediment bodies within these sequences grade vertically and laterally into each other at pedogenic boundaries, across which color, texture, and structures (sedimentary vs. pedogenic) change. Slickensides, unfilled (sealed) cracks, carbonate-filled cracks, and deeper cracks filled with sandstone; the latter features suggest thorough desiccation during aridification. Thin sandstones (Sms) in some sequences, typically as well as laminated to massive mudstones (Flm) with which they are interbedded in some cases, are interpreted as avulsion deposits. The termini of many beds of these lithofacies curve upward, parallel to nearby pedogenic slickensides, as the features we call ;turnups.; Turnups are overlain or surrounded by paleosols, but strata sheltered underneath beds with turnups retain primary sedimentary fabrics. Turnups were produced by movement along slickensides during pedogenesis, by differential compaction alongside pre-existing gilgai microhighs, or by a combination of both. Palustrine carbonates (lithofacies C) appear only in the highest or next-highest alluvial sequences, along with a deep paleo-Vertisol that exhibits partially preserved microrelief at the base of the overlying Poison Strip Member. The attributes of the Yellow Cat Member suggest comparatively low accommodation, slow accumulation, long hiatuses in clastic sedimentation, and substantial time intervals of subaerial exposure and pedogenesis; it appears to be distinct among the members of the Cedar Mountain Formation in these respects.

The use of synthetic bedding in children. Do strategies of change influence associations with asthma?

PubMed

Behrens, Thomas; Maziak, Wasim; Weiland, Stephan K; Siebert, Edith; Rzehak, Peter; Keil, Ulrich

2005-04-01

Epidemiological data suggest in contrast to clinical recommendations a negative effect of synthetic bedding on asthma and respiratory symptoms. To assess the effects of bedding filled with synthetic material on the risk of asthma and respiratory symptoms in 6- to 7-year-old children, taking into account allergy-related change of bedding material. We analyzed data from the ISAAC Phase III cross-sectional survey (1999/2000) in Münster, Germany. Data were collected by parental report from representative school-based samples of 6- to 7-year old children (n = 3,529). We calculated prevalence ratios with 95% confidence intervals for the association between respiratory symptoms suggestive of asthma and synthetic pillows and blankets and adjusting for potential confounders. In the preliminary analyses, synthetic pillows and synthetic blankets were positively associated with the studied respiratory outcomes. For example, a high number of wheezing attacks was positively associated with synthetic pillows (PR = 4.44; 95% CI 2.84-6.94) and synthetic blankets (PR = 3.80; 95% CI 2.48-5.82). However, in the restricted analysis, excluding participants reporting allergy-related change of bedding (pillows n = 440; blankets n = 437), the positive associations disappeared for all studied outcomes. Our findings suggest that allergy-related choice of bedding is an important factor in the assessment of the relation between synthetic bedding and asthma symptoms. Ignoring those changes can lead to false-positive risk estimates. Prospective studies that allow to disentangle the temporal sequence of disease, exposure, and change of bedding should help to further clarify this issue.

Flume Experiments on the Influence of Salmon Spawning Density on Grain Stability and Bedload Transport in Gravel-bed Streams

NASA Astrophysics Data System (ADS)

Buxton, T. H.

2015-12-01

Salmon spawning in streams involves the female salmon digging a pit in the bed where she deposits eggs for fertilization before covering them with gravel excavated from the next pit upstream. Sequences of pit excavation and filling winnow fines, loosen sediment, and move bed material into a tailspill mound resembling the shape of a dune. Research suggests salmonid nests (redds) destabilize streambeds by reducing friction between loosened grains and converging flow that elevates shear stress on redd topography. However, bed stability may be enhanced by form drag from redds in clusters that lower shear stress on the granular bed, but this effect will vary with the proportion of the bed surface that is occupied by redds (P). I used simulated redds and water-worked ("unspawned") beds in a laboratory flume to evaluate these competing influences on grain stability and bedload transport rates with P=0.12, 0.34, and 0.41. Results indicate that competence (largest-grain) and reference transport rate estimates of critical conditions for particle entrainment inversely relate to P. Bedload transport increased as exponential functions of P and excess boundary shear stress. Therefore, redd form drag did not overcome the destabilizing effects of spawning. Instead, grain mobility and bedload transport increased with P because larger areas of the bed were composed of relatively loose, unstable grains and redd topography that experienced elevated shear stress. Consequently, the presence of redds in fish-bearing streams likely reduces the effects of sedimentation from landscape disturbance on stream habitats that salmon use for reproduction.

Evaluation of the uncertainty in an EBT3 film dosimetry system utilizing net optical density.

PubMed

Marroquin, Elsa Y León; Herrera González, José A; Camacho López, Miguel A; Barajas, José E Villarreal; García-Garduño, Olivia A

2016-09-08

Radiochromic film has become an important tool to verify dose distributions for intensity-modulated radiotherapy (IMRT) and quality assurance (QA) procedures. A new radiochromic film model, EBT3, has recently become available, whose composition and thickness of the sensitive layer are the same as those of previous EBT2 films. However, a matte polyester layer was added to EBT3 to prevent the formation of Newton's rings. Furthermore, the symmetrical design of EBT3 allows the user to eliminate side-orientation dependence. This film and the flatbed scanner, Epson Perfection V750, form a dosimetry system whose intrinsic characteristics were studied in this work. In addition, uncertainties associated with these intrinsic characteristics and the total uncertainty of the dosimetry system were determined. The analysis of the response of the radiochromic film (net optical density) and the fitting of the experimental data to a potential function yielded an uncertainty of 2.6%, 4.3%, and 4.1% for the red, green, and blue channels, respectively. In this work, the dosimetry system presents an uncertainty in resolving the dose of 1.8% for doses greater than 0.8 Gy and less than 6 Gy for red channel. The films irradiated between 0 and 120 Gy show differences in the response when scanned in portrait or landscape mode; less uncertainty was found when using the portrait mode. The response of the film depended on the position on the bed of the scanner, contributing an uncertainty of 2% for the red, 3% for the green, and 4.5% for the blue when placing the film around the center of the bed of scanner. Furthermore, the uniformity and reproducibility radiochromic film and reproducibility of the response of the scanner contribute less than 1% to the overall uncertainty in dose. Finally, the total dose uncertainty was 3.2%, 4.9%, and 5.2% for red, green, and blue channels, respectively. The above uncertainty values were obtained by mini-mizing the contribution to the total dose uncertainty of the film orientation and film homogeneity. © 2016 The Authors.

Evaluation of the uncertainty in an EBT3 film dosimetry system utilizing net optical density

PubMed Central

Marroquin, Elsa Y. León; Herrera González, José A.; Camacho López, Miguel A.; Barajas, José E. Villarreal

2016-01-01

Radiochromic film has become an important tool to verify dose distributions for intensity‐modulated radiotherapy (IMRT) and quality assurance (QA) procedures. A new radiochromic film model, EBT3, has recently become available, whose composition and thickness of the sensitive layer are the same as those of previous EBT2 films. However, a matte polyester layer was added to EBT3 to prevent the formation of Newton's rings. Furthermore, the symmetrical design of EBT3 allows the user to eliminate side‐orientation dependence. This film and the flatbed scanner, Epson Perfection V750, form a dosimetry system whose intrinsic characteristics were studied in this work. In addition, uncertainties associated with these intrinsic characteristics and the total uncertainty of the dosimetry system were determined. The analysis of the response of the radiochromic film (net optical density) and the fitting of the experimental data to a potential function yielded an uncertainty of 2.6%, 4.3%, and 4.1% for the red, green, and blue channels, respectively. In this work, the dosimetry system presents an uncertainty in resolving the dose of 1.8% for doses greater than 0.8 Gy and less than 6 Gy for red channel. The films irradiated between 0 and 120 Gy show differences in the response when scanned in portrait or landscape mode; less uncertainty was found when using the portrait mode. The response of the film depended on the position on the bed of the scanner, contributing an uncertainty of 2% for the red, 3% for the green, and 4.5% for the blue when placing the film around the center of the bed of scanner. Furthermore, the uniformity and reproducibility radiochromic film and reproducibility of the response of the scanner contribute less than 1% to the overall uncertainty in dose. Finally, the total dose uncertainty was 3.2%, 4.9%, and 5.2% for red, green, and blue channels, respectively. The above uncertainty values were obtained by minimizing the contribution to the total dose uncertainty of the film orientation and film homogeneity. PACS number(s): 87.53.Bn PMID:27685125

Properties of gasification-derived char and its utilization for catalytic tar reforming

NASA Astrophysics Data System (ADS)

Qian, Kezhen

Char is a low-value byproduct of biomass gasification and pyrolysis with many potential applications, such as soil amendment and the synthesis of activated carbon. The overall goal of the proposed research was to develop novel methods to use char derived from gasification for high-value applications in syngas conditioning. The first objective was to investigate effects of gasification condition and feedstock on properties of char derived from fluidized bed gasification. Results show that the surface areas of most of the char were 1--10 m 2/g and increased as the equivalence ratio increased. Char moisture and fixed carbon contents decreased while ash content increased as equivalence ratio increased. The next objective was to study the properties of sorghum and red cedar char derived from downdraft gasifier. Red cedar char contained more aliphatic carbon and o-alkyl carbon than sorghum char. Char derived from downdraft gasification had higher heating values and lower ash contents than char derived from fluidized bed gasification. The gasification reactivity of red cedar char was higher than that of sorghum char. Then, red cedar char based catalysts were developed with different preparation method to reform toluene and naphthalene as model tars. The catalyst prepared with nickel nitrate was found to be better than that with nickel acetate. The nickel particle size of catalyst impregnated with nickel nitrate was smaller than that of catalyst impregnated with nickel acetate. The particle size of catalyst impregnated with nickel acetate decreased by hydrazine reduction. The catalyst impregnated with nickel nitrate had the highest toluene removal efficiency, which was 70%--100% at 600--800 °C. The presence of naphthalene in tar reduced the catalyst efficiency. The toluene conversion was 36--99% and the naphthalene conversion was 37%--93% at 700--900 °C. Finally, effects of atmosphere and pressure on catalytic reforming of lignin-derived tars over the developed catalyst were investigated. An increase in reaction temperature led to an increase in removal of most tar components except naphthalene. High pressure promoted the catalytic conditioning of lignin tar. Hydrogen promoted the conversion of lignin into non-condensable gas.

Neuropeptidomics of the Bed Bug Cimex lectularius.

PubMed

Predel, Reinhard; Neupert, Susanne; Derst, Christian; Reinhardt, Klaus; Wegener, Christian

2018-01-05

The bed bug Cimex lectularius is a globally distributed human ectoparasite with fascinating biology. It has recently acquired resistance against a broad range of insecticides, causing a worldwide increase in bed bug infestations. The recent annotation of the bed bug genome revealed a full complement of neuropeptide and neuropeptide receptor genes in this species. With regard to the biology of C. lectularius, neuropeptide signaling is especially interesting because it regulates feeding, diuresis, digestion, as well as reproduction and also provides potential new targets for chemical control. To identify which neuropeptides are translated from the genome-predicted genes, we performed a comprehensive peptidomic analysis of the central nervous system of the bed bug. We identified in total 144 different peptides from 29 precursors, of which at least 67 likely present bioactive mature neuropeptides. C. lectularius corazonin and myosuppressin are unique and deviate considerably from the canonical insect consensus sequences. Several identified neuropeptides likely act as hormones, as evidenced by the occurrence of respective mass signals and immunoreactivity in neurohemal structures. Our data provide the most comprehensive peptidome of a Heteropteran species so far and in comparison suggest that a hematophageous life style does not require qualitative adaptations of the insect peptidome.

Hydrodynamics of larval settlement: The influence of turbulent stress events at potential recruitment sites

USGS Publications Warehouse

Crimaldi, John P.; Thompson, Janet K.; Rosman, Johanna H.; Lowe, Ryan J.; Koseff, Jeffrey R.

2002-01-01

We describe a laboratory investigation into the effect of turbulent hydrodynamic stresses on clam larvae in the settlement phase of the recruitment process. A two-component laser-Doppler anemometer (LDA) was used to measure time histories of the instantaneous turbulence structure at potential recruitment sites within reconstructed beds of the adult Asian clam, Potamocorbula amurensis. Measurements were made for two flow speeds over beds with three different clam densities and two different clam heights. We analyze the statistical effect of the turbulence on the larval flux to the bed and on the probability of successful anchoring to the substrate. It is shown that the anchoring probability depends on the nature of the instantaneous stress events rather than on mean stresses. The instantaneous turbulence structure near the bed is altered by the flow rate and the spacing and height of adult clams living in the substrate. The ability to anchor quickly is therefore extremely important, since the time sequence of episodic turbulent stress events influences larval settlement success. The probability of successful larval settlement is predicted to decrease as the spacing between adults decreases, implying that the hydrodynamics impose negative feedback on clam bed aggregation dynamics.

Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi.

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-02-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas.

PubMed

Cumbo, Fabio; Fiscon, Giulia; Ceri, Stefano; Masseroli, Marco; Weitschek, Emanuel

2017-01-03

Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion in CSV, GTF, JSON, and XML standard formats. Furthermore, TCGA2BED extends TCGA data with information extracted from other genomic databases (i.e., NCBI Entrez Gene, HGNC, UCSC, and miRBase). We also provide and maintain an automatically updated data repository with publicly available Copy Number Variation, DNA-methylation, DNA-seq, miRNA-seq, and RNA-seq (V1,V2) experimental data of TCGA converted into the BED format, and their associated clinical and biospecimen meta data in attribute-value text format. The availability of the valuable TCGA data in BED format reduces the time spent in taking advantage of them: it is possible to efficiently and effectively deal with huge amounts of cancer genomic data integratively, and to search, retrieve and extend them with additional information. The BED format facilitates the investigators allowing several knowledge discovery analyses on all tumor types in TCGA with the final aim of understanding pathological mechanisms and aiding cancer treatments.

Environmental Changes Associated With Deccan Volcanism: evidences from the red bole record

NASA Astrophysics Data System (ADS)

Nikhil, Sharma; Valentin, Sordet; Thierry, Adatte; Gerta, Keller; Eric, Font; Blair, Schoene; Kyle, Samperton; Syed, Khadri

2017-04-01

Recent studies indicate that the bulk (80%) of Deccan trap eruptions occurred over a relatively short time interval in magnetic polarity C29r. U-Pb zircon geochronology shows that the main phase-2 began 250 ky before the Cretaceous-Tertiary (KT) mass extinction and continued into the early Danian suggesting a cause-and-effect relationship. Closer to the eruption center, the lava flows are generally separated by red weathered horizons known as red boles that mark quiescent periods between basalt flows. A typical red bole begins with the fresh underlying basalt and evolves into weathered basalt, then, a layer of basalt in a rounded shape called 'bole' surrounded by clays at the top, which is overlain by the next lava flow. Red boles have increasingly attracted the attention of researchers to understand the climatic and paleoenvironmental impact of Continental Flood Basalts (CFB). Recent advances in U-Pb dating of Deccan lava flows, studies of weathering patterns and paleoclimatic information gained from multiproxy analyses of red bole beds (e.g., lithology, mineralogy, geochemistry) yield crucial evidence of environmental changes triggered by volcanic activity. Red boles consist mainly of red silty clays characterized by concentrations of immobile elements such as Al and Fe3+ ions that are typical of paleo-laterites, which probably developed during the short periods of weathering between eruptions. Clay minerals consist mostly of smectite suggesting semi-arid monsoonal conditions. At least 30 thick red bole layers are present in C29r below the KT boundary between lava flows of phase-2 that erupted over a time span of about 250 ky. The short duration exposures of these red boles are reflected in the mineralogical and geochemical data that indicate rapid weathering (high CIA) linked to increasing acid rains. ∂D and ∂18O measured on smectite clays from the red boles approximate the meteoric water composition that prevailed during Deccan eruptions. Isotopic data from red boles deposited through the main phase-2 suggest significant and rapid changes in rainfall intensity and/or altitude linked to the accumulation of a 3100m thick basalt pile that erupted over a short period of time.

Phanerozoic Rifting Phases And Mineral Deposits

NASA Astrophysics Data System (ADS)

Hassaan, Mahmoud

2016-04-01

In North Africa occur Mediterranean and Red Sea metallogenic provinces. In each province distribute 47 iron- manganese- barite and lead-zinc deposits with tectonic-structural control. The author presents in this paper aspects of position of these deposits in the two provinces with Phanerozoic rifting . The Mediterranean Province belongs to two epochs, Hercynian and Alpine. The Hercynian Epoch manganese deposits in only Moroccoa- Algeria belong to Paleozoic tectonic zones and Proterozoic volcanics. The Alpine Epoch iron-manganese deposits are of post-orogenic exhalative-sedimentary origin. Manganese deposits in southern Morocco occur in Kabil-Rief quartz-chalcedony veins controlled by faults in andesitic sheets and in bedded pelitic tuffs, strata-form lenses and ore veins, in Precambrian schist and in Triassic and Cretaceous dolomites. Disseminated manganese with quartz and barite and effusive hydrothermal veins are hosted in Paleocene volcanics. Manganese deposits in Algeria are limited and unrecorded in Tunisia. Strata-form iron deposits in Atlas Heights are widespread in sub-rift zone among Jurassic sediments inter-bedding volcanic rocks. In Algeria, Group Beni-Saf iron deposits are localized along the Mediterranean coast in terrigenous and carbonate rocks of Jurassic, Cretaceous and Eocene age within faults and bedding planes. In Morocco strata-form hydrothermal lead-zinc deposits occur in contact zone of Tertiary andesite inter-bedding Cambrian shale, Lias dolomites and Eocene andesite. In both Algeria and Tunisia metasomatic Pb-Zn veins occur in Campanian - Maastrichtian carbonates, Triassic breccia, Jurassic limestone, Paleocene sandstones and limestone and Neogene conglomerates and sandstones. The Red Sea metallogenic province belongs to the Late Tertiary-Miocene times. In Wadi Araba hydrothermal iron-manganese deposits occur in Cretaceous sediments within 320°and 310 NW faults related to Tertiary basalt. Um-Bogma iron-manganese deposits are closely connected with NW,WNW and N-S faults genetically related to volcano-hydrothermal activity associated the Red Sea rifting. At Sherm EL-Sheikh hydrothermal manganese deposit occurs in Oligocene clastics within fault zone. Four iron-manganese-barite mineralization in Esh-Elmellaha plateau are controlled by faults trending NW,NE and nearly E-W intersecting Miocene carbonate rocks. Barite exists disseminated in the ores and as a vein in NW fault. In Shalatee - Halaib district 24 manganese deposits and barite veins with sulphide patches occur within Miocene carbonates distributed along two NW fault planes,trending 240°and 310° and occur in granite and basalt . Uranium -lead-zinc sulfide mineralization occur in Late Proterozoic granite, Late Cretaceous sandstones, and chiefly in Miocene clastic-carbonate-evaporate rocks. The occurrences of uranium- lead-zinc and iron-manganese-barite mineralization have the characteristic features of hypogene cavity filling and replacement deposits correlated with Miocene- Recent Aden volcanic rocks rifting. In western Saudi Arabia barite-lead-zinc mineralization occurs at Lat. 25° 45' and 25° 50'N hosted by Tertiary sediments in limestone nearby basaltic flows and NE-SW fault system. The mineralized hot brines in the Red Sea deeps considered by the author a part of this province. The author considers the constant rifting phases of Pangea and then progressive fragmentation of Western Gondwana during the Late Carboniferous-Lias, Late Jurassic-Early Aptian, Late Aptian - Albian and Late Eocene-Early Miocene and Oligocene-Miocene, responsible for formation of the mineral deposits constituting the M provinces. During these events, rifting, magmatism and hydrothermal activities took place in different peri-continental margins.

Whence the red panda?

PubMed

Flynn, J J; Nedbal, M A; Dragoo, J W; Honeycutt, R L

2000-11-01

The evolutionary history of the red panda (Ailurus fulgens) plays a pivotal role in the higher-level phylogeny of the "bear-like" arctoid carnivoran mammals. Characters from morphology and molecules have provided inconsistent evidence for placement of the red panda. Whereas it certainly is an arctoid, there has been major controversy about whether it should be placed with the bears (ursids), ursids plus pinnipeds (seals, sea lions, walrus), raccoons (procyonids), musteloids (raccoons plus weasels, skunks, otters, and badgers [mustelids]), or as a monotypic lineage of uncertain phylogenetic affinities. Nucleotide sequence data from three mitochondrial genes and one nuclear intron were analyzed, with more complete taxonomic sampling of relevant taxa (arctoids) than previously available in analyses of primary molecular data, to clarify the phylogenetic relationships of the red panda to other arctoid carnivorans. This study provides detailed phylogenetic analyses (both parsimony and maximum-likelihood) of primary character data for arctoid carnivorans, including bootstrap and decay indices for all arctoid nodes, and three statistical tests of alternative phylogenetic hypotheses for the placement of the red panda. Combined phylogenetic analyses reject the hypotheses that the red panda is most closely related to the bears (ursids) or to the raccoons (procyonids). Rather, evidence from nucleotide sequences strongly support placement of the red panda within a broad Musteloidea (sensu lato) clade, including three major lineages (the red panda, the skunks [mephitids], and a clearly monophyletic clade of procyonids plus mustelids [sensu stricto, excluding skunks]). Within the Musteloidea, interrelationships of the three major lineages are unclear and probably are best considered an unresolved trichotomy. These data provide compelling evidence for the relationships of the red panda and demonstrate that small taxonomic sample sizes can result in misleading or possibly erroneous (based on prior modeling, as well as conflict between the results of our analyses of less and more complete data sets) conclusions about phylogenetic relationships and taxonomy. Copyright 2000 Academic Press.

Multigene panel next generation sequencing in a patient with cherry red macular spot: Identification of two novel mutations in NEU1 gene causing sialidosis type I associated with mild to unspecific biochemical and enzymatic findings.

PubMed

Mütze, Ulrike; Bürger, Friederike; Hoffmann, Jessica; Tegetmeyer, Helmut; Heichel, Jens; Nickel, Petra; Lemke, Johannes R; Syrbe, Steffen; Beblo, Skadi

2017-03-01

Lysosomal storage diseases (LSD) often manifest with cherry red macular spots. Diagnosis is based on clinical features and specific biochemical and enzymatic patterns. In uncertain cases, genetic testing with next generation sequencing can establish a diagnosis, especially in milder or atypical phenotypes. We report on the diagnostic work-up in a boy with sialidosis type I, presenting initially with marked cherry red macular spots but non-specific urinary oligosaccharide patterns and unusually mild excretion of bound sialic acid. Biochemical, enzymatic and genetic tests were performed in the patient. The clinical and electrophysiological data was reviewed and a genotype-phenotype analysis was performed. In addition a systematic literature review was carried out. Cherry red macular spots were first noted at 6 years of age after routine screening myopia. Physical examination, psychometric testing, laboratory investigations as well as cerebral MRI were unremarkable at 9 years of age. So far no clinical myoclonic seizures occurred, but EEG displays generalized epileptic discharges and visual evoked potentials are prolonged bilaterally. Urine thin layer chromatography showed an oligosaccharide pattern compatible with different LSD including sialidosis, galactosialidosis, GM1 gangliosidosis or mucopolysaccharidosis type IV B. Urinary bound sialic acid excretion was mildly elevated in spontaneous and 24 h urine samples. In cultured fibroblasts, α-sialidase activity was markedly decreased to < 1%; however, bound and free sialic acid were within normal range. Diagnosis was eventually established by multigene panel next generation sequencing of genes associated to LSD, identifying two novel, compound heterozygous variants in NEU1 gene (c.699C > A, p.S233R in exon 4 and c.803A > G; p.Y268C in Exon 5 in NEU1 transcript NM_000434.3), leading to amino acid changes predicted to impair protein function. Sialidosis should be suspected in patients with cherry red macular spots, even with non-significant urinary sialic acid excretion. Multigene panel next generation sequencing can establish a definite diagnosis, allowing for counseling of the patient and family.

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.

An enigmatic source of hematitic carbonate beds containing vast amounts of iron oxidizers in a paleozoic metamorphic complex, South Hungary, Geresd-Hills, Ófalu.

NASA Astrophysics Data System (ADS)

Jáger, Viktor; Dabi, Gergely; Menyhárt, Adrienn

2013-04-01

Near the village of Ófalu, in the Geresd Hills, South Hungary, within the "Mecsekalja tectonic belt", low and intermediate grade paleozoic metamorphic complex (phyllite, gneiss) contains vein-like hematitic carbonate beds, up to 30 cm in thickness. The carbonate mineral is calcite. These hematitic carbonate beds cross-cut the foliation of the phyllite, and show no signs of any metamorphic alteration. In the studied section the red carbonate beds are associated with a vein system filled with multiple generations of vein carbonates(Dabi et al., 2011). The red carbonate beds contain a vaste number of twisted stalks of the iron oxidizing taxon of Gallionella. Rarely in some siliceous parts, Leptothrix-like microbial fossils can be found and these beds also contain numerous unidentifiable, hematitic foraminifers. According to ICP-AES measurements, the hematitic carbonate beds contains 8 % Fe, 0.86 % Mn and 0.12 % Ba. XRD and Raman measurements proved that the iron phase is hematite. The SEM observations revealed that the bacterial microfossils and foraminifers are built up of micron-submicron sized pseudohexagonal platy hematite. The bacterial microfossils of the Gallionella iron oxidizer are very well preserved and reaches about 80 µm length and about 2-3 µm width. The above observations raise the following issues: 1. how did these non metamorphic hematitic-carbonatic beds get inside into the metamorphic complex?, 2. what is the age of the formation of these beds?, and 3. what was the source of the iron? If we consider that the hematitic beds contain foraminifers and iron oxidizing bacteria, and no signs of metamorphic alteration nor foliations can be observed in these beds, the only answer for the first question is that the formations are fractures filled with lime-mud, i.e. neptunian dykes, which penetrated into the cracks of the phyllite. The presence of foraminifers and the geotectonic situation of the unit imply marine origin. Considering that these beds are neptunian dykes, their age must be younger than the paleozoic metamorphic event. They must be older than the Early Cretaceous dyke emplacement in the region, based on cross-cutting relation with limonite stained calcite veins, related to the volcanic activity (Dabi et al., 2011) In this region (Tisza-megaunit) continental rift-related alkali basaltic submarine volcanism was widespread during the Early Cretaceous epoch, when hypabyssal basaltic bodies (intrusive pillow basalts) intruded into unconsolidated sediments. Along these magmatic bodies low temperature hydrothermal circulation of seawater hydrolyzed basaltic glass and mafic minerals, and huge amount of Fe(II) was released and got into the lime mud that was saturated with anaerobic water, where iron oxidizing microorganisms thrived (Jáger et al., 2012).We propose a very similar paleoenvironmental model for Ófalu occurence, where low temperature, reductive iron-rich hydrothermal fluids penetrated soft sediments and contributed to the flourishing of iron-oxidizers. Due to subsequent tectonic events, these iron-rich sediments got into the fissures of the Ófalu metamorphic complex. This model is strenghtened by some borehole and outcrops where the Lower Cretaceous interpillow sediments and hyaloclastites rich in iron oxydes and intrusive pillow basalt can be found close to our investigated section. (Hetényi et al., 1976) This study was supported by the Developing Competitiveness of Universities in the South Transdanubian Region (SROP-4.2.1.B-10/2/KONV-2010-0002). Dabi, G., Siklósy, Z., Schubert, F., Bajnóczi, B., M. Tóth, T., 2011. The relevance of vein texture in understanding the past hydraulic behaviour of a crystalline rock mass: reconstruction of the palaeohydrology of the Mecsekalja Zone, South Hungary. Geofluids, 11, 309-327. Hetényi, R., Földi, M., Hámor, G., Nagy, I., Bilik, I., Jantsky, B. 1976. Magyarázó a Mecsek hegység földtani térképéhez 10 000-es sorozat. MÁFI Budapest (in hungarian). Jáger, V., Molnár, F., Buchs, D. & Koděra, P. 2012: The connection between iron ore formations and "mud-shrimp" colonizations around sunken wood debris and hydrothermal sediments in a Lower Cretaceous continental rift basin, Mecsek Mts., Hungary. — Earth-Science Reviews 114/3-4, 250-278.

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

USDA-ARS?s Scientific Manuscript database

Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker d...

Astronomical cycle origin of bedded chert: A middle Triassic bedded chert sequence, Inuyama, Japan

NASA Astrophysics Data System (ADS)

Ikeda, Masayuki; Tada, Ryuji; Sakuma, Hironobu

2010-09-01

Astronomical forcing is one of the main drivers of climate change, and astronomical cyclicity recorded in sediments provides a clue to understand the dynamics of the global climate system. Bedded cherts consist of rhythmic alternations of chert and shale beds. Although previous studies have hypothesized that the origin of bedded chert is related to astronomical cycles (e.g. Fischer, 1976; Hori et al., 1993), conclusive proof remains elusive. To explore this possibility, we established a continuous, high-resolution lithostratigraphy of middle Triassic bedded chert in Central Japan. The average duration of each chert-shale couplet is 20 kyr, similar to that of the precession cycle. Spectral analysis of a bed number series of thickness variations in chert beds was performed assuming that each chert-shale couplet represents a 20-kyr precession cycle. The results reveal cycles involving approximately 200, 20, 5, and 2-3 beds, corresponding to periodicities of approximately 4000, 400, 100, and 40-60 kyr, respectively. By further assuming that the 20-bed cycle represents a 405-kyr eccentricity cycle of constant and stable periodicity, we converted the bed number series to a time series. Spectral analysis of the time series revealed distinct periodicities of 3600, 117, 97, and 38 kyr, in addition to 405 kyr. Besides 3600 kyr, these periodicities agree well with the 120, 95, and 37 kyr periodicities for eccentricity cycles and the obliquity cycle during the Triassic. Moreover, we detected amplitude modulation of the approximately 100-kyr cycle of thickness variations in chert beds with a 405-kyr periodicity, which may correspond to amplitude modulation of 100-kyr climatic precession cycle with the 405-kyr periodicity. The approximately 3600-kyr periodicity described above and 1800-kyr periodicity manifested as the amplitude modulation of the 405-kyr cycle are correlated to present-day long-term eccentricity cycles of 2400 and 4800 kyr evolved by chaotic behavior of solar planets. Collectively, these similarities in the periodicities of dominant cycles, their hierarchy, and the nature of amplitude modulation of cycles in chert bed thickness with those of astronomical cycles strongly support the hypothesis that the sedimentary rhythm of bedded chert is paced by astronomical cycles, thereby indicating the potential of bedded chert as a template for a Mesozoic cyclostratigraphy.

Evolution of the Early Triassic marine depositional environment in the Croatian Dinarides

NASA Astrophysics Data System (ADS)

Aljinović, Dunja; Smirčić, Duje; Horacek, Micha; Richoz, Sylvain; Krystyn, Leopold; Kolar-Jurkovšek, Tea; Jurkovšek, Bogdan

2014-05-01

In the central part of the Dinarides in Croatia, the Early Triassic depositional sequence was investigated by means of litho-, bio- and chemostratigraphy at locality Plavno (ca. 1.000m thick). Conodont and δ13C-isotope analysis were a powerfull tool to determine stage and substage boundaries. The succession begins with the second conodont zone of the Griesbachian Isarcicella staeschei and I. isarcica with low δ13C-values and a steadily increase towards the Griesbachian-Dienerian boundary. Around that boundary a minor, short, negative excursion occurs. In the Dienerian the δ13C-values increase with a steepening of the slope towards the Dienerian-Smithian boundary. Around that boundary a maximum of +5o in shallow water carbonate occurs followed by a steep and continuous drop to low, often negative values in the Smithian. Just before the Smithian-Spathian boundary a steep rise to a second maximum is documented. It is followed by decline in the Spathian and a gentle increase to a rounded peak at the Spathian-Anisian boundary. In lithological sense Plavno succession has threefold division: 1) carbonates representing the oldest Early Triassic strata (early Griesbachian); 2) dominantly red clastics (shales, siltstones and sandstones) with intercalation of oncoid/ooid or bioclast rich grainstones (uppermost Griesbachian, Dienerian and Smithian) and 3) dominantly grey carbonaceous lime mudstones, marls and calcisiltites with ammonoids representing Spathian strata. In the oldest strata (Griesbachian) in macrocrystalline subhedral dolomites rare microspheres and foraminifers Earlandia and Cornuspira point to the stressful conditions related to the end Permian mass extinction. In the uppermost Griesbachian and Dienerian strata, within dominantly clastic deposition, rare coarse oncoliths with typical microbial cortices occur. Their presence fits to the interpretation of biotical-induced precipitation related to PTB extinction and can suggest still stressful condition. The Dienerian and Smithian are characterized by strong siliciclastic input and deposition of red shales, siltstones and sandstones with intercalation of oolithic and bioclastic grainstones. Hummocky-cross-strata witness the importance of storms. Presence of loadcasts and abundant casts of bivalve shells suggest quick deposition of terrigenous material and instant burying of epifauna during storms. Abundant trace fossils preserved in shales evidence intensive life activity in an overall shallow depositonal environment. During the Spathian deposition of lime mudstones and marls prevails. Two Spathian intervals bear ammonoid fauna suggest deposition in slightly deeper environment and a connection with the open sea testifying a transgression at the beginning of Spathian. Even in deeper environment storms play a significant role assuming deposition above storm wave base. The influence of storms in this deeper environment is recognized as accumulation of coarsegrained bioclastic lag at the base of storm beds, graded calcisiltites, gutter casts and hummocky-cross-stratified beds. Intense bioturbation suggest colonization by organisms between storms. Pending from nature and distribution of facies the Plavno sequence has been interpreted as epeiric ramp. An epeiric ramp is defined here as having a very low bathymetric slope (negligible in its inner regions), no grainy shoreface facies, water depths of tens of meters, a width of many hundreds of kilometers and depositional processes dominated by storms.

Plant pigment types, distributions, and influences on shallow water submerged aquatic vegetation mapping

NASA Astrophysics Data System (ADS)

Hall, Carlton R.; Bostater, Charles R., Jr.; Virnstein, Robert

2004-11-01

Development of robust protocols for use in mapping shallow water habitats using hyperspectral imagery requires knowledge of absorbing and scattering features present in the environment. These include, but are not limited to, water quality parameters, phytoplankton concentrations and species, submerged aquatic vegetation (SAV) species and densities, epiphytic growth on SAV, benthic microalgae and substrate reflectance characteristics. In the Indian River Lagoon, Fl. USA we conceptualize the system as having three possible basic layers, water column and SAV bed above the bottom. Each layer is occupied by plants with their associated light absorbing pigments that occur in varying proportions and concentrations. Phytoplankton communities are composed primarily of diatoms, dinoflagellates, and picoplanktonic cyanobacteria. SAV beds, including flowering plants and green, red, and brown macro-algae exist along density gradients ranging in coverage from 0-100%. SAV beds may be monotypic, or more typically, mixtures of the several species that may or may not be covered in epiphytes. Shallow water benthic substrates are colonized by periphyton communities that include diatoms, dinoflagellates, chlorophytes and cyanobacteria. Inflection spectra created form ASIA hyperspectral data display a combination of features related to water and select plant pigment absorption peaks.

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.

Age of Fishcreekian transgression

USGS Publications Warehouse

McDougall, K.

1995-01-01

The Fishcreekian transgression is one of a sequence of late Cenozoic marine transgressions recognized on the Alaskan Arctic Coastal Plain. The Fish Creek beds of northern Alaska, which were designated as the type section for this transgression, contain fossils interepreted as Pliocene in age. Analysis of the benthic foraminifers in the Fish Creek beds, however, indicates that deposition occurred in the latest Pliocene and early Pleistocene between 1.7 and 1.2 Ma during a "warm' interval which was characterized by climatic conditions similar to the present or slightly warmer where temperatures shifted within a relatively narow range. -from Author

Regional stratigraphy and petroleum potential, Ghadames basin, Algeria

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

Emme, J.J.; Sunderland, B.L.

1991-03-01

The Ghadames basin in east-central Algeria extends over 65,000 km{sup 2} (25,000 mi{sup 2}), of which 90% is covered by dunes of the eastern Erg. This intracratonic basin consists of up to 6000 m (20,000 ft) of dominantly clastic Paleozoic through Mesozoic strata. The Ghadames basin is part of a larger, composite basin complex (Ilizzi-Ghadames-Triassic basins) where Paleozoic strata have been truncated during a Hercynian erosional event and subsequently overlain by a northward-thickening wedge of Mesozoic sediments. Major reservoir rocks include Triassic sandstones that produce oil, gas, and condensate in the western Ghadames basin, Siluro-Devonian sandstones that produce mostly oilmore » in the shallower Ilizzi basin to the south, and Cambro-Ordovician orthoquartzites that produce oil at Hassi Messaoud to the northwest. Organic shales of the Silurian and Middle-Upper Devonian are considered primary source rocks. Paleozoic shales and Triassic evaporite/red bed sequences act as seals for hydrocarbon accumulations. The central Ghadames basin is underexplored, with less than one wildcat well/1700 km{sup 2} (one well/420,000 ac). Recent Devonian and Triassic oil discoveries below 3500 m (11,500 ft) indicate that deep oil potential exists. Exploration to date has concentrated on structural traps. Subcrop and facies trends indicate that potential for giant stratigraphic or combination traps exists for both Siluro-Devonian and Triassic intervals. Modern seismic acquisition and processing techniques in high dune areas can be used to successfully identify critical unconformity-bound sequences with significant stratigraphic trap potential. Advances in seismic and drilling technology combined with creative exploration should result in major petroleum discoveries in the Ghadames basin.« less

Reconnaissance geologic map of the Muwassam Quadrangle, sheet 16/42 D, Kingdom of Saudi Arabia

USGS Publications Warehouse

Blank, H. Richard

1985-01-01

All of the mapped area is occupied by coastal plain bordering the Red Sea. The flat coastal plain is covered by Quaternary surficial deposits overlying a sequence of Tertiary rocks as much as 5 km thick. The coastal plain is separated from the Red Sea by zone of supratidal sabkha deposits, offshore bars, islands, tidal md flats, and shallow lagoons. The sea is shallow, less than 200 m deep, and forms part of the shelf marginal to the main axial trough of the Red Sea.

Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

USDA-ARS?s Scientific Manuscript database

In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

PubMed

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-07-01

Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

First Molecular Characterization of Hypoderma actaeon in Cattle and Red Deer (Cervus elaphus) in Portugal.

PubMed

Ahmed, Haroon; Sousa, Sérgio Ramalho; Simsek, Sami; Anastácio, Sofia; Kilinc, Seyma Gunyakti

2017-12-01

Hypoderma spp. larvae cause subcutaneous myiasis in several animal species. The objective of the present investigation was to identify and characterize morphologically and molecularly the larvae of Hypoderma spp. collected from cattle (Bos taurus taurus) and red deer (Cervus elaphus) in the district of Castelo Branco, Portugal. For this purpose, a total of 8 larvae were collected from cattle (n=2) and red deer (n=6). After morphological identification of Hypoderma spp. larvae, molecular characterization was based on PCR-RFLP and mitochondrial CO1 gene sequence analysis. All larvae were morphologically characterized as the third instar larvae (L3) of H. actaeon. Two restriction enzymes were used for molecular identification of the larvae. TaqI restriction enzyme was not able to cut H. actaeon. However, MboII restriction enzyme differentiated Hypoderma species showing 210 and 450 bp bands in H. actaeon. Furthermore, according to the alignment of the mt-CO1 gene sequences of Hypoderma species and to PCR-RFLP findings, all the identified Hypoderma larvae were confirmed as H. actaeon. This is the first report of identification of Hypoderma spp. (Diptera; Oestridae) from cattle and red deer in Portugal, based on morphological and molecular analyses.

Distribution and diversity of Prochlorococcus ecotypes in the Red Sea.

PubMed

Shibl, Ahmed A; Thompson, Luke R; Ngugi, David K; Stingl, Ulrich

2014-07-01

Photosynthetic prokaryotes of the genus Prochlorococcus play a major role in global primary production in the world's oligotrophic oceans. A recent study on pelagic bacterioplankton communities in the northern and central Red Sea indicated that the predominant cyanobacterial 16S rRNA gene sequence types were from Prochlorococcus cells belonging to a high-light-adapted ecotype (HL II). In this study, we analyzed microdiversity of Prochlorococcus sp. at multiple depths within and below the euphotic zone in the northern, central, and southern regions of the Red Sea, as well as in surface waters in the same locations, but in a different season. Prochlorococcus dominated the communities in clone libraries of the amplified 16S-23S rRNA internal transcribed spacer (ITS) region. Almost no differences were found between samples from coastal or open-water sites, but a high diversity of Prochlorococcus ecotypes was detected at 100-meter depth in the water column. In addition, an unusual dominance of HL II-related sequences was observed in deeper waters. Our results indicate that the Red Sea harbors diverse Prochlorococcus lineages, but no novel ecotypes, despite its unusual physicochemical properties. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Uranium in the Islamic Republic of Mauritania (phase V, deliverable 81): Chapter N in Second projet de renforcement institutionnel du secteur minier de la République Islamique de Mauritanie (PRISM-II)

USGS Publications Warehouse

Fernette, Gregory

2015-01-01

Uranium occurrences are also reported in the Tasiast-Tijirit Terrane of the Archean Rgueïbat Shield, the Mauritanide Belt, and the Coastal Basin. Geologic environments permissive for eight types of uranium deposits are recognized in Mauritania. These deposit types include: calcrete, granite-hosted vein/shear, alkaline intrusive, unconformity-associated, quartz pebble conglomerate, phosphate, sandstone, and red bed-type uranium deposits.

[Structural changes in the tissues of white rats after capsaicin administration].

PubMed

Vorob'eva, N F; Kniazev, G G; Lazarev, V A; Spiridonov, V K

1997-01-01

Tissue structure of albino rat lung, skin and cornea changing after administration of capsaicin (neurotoxin isolated from red pepper) was studied using light and electron microscope. 5 mg/kg dose causes tissue swelling and microcirculatory bed reaction. 200 mg/kg dose leads to more significant dystrophic tissue alterations. Fibrosclerosis signs were found in certain cases. Microcirculatory disorders are proposed as the main reason for tissue structure alterations observed, although the mechanism of their development is still unclear.

Final Remedial Investigation Report Area of Contamination (AOC) 57. Volume I. Text Sections 1 Through 10, Figures and Tables

DTIC Science & Technology

2000-06-01

duckweed ( Lemna minor ), and bur-reed (Sparganium sp.). The forested wetland to the southeast of Cold Spring Brook has a sparse canopy cover of red...FORMATION (Lower Devonian and Silurian) Carbonaceous slate and phyllite, with minor metagraywacke to the west (Zen, 1983; Peck, 1975). Bedding is...Allmendinger (1975). So OAKDALE FORMATION (Silurian) Metasiltstone and phyllite. It is fine- grained and consists of quartz and minor feldspar and ankerite, and

Installation Restoration Program. Phase 1. Records Search Andrews AFB. Maryland

DTIC Science & Technology

1985-06-01

red to silvery-qrey, functions ma a conf ining bed. Formation. ~Va plastics thin lonses of pole gray silt. Ann"a Formation. ye (0-210 sand, qrsenieh...the Nanjemoy Formation (a clayey glauconi- tic sand, two to thirty feet thick) and the Marlboro Clay (a plastic clay with silt partings, two to... plastics , empty 55-gallon drums, waste lumber, tires, pipes, and hospital wastes such as unused needles and chemical reagents. In the past, Site D-4 was

The legacy of lead (Pb) in fluvial bed sediments of an urban drainage basin, Oahu, Hawaii.

PubMed

Hotton, Veronica K; Sutherland, Ross A

2016-03-01

The study of fluvial bed sediments is essential for deciphering the impact of anthropogenic activities on water quality and drainage basin integrity. In this study, a systematic sampling design was employed to characterize the spatial variation of lead (Pb) concentrations in bed sediment of urban streams in the Palolo drainage basin, southeastern Oahu, Hawaii. Potentially bioavailable Pb was assessed with a dilute 0.5 N HCl extraction of the <63 μm grain-size fraction from the upper bed sediment layer of 169 samples from Palolo, Pukele, and Waiomao streams. Contamination of bed sediments was associated with the direct transport of legacy Pb from the leaded gasoline era to stream channels via a dense network of storm drains linked to road surfaces throughout the basin. The Palolo Stream had the highest median Pb concentration (134 mg/kg), and the greatest road and storm drain densities, the greatest population, and the most vehicle numbers. Lower median Pb concentrations were associated with the less impacted Pukele Stream (24 mg/kg), and Waiomao Stream (7 mg/kg). The median Pb enrichment ratio values followed the sequence of Palolo (68) > Pukele (19) > Waiomao (8). Comparisons to sediment quality guidelines and potential toxicity estimates using a logistic regression model (LRM) indicated a significant potential risk of Palolo Stream bed sediments to bottom-dwelling organisms.

De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora)

PubMed Central

Liu, Le; Zhang, Shijie; Lian, Chunlan

2015-01-01

Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora. PMID:26690126

A Definitive Optical Detection of a Supercluster at Z ~ 0.91

NASA Astrophysics Data System (ADS)

Lubin, Lori M.; Brunner, Robert; Metzger, Mark R.; Postman, Marc; Oke, J. B.

2000-03-01

We present the results from a multiband optical imaging program that has definitively confirmed the existence of a supercluster at z~0.91. Two massive clusters of galaxies, Cl 1604+4304 at z=0.897 and Cl 1604+4321 at z=0.924, were originally observed in the high-redshift cluster survey of Oke, Postman, & Lubin. They are separated by 4300 km s-1 in radial velocity and 17' on the plane of the sky. Their physical and redshift proximity suggested a promising supercluster candidate. Deep BRi imaging of the region between the two clusters indicates a large population of red galaxies. This population forms a tight, red sequence in the color-magnitude diagram at (R-i)~1.4. The characteristic color is identical to that of the spectroscopically confirmed early-type galaxies in the two member clusters. The red galaxies are spread throughout the 5 h-1 Mpc region between Cl 1604+4304 and Cl 1604+4321. Their spatial distribution delineates the entire large-scale structure with high concentrations at the cluster centers. In addition, we detect a significant overdensity of red galaxies directly between Cl 1604+4304 and Cl 1604+4321 which is the signature of a third, rich cluster associated with this system. The strong sequence of red galaxies and their spatial distribution clearly indicate that we have discovered a supercluster at z~0.91.

Life style and biochemical adaptation in Antarctic fishes

NASA Astrophysics Data System (ADS)

di Prisco, Guido

2000-12-01

Respiration and metabolism are under investigation in Antarctic fish, in an effort to understand the interplay between ecology and biochemical and physiological processes. Fish of the dominant suborder Notothenioidei are red-blooded, except Channichthyidae (the most phyletically derived family), whose genomes retain transcriptionally inactive DNA sequences closely related to the α-globin gene of red-blooded notothenioids and have lost the β-globin locus. Our structure/function studies on 38 of the 80 red-blooded species are aimed at correlating sequence, multiplicity and oxygen binding with ecological constraints and at obtaining phylogenetic information on evolution. For comparative purposes, this work has been extended to non-Antarctic notothenioids. All sluggish bottom dwellers have a single major hemoglobin (Hb) and often a minor, functionally similar one. Three species of the family Nototheniidae have different life styles. They have uniquely specialised oxygen-transport systems, adjusted to the mode of life of each species. Artedidraconidae have a single Hb, lacking oxygen-binding cooperativity, similar to the ancestral hemoproteins of primitive organisms. The amino acid sequences are currently used in the molecular modelling approach. The study of several enzymes with key roles in metabolism (e.g. glucose-6-phosphate dehydrogenase, L-glutamate dehydrogenase, phosphorylase b, carbonic anhydrase) indicate that some aspects of the molecular structure (e.g. molecular mass, number of subunits, amino acid sequence, temperature of irreversible heat inactivation) have been conserved during development of cold adaptation. However, high catalytic efficiency, possibly due to subtle molecular changes, is observed at low temperature.

Shoreface to estuarine sedimentation in the late Paleocene Matanomadh Formation, Kachchh, western India

NASA Astrophysics Data System (ADS)

Srivastava, V. K.; Singh, B. P.

2017-04-01

Late Paleocene sedimentation in the pericratonic Kachchh Basin marks the initial marine transgression during the Cenozoic era. A 17 m thick sandstone-dominated succession, known as the clastic member (CM) of the Matanomadh Formation (MF), is exposed sporadically in the basin. Three facies associations are reconstructed in the succession in three different sections. Facies association-1 contains matrix-supported pebbly conglomerate facies, horizontally-laminated sandstone-mudstone alternation facies, hummocky- and swaley cross-bedded sandstone facies, wave-rippled sandstone facies and climbing ripple cross-laminated sandstone facies. This facies association developed between shoreface and foreshore zone under the influence of storms on a barrier ridge. Facies association-2 contains sigmoidal cross-bedded sandstone facies, sandstone-mudstone alternation facies, flaser-bedded sandstone facies, herringbone cross-bedded sandstone facies and tangential cross-bedded sandstone facies. This facies association possessing tidal bundles and herringbone cross-beds developed on a tidal flat with strong tidal influence. Facies association-3 comprises pebbly sandstone facies, horizontally-bedded sandstone facies, tangential cross-bedded sandstone facies exhibiting reactivation surfaces and tabular cross-bedded sandstone facies. This facies association represents sedimentation in a river-dominated estuary and reactivation surfaces and herringbone cross-beds indicating tidal influence. The bipolar paleocurrent pattern changes to unipolar up-section because of the change in the depositional currents from tidal to fluvial. The sedimentation took place in an open coast similar to the Korean coast. The presence of neap-spring tidal rhythmites further suggests that a semidiurnal system similar to the modern day Indian Ocean was responsible for the sedimentation. Here, the overall sequence developed during the transgressive phase where barrier ridge succession is succeeded by the tidal flat succession and the latter, in turn, is succeeded by the estuarine succession. This study resolves the most debated issue of initial marine transgression in the Kachchh Basin during the Cenozoic.

Ecophysiology, secondary pigments and ultrastructure of Chlainomonas sp. (Chlorophyta) from the European Alps compared with Chlamydomonas nivalis forming red snow

PubMed Central

Remias, Daniel; Pichrtová, Martina; Pangratz, Marion; Lütz, Cornelius; Holzinger, Andreas

2016-01-01

Red snow is a well-known phenomenon caused by microalgae thriving in alpine and polar regions during the melting season. The ecology and biodiversity of these organisms, which are adapted to low temperatures, high irradiance and freeze–thaw events, are still poorly understood. We compared two different snow habitats containing two different green algal genera in the European Alps, namely algae blooming in seasonal rock-based snowfields (Chlamydomonas nivalis) and algae dominating waterlogged snow bedded over ice (Chlainomonas sp.). Despite the morphological similarity of the red spores found at the snow surface, we found differences in intracellular organization investigated by light and transmission electron microscopy and in secondary pigments investigated by chromatographic analysis in combination with mass spectrometry. Spores of Chlainomonas sp. show clear differences from Chlamydomonas nivalis in cell wall arrangement and plastid organization. Active photosynthesis at ambient temperatures indicates a high physiological activity, despite no cell division being present. Lipid bodies containing the carotenoid astaxanthin, which produces the red color, dominate cells of both species, but are modified differently. While in Chlainomonas sp. astaxanthin is mainly esterified with two fatty acids and is more apolar, in Chamydomonas nivalis, in contrast, less apolar monoesters prevail. PMID:26884467

RED GIANTS IN ECLIPSING BINARY AND MULTIPLE-STAR SYSTEMS: MODELING AND ASTEROSEISMIC ANALYSIS OF 70 CANDIDATES FROM KEPLER DATA

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

Gaulme, P.; McKeever, J.; Rawls, M. L.

2013-04-10

Red giant stars are proving to be an incredible source of information for testing models of stellar evolution, as asteroseismology has opened up a window into their interiors. Such insights are a direct result of the unprecedented data from space missions CoRoT and Kepler as well as recent theoretical advances. Eclipsing binaries are also fundamental astrophysical objects, and when coupled with asteroseismology, binaries provide two independent methods to obtain masses and radii and exciting opportunities to develop highly constrained stellar models. The possibility of discovering pulsating red giants in eclipsing binary systems is therefore an important goal that could potentiallymore » offer very robust characterization of these systems. Until recently, only one case has been discovered with Kepler. We cross-correlate the detected red giant and eclipsing-binary catalogs from Kepler data to find possible candidate systems. Light-curve modeling and mean properties measured from asteroseismology are combined to yield specific measurements of periods, masses, radii, temperatures, eclipse timing variations, core rotation rates, and red giant evolutionary state. After using three different techniques to eliminate false positives, out of the 70 systems common to the red giant and eclipsing-binary catalogs we find 13 strong candidates (12 previously unknown) to be eclipsing binaries, one to be a non-eclipsing binary with tidally induced oscillations, and 10 more to be hierarchical triple systems, all of which include a pulsating red giant. The systems span a range of orbital eccentricities, periods, and spectral types F, G, K, and M for the companion of the red giant. One case even suggests an eclipsing binary composed of two red giant stars and another of a red giant with a {delta}-Scuti star. The discovery of multiple pulsating red giants in eclipsing binaries provides an exciting test bed for precise astrophysical modeling, and follow-up spectroscopic observations of many of the candidate systems are encouraged. The resulting highly constrained stellar parameters will allow, for example, the exploration of how binary tidal interactions affect pulsations when compared to the single-star case.« less

Optimal MRI sequences for 68Ga-PSMA-11 PET/MRI in evaluation of biochemically recurrent prostate cancer.

PubMed

Lake, Spencer T; Greene, Kirsten L; Westphalen, Antonio C; Behr, Spencer C; Zagoria, Ronald; Small, Eric J; Carroll, Peter R; Hope, Thomas A

2017-09-19

PET/MRI can be used for the detection of disease in biochemical recurrence (BCR) patients imaged with 68 Ga-PSMA-11 PET. This study was designed to determine the optimal MRI sequences to localize positive findings on 68 Ga-PSMA-11 PET of patients with BCR after definitive therapy. Fifty-five consecutive prostate cancer patients with BCR imaged with 68 Ga-PSMA-11 3.0T PET/MRI were retrospectively analyzed. Mean PSA was 7.9 ± 12.9 ng/ml, and mean PSA doubling time was 7.1 ± 6.6 months. Detection rates of anatomic correlates for prostate-specific membrane antigen (PSMA)-positive foci were evaluated on small field of view (FOV) T2, T1 post-contrast, and diffusion-weighted images. For prostate bed recurrences, the detection rate of dynamic contrast-enhanced (DCE) imaging for PSMA-positive foci was evaluated. Finally, the detection sensitivity for PSMA-avid foci on 3- and 8-min PET acquisitions was compared. PSMA-positive foci were detected in 89.1% (49/55) of patients evaluated. Small FOV T2 performed best for lymph nodes and detected correlates for all PSMA-avid lymph nodes. DCE imaging performed the best for suspected prostate bed recurrence, detecting correlates for 87.5% (14/16) of PSMA-positive prostate bed foci. The 8-min PET acquisition performed better than the 3-min acquisition for lymph nodes smaller than 1 cm, detecting 100% (57/57) of lymph nodes less than 1 cm, compared to 78.9% (45/57) for the 3-min acquisition. PSMA PET/MRI performed well for the detection of sites of suspected recurrent disease in patients with BCR. Of the MRI sequences obtained for localization, small FOV T2 images detected the greatest proportion of PSMA-positive abdominopelvic lymph nodes and DCE imaging detected the greatest proportion of PSMA-positive prostate bed foci. The 8-min PET acquisition was superior to the 3 min acquisition for detection of small lymph nodes.

Integrated biostratigraphy of foraminifers, radiolarians and conodonts in shallow and deep water Middle Permian (Capitanian) deposits of the "Rader slide", Guadalupe Mountains, West Texas

USGS Publications Warehouse

Nestell, M.K.; Nestell, G.P.; Wardlaw, B.R.; Sweatt, M.J.

2006-01-01

A diverse assemblage of microfossils is present in a 6m thick sequence of three debris flow deposits interbedded with thin turbidite limestone beds and fine grained siliciclastics exposed above the megaconglomerate in a section (known as the "Rader Slide" in numerous guidebook stops) of the Rader Limestone Member of the Bell Canyon Formation of Capitanian age (Middle Permian) in the Guadalupe Mountains of West Texas. Each debris flow, derived from nearby Capitan Reef shelf-margin and slope deposits, contains a distinct microfossil assemblage. Small foraminifers and fusulinaceans, conodonts, radiolarians, sponge spicules, fish dermal plates and teeth, and other fragmental fossils are present in this sequence. Conodonts are relatively scarce in the first (or lowest) debris flow, except in its upper part, but they are common to abundant in the other two debris flows, and very abundant in several of the thin turbidite limestone beds. All of the conodonts present appear to be morphotypes of one population of the species Jinogondolella postserrata, except for one new conodont species, and the Jinogondolella postserrata Zone is clearly documented in this sequence. The debris flows contain the fusulinaceans Rauserella, rare Codonofusiella, Polydiexodina, Leella? and various species of the small foraminifers Globivalvulina, Hemigordius, Baisalina, Abadehella, Deckerella, Neoendothyranella, Vachardella, Geinitzina, and Polarisella. Some of the thin turbidite limestone beds contain a foraminiferal assemblage similar to that found in the debris flows, but with lower diversity. Many small foraminiferal species appear to be endemic, although a few are closely related to species known in Permian age strata in Italy, Greenland, the Russian Far East, northeastern part of Russia (Omolon massif), and the Zechstein of Germany and the Baltic area. Two thin limestone beds above the second debris flow contain primarily radiolarian species known from the Follicucullus japonicus Zone of Japan. Nine new species of small foraminifers (Bisphaera? improvisa, Vissariotaxis? nativus, Multidiscus raderensis, Baisalina miscella, Agathammina minuscula, Polarisella globosa, Geinitzina jucunda, Robustopachyphloia texana and Spireitlina capitanensis) and one new conodont species Jinogondolella gladirobusta are described.

Exobasidium maculosum, a new species causing leaf and fruit spots on blueberry in the southeastern USA and its relationship with other Exobasidium spp. parasitic to blueberry and cranberry.

PubMed

Brewer, Marin Talbot; Turner, Ashley N; Brannen, Phillip M; Cline, William O; Richardson, Elizabeth A

2014-01-01

Exobasidium leaf and fruit spot of blueberry (Vaccinium section Cyanococcus) is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA. To determine whether this disease is caused by a new species of Exobasidium, we studied the morphology and phylogenetic relationship of the causal fungus compared with other members of the genus, including the type species E. vaccinii and other species that parasitize blueberry and cranberry (V. macrocarpon). Both scanning electron microscopy and light microscopy were used for morphological characterization. For phylogenetic analyses, we sequenced the large subunit of the rDNA (LSU) from 10 isolates collected from leaf or fruit spots of rabbiteye blueberry (V. virgatum), highbush blueberry (V. corymbosum) and southern highbush blueberry (Vaccinium interspecific hybrid) from Georgia and North Carolina and six isolates from leaf spots of lowbush blueberry (V. angustifolium) from Maine and Nova Scotia, Canada. LSU was sequenced from isolates causing red leaf disease of lowbush blueberry and red leaf spot (E. rostrupii) and red shoot (E. perenne) of cranberry. In addition, LSU sequences from GenBank, including sequences with high similarity to the emerging parasite and from Exobasidium spp. parasitizing other Vaccinium spp. and related hosts, were obtained. All sequences were aligned and subjected to phylogenetic analyses. Results indicated that the emerging parasite in the southeastern USA differs morphologically and phylogenetically from other described species and is described herein as Exobasidium maculosum. Within the southeastern USA, clustering based on host species, host tissue type (leaf or fruit) or geographic region was not detected; however, leaf spot isolates from lowbush blueberry were genetically different and likely represent a unique species. © 2014 by The Mycological Society of America.

Effect of red clay on diesel bioremediation and soil bacterial community.

PubMed

Jung, Jaejoon; Choi, Sungjong; Hong, Hyerim; Sung, Jung-Suk; Park, Woojun

2014-08-01

Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.

Coevolution of bed surface patchiness and channel morphology: 1. Mechanisms of forced patch formation

USGS Publications Warehouse

Nelson, Peter A.; McDonald, Richard R.; Nelson, Jonathan M.; Dietrich, William E.

2015-01-01

Riverbeds frequently display a spatial structure where the sediment mixture composing the channel bed has been sorted into discrete patches of similar grain size. Even though patches are a fundamental feature in gravel bed rivers, we have little understanding of how patches form, evolve, and interact. Here we present a two-dimensional morphodynamic model that is used to examine in greater detail the mechanisms responsible for the development of forced bed surface patches and the coevolution of bed morphology and bed surface patchiness. The model computes the depth-averaged channel hydrodynamics, mixed-grain-size sediment transport, and bed evolution by coupling the river morphodynamic model Flow and Sediment Transport with Morphological Evolution of Channels (FaSTMECH) with a transport relation for gravel mixtures and the mixed-grain-size Exner equation using the active layer assumption. To test the model, we use it to simulate a flume experiment in which the bed developed a sequence of alternate bars and temporally and spatially persistent forced patches with a general pattern of coarse bar tops and fine pools. Cross-stream sediment flux causes sediment to be exported off of bars and imported into pools at a rate that balances downstream gradients in the streamwise sediment transport rate, allowing quasi-steady bar-pool topography to persist. The relative importance of lateral gravitational forces on the cross-stream component of sediment transport is a primary control on the amplitude of the bars. Because boundary shear stress declines as flow shoals over the bars, the lateral sediment transport is increasingly size selective and leads to the development of coarse bar tops and fine pools.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae.

PubMed

Boo, Ga Hun; Hughey, Jeffery R; Miller, Kathy Ann; Boo, Sung Min

2016-10-14

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43-44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae

PubMed Central

Boo, Ga Hun; Hughey, Jeffery R.; Miller, Kathy Ann; Boo, Sung Min

2016-01-01

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution. PMID:27739454

Chromosomal Mapping of Canine-Derived BAC Clones to the Red Fox and American Mink Genomes

PubMed Central

Vorobieva, Nadegda V.; Beklemisheva, Violetta R.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Yudkin, Dmitry V.; Trut, Lyudmila N.; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D.; Acland, Gregory M.; Graphodatsky, Alexander S.

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene–containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations. PMID:19546120

Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes.

PubMed

Kukekova, Anna V; Vorobieva, Nadegda V; Beklemisheva, Violetta R; Johnson, Jennifer L; Temnykh, Svetlana V; Yudkin, Dmitry V; Trut, Lyudmila N; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D; Acland, Gregory M; Graphodatsky, Alexander S

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

Coinfection of Ugandan Red Colobus (Procolobus [Piliocolobus] rufomitratus tephrosceles) with Novel, Divergent Delta-, Lenti-, and Spumaretroviruses ▿

PubMed Central

Goldberg, Tony L.; Sintasath, David M.; Chapman, Colin A.; Cameron, Kenneth M.; Karesh, William B.; Tang, Shaohua; Wolfe, Nathan D.; Rwego, Innocent B.; Ting, Nelson; Switzer, William M.

2009-01-01

Nonhuman primates host a plethora of potentially zoonotic microbes, with simian retroviruses receiving heightened attention due to their roles in the origins of human immunodeficiency viruses type 1 (HIV-1) and HIV-2. However, incomplete taxonomic and geographic sampling of potential hosts, especially the African colobines, has left the full range of primate retrovirus diversity unexplored. Blood samples collected from 31 wild-living red colobus monkeys (Procolobus [Piliocolobus] rufomitratus tephrosceles) from Kibale National Park, Uganda, were tested for antibodies to simian immunodeficiency virus (SIV), simian T-cell lymphotrophic virus (STLV), and simian foamy virus (SFV) and for nucleic acids of these same viruses using genus-specific PCRs. Of 31 red colobus tested, 22.6% were seroreactive to SIV, 6.4% were seroreactive to STLV, and 97% were seroreactive to SFV. Phylogenetic analyses of SIV polymerase (pol), STLV tax and long terminal repeat (LTR), and SFV pol and LTR sequences revealed unique SIV and SFV strains and a novel STLV lineage, each divergent from corresponding retroviral lineages previously described in Western red colobus (Procolobus badius badius) or black-and-white colobus (Colobus guereza). Phylogenetic analyses of host mitochondrial DNA sequences revealed that red colobus populations in East and West Africa diverged from one another approximately 4.25 million years ago. These results indicate that geographic subdivisions within the red colobus taxonomic complex exert a strong influence on retroviral phylogeny and that studying retroviral diversity in closely related primate taxa should be particularly informative for understanding host-virus coevolution. PMID:19692478

Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

PubMed

Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

2017-12-01

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

Genetic Basis for Red Coloration in Birds.

PubMed

Lopes, Ricardo J; Johnson, James D; Toomey, Matthew B; Ferreira, Mafalda S; Araujo, Pedro M; Melo-Ferreira, José; Andersson, Leif; Hill, Geoffrey E; Corbo, Joseph C; Carneiro, Miguel

2016-06-06

The yellow and red feather pigmentation of many bird species [1] plays pivotal roles in social signaling and mate choice [2, 3]. To produce red pigments, birds ingest yellow carotenoids and endogenously convert them into red ketocarotenoids via an oxidation reaction catalyzed by a previously unknown ketolase [4-6]. We investigated the genetic basis for red coloration in birds using whole-genome sequencing of red siskins (Spinus cucullata), common canaries (Serinus canaria), and "red factor" canaries, which are the hybrid product of crossing red siskins with common canaries [7]. We identified two genomic regions introgressed from red siskins into red factor canaries that are required for red coloration. One of these regions contains a gene encoding a cytochrome P450 enzyme, CYP2J19. Transcriptome analysis demonstrates that CYP2J19 is significantly upregulated in the skin and liver of red factor canaries, strongly implicating CYP2J19 as the ketolase that mediates red coloration in birds. Interestingly, a second introgressed region required for red feathers resides within the epidermal differentiation complex, a cluster of genes involved in development of the integument. Lastly, we present evidence that CYP2J19 is involved in ketocarotenoid formation in the retina. The discovery of the carotenoid ketolase has important implications for understanding sensory function and signaling mediated by carotenoid pigmentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Backwater control on riffle pool hydraulics, fish habitat quality, and sediment transport regime in gravel-bed rivers

NASA Astrophysics Data System (ADS)

Pasternack, Gregory B.; Bounrisavong, Michael K.; Parikh, Kaushal K.

2008-07-01

SummaryThe importance of channel non-uniformity to natural hydrogeomorphic and ecological processes in gravel-bed rivers is becoming increasingly known, but its use in channel rehabilitation lags behind. Many projects still use methods that assume steady, uniform flow and simple channel geometries. One aspect of channel non-uniformity that has not been considered much is its role in controlling backwater conditions and thus potentially influencing patterns of physical habitat and channel stability in sequences of riffles and pools. In this study, 2D hydrodynamic models of two non-uniform pool-riffle-pool configurations were used to systematically explore the effects of four different downstream water surface elevations at three different discharges (24 total simulations) on riffle-pool ecohydraulics. Downstream water surface elevations tested included backwater, uniform, accelerating, and critical conditions, which are naturally set by downstream riffle-crest morphology but may also be re-engineered artificially. Discharges included a fish-spawning low flow, summer fish-attraction flow, and a peak snowmelt pulse. It was found that the occurrence of a significant area of high-quality fish spawning habitat at low flow depends on riffles being imposed upon by backwater conditions, which also delay the onset of full bed mobility on riffles during floods. The assumption of steady, uniform flow was found to be inappropriate for gravel-bed rivers, since their non-uniformity controls spatial patterns of habitat and sediment transport. Also, model results indicated that a "reverse domino" mechanism can explain catastrophic failure and re-organization of a sequence of riffles based on the water surface elevation response to scour on downstream riffles, which then increases scour on upstream riffles.

[Combined internal-external radiotherapy (CIERT) in a cell model].

PubMed

Oehme, Liane; Bartzsch, Thomas; Maucksch, Ute; Freudenberg, Robert; Wunderlich, Gerd; Kotzerke, Jörg

2018-06-01

Combined internal-external radiotherapy (CIERT) requires a unified assessment of biologic radiation effects in addition to the total dose. The concept of biological effective dose (BED) was evaluated in a cell model. The thyroid NIS-positive cell line FRTL-5 was irradiated with X-ray and the radiotracer Tc-99m pertechnetate either alone or in combination. The cellular uptake of the radionuclide during the incubation time of 24 h was controlled by the presence or absence of perchlorate. Dose calculation was performed based on measured uptake values. Cell specific radiobiologic parameters were derived from dose effect curves using the colony forming assay as biological endpoint. For the combination of the radiation qualities the sequence and time difference were varied. Cell survival was compared with the prediction of the BED model. The radiobiologic parameters from X-ray dose response were α = (0.22 ± 0.02) Gy -1 and β = (0.021 ± 0.001) Gy -2 . The half life for repair was (1.51 ± 0.21) h. These values could also explain the dose response curves for Tc-99m-irradiation with exponential decreasing dose rate. CIERT experiments showed no significant differences in cell survival regarding sequence and irradiation break. When the radionuclide uptake was not prevented the cell survival for the combination of X-ray and Tc-99m was lower than the prediction by BED calculations. The validity of the BED formalism for different dose rates and radiation qualities was verified. Supraaddive effects measured in the combination of X-ray and intracellular Tc-99m might be caused by Auger and conversion electrons, however further experiments are necessary. Schattauer GmbH.

Genome sequencing and analyses of the postharvest fungus Penicillium expansum R21

USDA-ARS?s Scientific Manuscript database

Blue mold is the vernacular name of a common postharvest disease of stored apples, pears and quince that is caused by several common species of Penicillium. This study reports the draft genome sequence of Penicillium expansum strain R21, a strain isolated from a Red Delicious apple in 2011 in Pennsy...

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

A sample of potential disk hosting first ascent red giants

NASA Astrophysics Data System (ADS)

Steele, Amy; Debes, John

2018-01-01

Observations of (sub)giants with planets and disks provide the first set of proof that disks can survive the first stages of post-main-sequence evolution, even though the disks are expected to dissipate by this time. The infrared (IR) excesses present around a number of post-main-sequence (PMS) stars could be due to a traditional debris disk with planets (e.g. kappa CrB), some remnant of enhanced mass loss (e.g. the shell-like structure of R Sculptoris), and/or background contamination. We present a sample of potential disk hosting first ascent red giants. These stars all have infrared excesses at 22 microns, and possibly host circumstellar debris. We summarize the characteristics of the sample to better inform the incidence rates of thermally emitting material around giant stars. A thorough follow-up study of these candidates would serve as the first step in probing the composition of the dust in these systems that have left the main sequence, providing clues to the degree of disk processing that occurs beyond the main-sequence.

Structural Analyses of the Kahiltna Terrane: A Kinematic Record of the Collision of the Talkeetna Superterrane

NASA Astrophysics Data System (ADS)

Bier, S. E.; Fisher, D.

2002-12-01

Macro-, meso-, and microscale structural analyses from several localities across the ~1000 km Kahiltna Terrane provide valuable kinematic insights into the late Cretaceous collision between the Talkeetna superterrane and North America. The Kahiltna Terrane, a Jurassic-Cretaceous flysch basin inboard of the Talkeetna superterrane (Wrangellia, Peninsular, and Alexander terranes), contains incremental strain indicators that record a history of oblique collision and subsequent deformation in a strike-slip regime. A comparison of structural data from localities across the Kahiltna terrane suggests a unique history not yet described in previous work on south-central Alaskan tectonics. Data was collected from the Reindeer Hills area, the northwestern Talkeetna Mountains, Denali National Park, the Peters Hills, and the Tordrillo Mountains. In the Reindeer Hills, a melange zone occurs as a series of exposures dismembered by ongoing strike slip faulting between the flysch of the Kahiltna terrane and the precollisional edge of the North American continent. This melange is characterized by fault-bounded blocks of Paleozoic limestone and sandstone within an argillite matrix with a conspicuous scaly fabric. The blocks range in size from 10 cm to tens of meters; and melange fish indicate a south-directed shear sense. The melange is overlain by a red and green (Triassic-Jurassic?) conglomerate along an unconformity that likely marks the base of a perched slope basin near the toe of an accretionary wedge. The strike of bedding and cleavage in this area trends EW. The fold axes trend NW-SE and folds verge to the south. In the northwest corner of the Talkeetna Mountains, the structure is dominated by north vergent folds and faults. The strike of bedding trends ~025°; whereas the strike of the cleavage is ~060°. Both cleavage and bedding dip to the southeast. The fold axes trend roughly NE-SW. North of the Denali Fault System, in Denali National Park, strike of bedding is ~122° and the dip is to the southwest. Folds can be divided into two sets: 1) tight folds with axes trending E-W and 2) open folds with axes that trend N-S. Cleavage is axial planar to the first set of folds. Crenulation cleavage that trends E-W may also be associated with the first set of folds. In the Peters Hills, reversals in facing direction indicate the presence of multiple macroscale folds. The strike of bedding and cleavage trend ~240° and dip to the northwest. Outcrop observations of smaller scale north-vergent folds and larger scale south-vergent folds suggest multiple deformation events. Stretching lineations trend NE-SW, and incremental strain indicators record indicate a dextral shearing event. The Kahiltna terrane exposed in the vicinity of the Tordrillo Mountains consists of alternating volcaniclastic sandstones and turbidite sequences. The strike of bedding and cleavage is ~240°, and they dip steeply to the northwest. Small isoclinal folds and faults indicate northwestward transport and deformation overprinted by large-scale open folds that verge to the east. Observations of the melange indicate precollisional northward-dipping subduction beneath an accretionary assemblage of Triassic(?) material. Structural observations from multiple localities across the Kahiltna terrane indicate northward-directed thrusting related to dextral transpression and oblique collision of the Talkeetna superterrane, with varying amounts of obliquity along the margin.

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

PubMed Central

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-01-01

Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

The ATLAS3D project - XXVII. Cold gas and the colours and ages of early-type galaxies

NASA Astrophysics Data System (ADS)

Young, Lisa M.; Scott, Nicholas; Serra, Paolo; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Cappellari, Michele; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; McDermid, Richard M.; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Weijmans, Anne-Marie

2014-11-01

We present a study of the cold gas contents of the ATLAS3D early-type galaxies, in the context of their optical colours, near-ultraviolet colours and Hβ absorption line strengths. Early-type (elliptical and lenticular) galaxies are not as gas poor as previously thought, and at least 40 per cent of local early-type galaxies are now known to contain molecular and/or atomic gas. This cold gas offers the opportunity to study recent galaxy evolution through the processes of cold gas acquisition, consumption (star formation) and removal. Molecular and atomic gas detection rates range from 10 to 34 per cent in red sequence early-type galaxies, depending on how the red sequence is defined, and from 50 to 70 per cent in blue early-type galaxies. Notably, massive red sequence early-type galaxies (stellar masses >5 × 1010 M⊙, derived from dynamical models) are found to have H I masses up to M(H I)/M* ˜ 0.06 and H2 masses up to M(H2)/M* ˜ 0.01. Some 20 per cent of all massive early-type galaxies may have retained atomic and/or molecular gas through their transition to the red sequence. However, kinematic and metallicity signatures of external gas accretion (either from satellite galaxies or the intergalactic medium) are also common, particularly at stellar masses ≤5 × 1010 M⊙, where such signatures are found in ˜50 per cent of H2-rich early-type galaxies. Our data are thus consistent with a scenario in which fast rotator early-type galaxies are quenched former spiral galaxies which have undergone some bulge growth processes, and in addition, some of them also experience cold gas accretion which can initiate a period of modest star formation activity. We discuss implications for the interpretation of colour-magnitude diagrams.

Resistance to Change and Preference for Variable versus Fixed Response Sequences

ERIC Educational Resources Information Center

Arantes, Joana; Berg, Mark E.; Le, Dien; Grace, Randolph C.

2012-01-01

In Experiment 1, 4 pigeons were trained on a multiple chain schedule in which the initial link was a variable-interval (VI) 20-s schedule signalled by a red or green center key, and terminal links required four responses made to the left (L) and/or right (R) keys. In the REPEAT component, signalled by red keylights, only LRLR terminal-link…

Molecular and histopathological detection of Hepatozoon canis in red foxes (Vulpes vulpes) from Portugal.

PubMed

Cardoso, Luís; Cortes, Helder C E; Eyal, Osnat; Reis, Antónia; Lopes, Ana Patrícia; Vila-Viçosa, Maria João; Rodrigues, Paula A; Baneth, Gad

2014-03-24

Hepatozoon canis is a protozoan tick-borne pathogen of dogs and wild canids. Hepatozoon spp. have been reported to infect foxes in different continents and recent studies have mostly used the polymerase chain reaction (PCR) for the detection and characterization of the infecting species. Surveying red foxes (Vulpes vulpes) may contribute to better understanding the epidemiology of canine vector-borne diseases, including hepatozoonosis caused by H. canis in domestic dogs. The present study investigated the prevalence of Hepatozoon spp. by means of histopathology and molecular analysis of different tissues in red foxes from different parts of Portugal. Blood and tissues including bone marrow, heart, hind leg muscle, jejunum, kidney, liver, lung, popliteal or axillary lymph nodes, spleen and/or tongue were collected from 91 red foxes from eight districts in northern, central and southern Portugal. Tissues were formalin-fixed, paraffin-embedded, cut and stained with hematoxylin and eosin. Polymerase chain reaction (PCR) amplified a ~650 bp fragment of the 18S rRNA gene of Hepatozoon spp. and the DNA products were sequenced. Hepatozoon canis was detected in 68 out of 90 foxes (75.6%) from all the sampled areas by PCR and sequencing. Histopathology revealed H. canis meronts similar in shape to those found in dogs in the bone marrow of 11 (23.4%) and in the spleen of two (4.3%) out of 47 foxes (p = 0.007). All the 11 foxes found positive by histopathology were also positive by PCR of bone marrow and/or blood. Positivity by PCR (83.0%) was significantly higher (p < 0.001) than by histopathological examination (23.4%) in paired bone marrow samples from the same 47 foxes. Sequences of the 18S rRNA gene of H. canis were 98-99% identical to those in GenBank. Hepatozoon canis was found to be highly prevalent in red fox populations from northern, central and southern Portugal. Detection of the parasite by histopathology was significantly less sensitive than by PCR. Red foxes are a presumptive reservoir of H. canis infection for domestic dogs.

Molecular and histopathological detection of Hepatozoon canis in red foxes (Vulpes vulpes) from Portugal

PubMed Central

2014-01-01

Background Hepatozoon canis is a protozoan tick-borne pathogen of dogs and wild canids. Hepatozoon spp. have been reported to infect foxes in different continents and recent studies have mostly used the polymerase chain reaction (PCR) for the detection and characterization of the infecting species. Surveying red foxes (Vulpes vulpes) may contribute to better understanding the epidemiology of canine vector-borne diseases, including hepatozoonosis caused by H. canis in domestic dogs. The present study investigated the prevalence of Hepatozoon spp. by means of histopathology and molecular analysis of different tissues in red foxes from different parts of Portugal. Methods Blood and tissues including bone marrow, heart, hind leg muscle, jejunum, kidney, liver, lung, popliteal or axillary lymph nodes, spleen and/or tongue were collected from 91 red foxes from eight districts in northern, central and southern Portugal. Tissues were formalin-fixed, paraffin-embedded, cut and stained with hematoxylin and eosin. Polymerase chain reaction (PCR) amplified a ~650 bp fragment of the 18S rRNA gene of Hepatozoon spp. and the DNA products were sequenced. Results Hepatozoon canis was detected in 68 out of 90 foxes (75.6%) from all the sampled areas by PCR and sequencing. Histopathology revealed H. canis meronts similar in shape to those found in dogs in the bone marrow of 11 (23.4%) and in the spleen of two (4.3%) out of 47 foxes (p = 0.007). All the 11 foxes found positive by histopathology were also positive by PCR of bone marrow and/or blood. Positivity by PCR (83.0%) was significantly higher (p < 0.001) than by histopathological examination (23.4%) in paired bone marrow samples from the same 47 foxes. Sequences of the 18S rRNA gene of H. canis were 98–99% identical to those in GenBank. Conclusions Hepatozoon canis was found to be highly prevalent in red fox populations from northern, central and southern Portugal. Detection of the parasite by histopathology was significantly less sensitive than by PCR. Red foxes are a presumptive reservoir of H. canis infection for domestic dogs. PMID:24655375

AKARI OBSERVATION OF THE NORTH ECLIPTIC POLE (NEP) SUPERCLUSTER AT z = 0.087: MID-INFRARED VIEW OF TRANSITION GALAXIES

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

Ko, Jongwan; Im, Myungshin; Lee, Hyung Mok

2012-02-01

We present the mid-infrared (MIR) properties of galaxies within a supercluster in the north ecliptic pole region at z {approx} 0.087 observed with the AKARI satellite. We use data from the AKARI NEP-Wide (5.4 deg{sup 2}) IR survey and the CLusters of galaxies EVoLution studies (CLEVL) mission program. We show that near-IR (3 {mu}m)-mid-IR (11 {mu}m) color can be used as an indicator of the specific star formation rate and the presence of intermediate-age stellar populations. From the MIR observations, we find that red-sequence galaxies consist not only of passively evolving red early-type galaxies, but also of (1) 'weak-SFGs' (disk-dominatedmore » star-forming galaxies that have star formation rates lower by {approx}4 Multiplication-Sign than blue-cloud galaxies) and (2) 'intermediate-MXGs' (bulge-dominated galaxies showing stronger MIR dust emission than normal red early-type galaxies). These two populations can be a set of transition galaxies from blue, star-forming, late-type galaxies evolving into red, quiescent, early-type ones. We find that the weak-SFGs are predominant at intermediate masses (10{sup 10} M{sub Sun} < M{sub *} < 10{sup 10.5} M{sub Sun }) and are typically found in local densities similar to the outskirts of galaxy clusters. As much as 40% of the supercluster member galaxies in this mass range can be classified as weak-SFGs, but their proportion decreases to <10% at larger masses (M{sub *} > 10{sup 10.5} M{sub Sun }) at any galaxy density. The fraction of the intermediate-MXG among red-sequence galaxies at 10{sup 10} M{sub Sun} < M{sub *} < 10{sup 11} M{sub Sun} also decreases as the density and mass increase. In particular, {approx}42% of the red-sequence galaxies with early-type morphologies are classified as intermediate-MXGs at intermediate densities. These results suggest that the star formation activity is strongly dependent on the stellar mass, but that the morphological transformation is mainly controlled by the environment.« less

iss016e019394

NASA Image and Video Library

2008-05-02

ISS016-E-019394 (30 Dec. 2007) --- Al Wadj Bank, Saudi Arabia is featured in this image photographed by an Expedition 16 crewmember on the International Space Station. Saudi Arabia boasts the most coral reefs of any Middle Eastern country, as it includes coastline along both the Red Sea and Gulf of Arabia. This high resolution image depicts a portion of the Al Wadj Bank, located along the northern Red Sea coast. Despite the relatively high salinity of Red Sea water (compared to other oceans), approximately 260 species of coral are found here, according to scientists. Large tracts of the Saudi Arabian coastline are undeveloped, and reefs in these areas are in generally good ecological health. However, reefs located near large urban centers like Jeddeh have suffered degradation due to land reclamation, pollution, and increased terrigeneous sediment input. The Al Wadj Bank includes a healthy and diverse reef system, extensive seagrass beds, and perhaps the largest population of dugong -- a marine mammal similar to the North American manatee -- in the eastern Red Sea. The portion of the Bank in this image illustrates the complex form and topography of the reef system. Several emergent islands (tan) - surrounded primarily by dark green seagrass - are visible, the largest located at top left. Only the islands are above the waterline -- over the reef structures the water color ranges from light teal (shallow) to turquoise (increasing depth). The southern edge of the reef is well indicated by the deep, dark blue water of the Red Sea at image top.

Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure.

PubMed

Donaldson, Michael E; Rico, Yessica; Hueffer, Karsten; Rando, Halie M; Kukekova, Anna V; Kyle, Christopher J

2018-01-01

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

Evolutionary paths among different red galaxy types at 0.3 < z < 1.5 and the build-up of massive E-S0's

NASA Astrophysics Data System (ADS)

Gallego, Jesús; Prieto, Mercedes; Eliche-Moral, M. Carmen; Balcells, Marc; Cristóbal-Hornillos, David; Erwin, Peter; Abreu, David; Domínguez-Palmero, Lilian; Hempel, Angela; López-Sanjuan, Carlos; Guzmán, Rafael; Pérez-González, Pablo G.; Barro, Guillermo; Zamorano, Jaime

2013-07-01

Some recent observations seem to disagree with hierarchical theories of galaxy formation on the role of major mergers in a late build-up of massive early-type galaxies. We re-address this question by analysing the morphology, structural distortion level, and star formation enhancement of a sample of massive galaxies (M* > 5 × 1010M⊙) lying on the Red Sequence and its surroundings at 0.3 < z < 1.5. We have used an initial sample of ~1800 sources with Ks < 20.5 mag over an area ~155 arcmin2 on the Groth Strip, combining data from the Rainbow Extragalactic Database and the GOYA Survey. Red galaxy classes that can be directly associated to intermediate stages of major mergers and to their final products have been defined. For the first time we report observationally the existence of a dominant evolutionary path among massive red galaxies at 0.6 < z < 1.5, consisting in the conversion of irregular disks into irregular spheroids, and of these ones into regular spheroids. This result points to: 1) the massive red regular galaxies at low redshifts derive from the irregular ones populating the Red Sequence and its neighbourhood at earlier epochs up to z ~ 1.5; 2) the progenitors of the bulk of present-day massive red regular galaxies have been blue disks that have migrated to the Red Sequence majoritarily through major mergers at 0.6 < z < 1.2 (these mergers thus starting at z ~ 1.5); 3) the formation of E-S0's that end up with M* > 1011M⊙ at z = 0 through gas-rich major mergers has frozen since z ~ 0.6. Our results support that major mergers have played the dominant role in the definitive build-up of present-day E-S0's with M* > 1011M⊙ at 0.6 < z < 1.2, in good agreement with the hierarchical scenario proposed in the Eliche-Moral et al. (2010a) model (see also Eliche-Moral et al. 2010b). This study is published in Prieto et al. (2012). Supported by the Spanish Ministry of Science and Innovation (MICINN) under projects AYA2009-10368, AYA2006-12955, AYA2010-21887-C04-04, and AYA2009-11137, by the Madrid Regional Government through the AstroMadrid Project (CAM S2009/ESP-1496), and by the Spanish MICINN under the Consolider-Ingenio 2010 Program grant CSD2006-00070: ``First Science with the GTC'' (http://www.iac.es/consolider-ingenio-gtc/). S. D. H. & G.

A 454 Survey Reveals the Community Composition and Core Microbiome of the Common Bed Bug (Cimex lectularius) across an Urban Landscape

PubMed Central

Meriweather, Matthew; Matthews, Sara; Rio, Rita; Baucom, Regina S.

2013-01-01

Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs. PMID:23585900

A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an Urban Landscape.

PubMed

Meriweather, Matthew; Matthews, Sara; Rio, Rita; Baucom, Regina S

2013-01-01

Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4-V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.

A 600-year-long stratigraphic record of tsunamis in south-central Chile

USGS Publications Warehouse

Hong, Isabel; Dura, Tina; Ely, Lisa L.; Horton, Benajamin P.; Nelson, Alan R.; Cisternas, Marco; Nikitina, Daria; Wesson, Robert L.

2017-01-01

The stratigraphy within coastal river valleys in south-central Chile clarifies and extends the region’s history of large, earthquakes and accompanying tsunamis. Our site at Quidico (38.1°S, 73.3°W) is located in an overlap zone between ruptures of magnitude 8–9 earthquakes in 1960 and 2010, and, therefore, records tsunamis originating from subduction-zone ruptures north and south of the city of Concepción. Hand-dug pits and cores in a 3-m-thick sequence of freshwater peat in an abandoned meander (a little-examined depositional environment for tsunami deposits) and exposures along the Quidico River show five sand beds that extend as much as 1.2 km inland. Evidence for deposition of the beds by tsunamis includes tabular sand beds that are laterally extensive (>100 m), well sorted, fine upward, have sharp lower contacts, and contain diatom assemblages dominated by brackish and marine taxa. Using eyewitness accounts of tsunami inundation, 137Cs analyses, and 14C dating, we matched the upper four sand beds with historical tsunamis in 2010, 1960, 1835, and 1751. The oldest prehistoric bed dates to 1445–1490 CE and correlates with lacustrine and coastal records of similar-aged earthquakes and tsunamis in south-central Chile.

The stratigraphic distribution of large marine vertebrates and shell beds in the Pliocene of Tuscany

NASA Astrophysics Data System (ADS)

Dominici, Stefano; Benvenuti, Marco; Danise, Silvia

2015-04-01

The record of 337 shark fossils, 142 cetaceans and 10 sea cows from the Pliocene of Tuscany, mostly from historical museum collections, is revised. The majority of these fossils are concentrated at a few geographic sites from separated hinterland basins, on the South-Western side of the Northern Apennines. To better understand the meaning of these concentrations, the sequence stratigraphic distribution of more recent findings of large marine vertebrates is reconstructed against a high-resolution framework based on sedimentary facies analysis. These remains are usually covered by, or included in mudstones deposited far from the coast (N=12), skeletons being usually articulated, slightly displaced, and often bioeroded. A minor part of better preserved articulated skeletons is associated with sandstones from deltaic paleonenvironments (N=2). Marine mammal and shark remains may be associated with laterally-continuous shell accumulations, a type of concentration occurring at maximum flooding surfaces, separating relatively coarse-grained facies from open marine mudstones. Shell beds were bulk-sampled at 66 locations from six basins, covering a wide range of sedimentary facies, and spanning a chronologic interval of about 2.5 million years. A dataset of 62,655 mollusc specimens belonging to 496 species formed the basis of a statistical study to reconstruct the structure of the benthic communities, and to estimate paleodepths from intertidal to upper bathyal settings. Mollusc associations closely mirror the distribution of sedimentary facies, allowing for a fine tuning of the sequence stratigraphic architecture. Merging paleogeographic, stratigraphic and paleoecologic data, we conclude that the more abundant and diverse accumulations of large vertebrates took place in settings under the influence of coastal upwelling. A modern analogue occurs today in the Ligurian Sea, on the Tuscan offshore, where abundant nutrients carried by deep-marine currents of Western origin, within an otherwise oligotrophic Mediterranean Sea, sustain a rich and diverse cetacean and shark, epipelagic and mesopelagic community. The modern steep bathymetric gradient was displaced towards the East during the Pliocene, before the latest phases of uplift of the Northern Apennines. An open marine, nutrient-rich ecosystem influenced hinterland basins during major transgressive pulses, leading to a higher productivity and the formation of laterally-continuos accumulations of biogenic hard parts. A comparison with the few available studies on the sequence-stratigraphic distribution of large marine vertebrates and shell beds suggests that a model integrating high-productivity and sea level rise, favouring bone bed and shell bed formation, can be applied at other settings, and other geologic intervals.

Hydrocarbon Liquid Production via Catalytic Hydroprocessing of Phenolic Oils Fractionated from Fast Pyrolysis of Red Oak and Corn Stover

DOE PAGES

Elliott, Douglas C.; Wang, Huamin; Rover, Majorie; ...

2015-04-13

Phenolic oils were produced from fast pyrolysis of two different biomass feedstocks, red oak and corn stover and evaluated in hydroprocessing tests for production of liquid hydrocarbon products. The phenolic oils were produced with a bio-oil fractionating process in combination with a simple water wash of the heavy ends from the fractionating process. Phenolic oils derived from the pyrolysis of red oak and corn stover were recovered with yields (wet biomass basis) of 28.7 wt% and 14.9 wt%, respectively, and 54.3% and 58.6% on a carbon basis. Both precious metal catalysts and sulfided base metal catalyst were evaluated for hydrotreatingmore » the phenolic oils, as an extrapolation from whole bio-oil hydrotreatment. They were effective in removing heteroatoms with carbon yields as high as 81% (unadjusted for the 90% carbon balance). There was nearly complete heteroatom removal with residual O of only 0.4% to 5%, while N and S were reduced to less than 0.05%. Use of the precious metal catalysts resulted in more saturated products less completely hydrotreated compared to the sulfided base metal catalyst, which was operated at higher temperature. The liquid product was 42-52% gasoline range molecules and about 43% diesel range molecules. Particulate matter in the phenolic oils complicated operation of the reactors, causing plugging in the fixed-beds especially for the corn stover phenolic oil. This difficulty contrasts with the catalyst bed fouling and plugging, which is typically seen with hydrotreatment of whole bio-oil. This problem was substantially alleviated by filtering the phenolic oils before hydrotreating. More thorough washing of the phenolic oils during their preparation from the heavy ends of bio-oil or on-line filtration of pyrolysis vapors to remove particulate matter before condensation of the bio-oil fractions is recommended.« less

Hydrocarbon Liquid Production via Catalytic Hydroprocessing of Phenolic Oils Fractionated from Fast Pyrolysis of Red Oak and Corn Stover

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

Elliott, Douglas C.; Wang, Huamin; Rover, Majorie

Phenolic oils were produced from fast pyrolysis of two different biomass feedstocks, red oak and corn stover and evaluated in hydroprocessing tests for production of liquid hydrocarbon products. The phenolic oils were produced with a bio-oil fractionating process in combination with a simple water wash of the heavy ends from the fractionating process. Phenolic oils derived from the pyrolysis of red oak and corn stover were recovered with yields (wet biomass basis) of 28.7 wt% and 14.9 wt%, respectively, and 54.3% and 58.6% on a carbon basis. Both precious metal catalysts and sulfided base metal catalyst were evaluated for hydrotreatingmore » the phenolic oils, as an extrapolation from whole bio-oil hydrotreatment. They were effective in removing heteroatoms with carbon yields as high as 81% (unadjusted for the 90% carbon balance). There was nearly complete heteroatom removal with residual O of only 0.4% to 5%, while N and S were reduced to less than 0.05%. Use of the precious metal catalysts resulted in more saturated products less completely hydrotreated compared to the sulfided base metal catalyst, which was operated at higher temperature. The liquid product was 42-52% gasoline range molecules and about 43% diesel range molecules. Particulate matter in the phenolic oils complicated operation of the reactors, causing plugging in the fixed-beds especially for the corn stover phenolic oil. This difficulty contrasts with the catalyst bed fouling and plugging, which is typically seen with hydrotreatment of whole bio-oil. This problem was substantially alleviated by filtering the phenolic oils before hydrotreating. More thorough washing of the phenolic oils during their preparation from the heavy ends of bio-oil or on-line filtration of pyrolysis vapors to remove particulate matter before condensation of the bio-oil fractions is recommended.« less

Direct dating of paleomagnetic results from Precambrian sediments in the Amazon craton: Evidence for Grenvillian emplacement of exotic crust in SE Appalachians of North America

NASA Astrophysics Data System (ADS)

D'Agrella-Filho, Manoel S.; Tohver, Eric; Santos, João O. S.; Elming, Sten-Åke; Trindade, Ricardo I. F.; Pacca, Igor I. G.; Geraldes, Mauro C.

2008-03-01

We apply a new diagenetic dating technique to determine the age of magnetization for Precambrian sedimentary rocks in the SW Amazon craton. Two new paleomagnetic poles are reported from the rocks of the Aguapeí Gp.: red beds of the Fortuna Fm. (Plat = 59.8°N, Plon = 155.9°E, A95 = 9.5, K = 14, 18 sites, N/n 128/115, Q = 5) and the reverse-polarity mudstones of the overlying Vale da Promissão Formation (Plat = 49.5°N, Plon = 89.3°E, A95 = 12.5, K = 30, 6 sites, N/n = 94/80, Q = 4). The Fortuna Fm. magnetization is hosted by massive, interstitial hematite cement and constitutes a post-depositional remanence. The age of diagenesis of the red beds is well-constrained by the 1149 ± 7 Ma U-Pb age of authigenic xenotime rims on detrital zircons determined by SHRIMP analysis. The magnetite-hosted remanence of the Vale da Promissão Fm. may be detrital in origin, but the age of deposition is poorly constrained. The reliable and precisely-dated Fortuna Fm. paleomagnetic pole fixes the paleogeographic position of the Amazon craton near the SE Appalachians portion of North America at 1.15 Ga. These data demonstrate a mobile Grenvillian link between these two cratons, and support the recent identification of Amazon crust in the Blue Ridge province region of North America.

SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

PubMed

Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

2013-06-01

The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

Early alterations of red blood cell rheology in critically ill patients.

PubMed

Reggiori, Giulia; Occhipinti, Giovanna; De Gasperi, Andrea; Vincent, Jean-Louis; Piagnerelli, Michael

2009-12-01

To investigate red blood cell rheology in a large intensive care unit population on admission, and to assess the possible influence of comorbidities on the rheology. : Prospective study. Medico-surgical intensive care unit with 31 beds. All intensive care unit admissions during a 5-month period and 20 healthy volunteers. Blood sampling. A total of 196 intensive care patients (160 without and 36 with sepsis) and 20 healthy volunteers were studied. Red blood cell rheology (deformability and aggregation) was assessed ex vivo using the laser-assisted optical rotational cell analyzer (LORCA; Mechatronics Instruments BV, AN Zwaag, Netherlands) within the first 24 hrs after intensive care unit admission. Red blood cell deformability was determined by the elongation index in relation to the shear stress (0.3 to 50 Pa) applied on the red blood cell membrane surface. Aggregation was assessed by the aggregation index. Septic patients were more likely to have anemia, coagulation abnormalities, and comorbidities than were nonseptic patients. Red blood cell deformability was significantly altered in septic compared to nonseptic patients and volunteers for the majority of shear stress rates studied. The aggregation index was greater in septic patients than in volunteers (67.9% [54.7-73.5] vs. 61.8% [58.2-68.4]; p < .05). Only sepsis and hematologic disease influenced the elongation index (both p < .01). Other comorbidities, like cancer, diabetes mellitus, cirrhosis, and terminal renal failure, had no effect on the elongation index. Aggregation index was related to the degree of organ failure (Sequential Organ Failure Assessment score), the red blood cell count, and fibrinogen concentrations. Early alterations of red blood cell rheology are common in intensive care unit patients, especially in those with sepsis. Comorbidities (other than hematologic diseases) do not significantly influence these abnormalities. These alterations could contribute to the microcirculatory alterations observed in critically ill patients.

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.

Mass-losing peculiar red giants - The comparison between theory and observations

NASA Technical Reports Server (NTRS)

Jura, M.

1989-01-01

The mass loss from evolved red giants is considered. It seems that red giants on the Asymptotic Giant Branch (AGB) are losing between 0.0003 and 0.0006 solar mass/sq kpc yr in the solar neighborhood. If all the main sequence stars between 1 and 5 solar masses ultimately evolve into white dwarfs with masses of 0.7 solar mass, the predicted mass loss rate in the solar neighborhood from these stars is 0.0008 solar mass/sq kpc yr. Although there are still uncertainties, it appears that there is no strong disagreement between theory and observation.

Polydactylous Transverse Erythronychia: Report of a Patient with Multiple Horizontal Red Bands Affecting the Fingernails.

PubMed

Chang, Carina; Beutler, Bryce D; Cohen, Philip R

2017-06-01

Redness of the nail plate-erythronychia-is a common condition involving one or multiple digits. It may affect the entire nail or present as longitudinal red bands that extend from the proximal nail fold to the distal tip of the nail plate. Rarely, red bands may traverse the nail bed horizontally. Although erythronychia is often idiopathic, it has also been associated with amyloidosis, Darier's disease, lichen planus, and various other cutaneous conditions. We describe the clinical features of a 64-year-old Caucasian man who presented with transverse and longitudinal erythronychia affecting his fingernails. In addition, we review the classification of erythronychia and summarize the acute and chronic conditions that have been associated with this clinical finding. The features of a man with polydactylous transverse and longitudinal erythronychia are presented. In addition, PubMed was used to search the following terms: erythronychia, longitudinal erythronychia, red lunulae, and subungual. All papers were reviewed, and relevant articles, along with their references, were evaluated. Informed consent was obtained from the patient for being included in the study. A 64-year-old Caucasian man with a past medical history significant for testicular cancer and pulmonary embolism presented with multiple horizontal pink-red bands affecting his fingernails. The discoloration was most prominent in the region distal to the lunula. In addition, the nails of the fifth digit of his left hand and third digit of his right hand featured longitudinal red bands extending from the distal curvature of the lunula to the free edge of the nail plate. A diagnosis of polydactylous longitudinal and transverse erythronychia, based on the clinical presentation, was established. Our patient's red bands were asymptomatic and he was not concerned about the cosmetic appearance of his nails; therefore, no additional investigation or treatment was required. Polydactylous transverse erythronychia is a rare condition characterized by the development of horizontal red bands affecting the fingernails or toe nails. It has only been previously described in a man with multiple system atrophy. In our patient, both transverse and longitudinal red bands were present simultaneously. Therefore, it is possible that horizontal erythronychia is an early clinical manifestation of longitudinal erythronychia.

Understanding the degradation of Congo red and bacterial diversity in an air-cathode microbial fuel cell being evaluated for simultaneous azo dye removal from wastewater and bioelectricity generation.

PubMed

Sun, Jian; Li, Youming; Hu, Yongyou; Hou, Bin; Zhang, Yaping; Li, Sizhe

2013-04-01

We investigated the mechanism of Congo red degradation and bacterial diversity in a single-chambered microbial fuel cell (MFC) incorporating a microfiltration membrane and air-cathode. The MFC was operated continuously for more than 4 months using a mixture of Congo red and glucose as fuel. We demonstrated that the Congo red azo bonds were reduced at the anode to form aromatic amines. This is consistent with the known mechanism of anaerobic biodegradation of azo dyes. The MFC developed a less dense biofilm at the anode in the presence of Congo red compared to its absence indicating that Congo red degradation negatively affected biofilm formation. Denaturing gradient gel electrophoresis and direct 16S ribosomal DNA gene nucleotide sequencing revealed that the microbial communities differed depending on whether Congo red was present in the MFC. Geobacter-like species known to generate electricity were detected in the presence or absence of Congo red. In contrast, Azospirillum, Methylobacterium, Rhodobacter, Desulfovibrio, Trichococcus, and Bacteroides species were only detected in its presence. These species were most likely responsible for degrading Congo red.

Complete mitochondrial genomes of the yellow-bellied slider turtle Trachemys scripta scripta and anoxia tolerant red-eared slider Trachemys scripta elegans.

PubMed

Yu, Danna; Fang, Xindong; Storey, Kenneth B; Zhang, Yongpu; Zhang, Jiayong

2016-05-01

The complete mitochondrial genomes of the yellow-bellied slider (Trachemys scripta scripta) and anoxia tolerant red-eared slider (Trachemys scripta elegans) turtles were sequenced to analyze gene arrangement. The complete mt genomes of T. s. scripta and elegans were circular molecules of 16,791 bp and 16,810 bp in length, respectively, and included an A + 1 frameshift insertion in ND3 and ND4L genes. The AT content of the overall base composition of scripta and elegans was 61.2%. Nucleotide sequence divergence of the mt-genome (p distance) between scripta and elegans was 0.4%. A detailed comparison between the mitochondrial genomes of the two subspecies is shown.

Steam Reforming of Acetic Acid over Co-Supported Catalysts: Coupling Ketonization for Greater Stability

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

Davidson, Stephen D.; Spies, Kurt A.; Mei, Donghai

We report on the markedly improved stability of a novel 2-bed catalytic system, as compared to a conventional 1-bed steam reforming catalyst, for the production of H2 from acetic acid. The 2-bed catalytic system comprises of i) a basic oxide ketonization catalyst for the conversion of acetic acid to acetone, and a ii) Co-based steam reforming catalyst, both catalytic beds placed in sequence within the same unit operation. Steam reforming catalysts are particularly prone to catalytic deactivation when steam reforming acetic acid, used here as a model compound for the aqueous fraction of bio-oil. Catalysts comprising MgAl2O4, ZnO, CeO2, andmore » activated carbon (AC) both with and without Co-addition were evaluated for conversion of acetic acid and acetone, its ketonization product, in the presence of steam. It was found that over the bare oxide support only ketonization activity was observed and coke deposition was minimal. With addition of Co to the oxide support steam reforming activity was facilitated and coke deposition was significantly increased. Acetone steam reforming over the same Co-supported catalysts demonstrated more stable performance and with less coke deposition than with acetic acid feedstock. DFT analysis suggests that over Co surface CHxCOO species are more favorably formed from acetic acid versus acetone. These CHxCOO species are strongly bound to the Co catalyst surface and could explain the higher propensity for coke formation from acetic acid. Based on these findings, in order to enhance stability of the steam reforming catalyst a dual-bed (2-bed) catalyst system was implemented. Comparing the 2-bed and 1-bed (Co-supported catalyst only) systems under otherwise identical reaction conditions the 2-bed demonstrated significantly improved stability and coke deposition was decreased by a factor of 4.« less

Explosion of a supernova with a red giant companion

NASA Technical Reports Server (NTRS)

Livne, E.; Tuchman, Y.; Wheeler, J. C.

1992-01-01

Two-dimensional numerical simulations of the collision between spherical ejecta from a supernova and a red giant companion are presented. In contrast to previous numerical studies, in which the companion was a main-sequence star or a compact object, the collision consequences are found to have a dramatic impact upon the red giant. In most cases the red giant companion loses most of its envelope in a time scale of 10 exp 7 s with typical velocities about an order of magnitude less than those of the expanding velocity of the supernova shell. We confirm the conclusion of Chugai (1986) that the stripped hydrogen tends to come off as a low-velocity component interior to the supernova ejecta. Possible observational consequences of the results are discussed.

Rejuvenation Stage Volcanics at Laeo Kilauea, Kauai, Hawaii

NASA Astrophysics Data System (ADS)

Thordarson, T.; Garcia, M.; Wanless, D.; Tagami, T.; Sano, H.

2005-12-01

The Plio-Pleistocene Koloa volcanic series represents the rejuvenated volcanism on Kauai, one of the oldest main Hawaiian Islands. The Koloa series is made up of highly alkalic basalt and associated sedimentary rocks that rest unconformably on the shield-building Waimea Canyon volcanic series. Koloa vents are dispersed across the eastern two-thirds of the island and typically consist of scoria or lava cones that fed broad lava flow fields blanketing the marginal lowlands on the south, east and north side of the island. The northernmost subaerial Koloa vents are found at Laeo Kilauea on the north shore of the island. At Laeo Kilauea the volcanic succession is unusual in that it contains the only phreatomagmatic vent structures of the Koloa series. Here an ~2-km-long costal cliff face reveals a bedded phreatomagmatic tephra sequence that is >90-m-thick and represents the remnant of an a much large tuff cone (>2-km in diameter). The tuff cone sequence is characterized by decimeter to meters thick layers, where cross-bedded ash beds alternate with massive and poorly sorted lapilli tuff beds. The cross-bedded deposits were produced by dry and wet surges, whereas the poorly sorted beds represent fall deposits produced by sustained eruption column (i.e. continuous up-rush) or tephra jets (i.e. rooster-tail explosions). The juvenile clast population of the tephra consists of olivine-phyric foidite, but it also contains abundant wall-rock lithics, including fragments of reef-limestone. The base of the tuff cone outcrops at Mokolea point on the east side of the outcrop, where phreatomagmatic tephra rests directly on an older Koloa pahoehoe flow, a olivine- and mellelite-phyric foidite lava. The tephra sequence is cut by an ~1-m-thick olivine-bearing basanite dike, which acted as a feeder for the fountain-fed spatter and lava (up to 100-m-thick) that cap the phreatomagmatic tephra sequence. These units are separated by a 2-3 m thick soil horizon formed by weathering of the tuff. These three formations have been dated by Ar-Ar giving 2.65 +/- 0.35 Ma for the age of the basal foidite lava, 1.68 +/- 0.11 Ma for the tuff cone and 0.69 +/- 0.03 Ma for the overlying fountain-fed basanite lava. Important conclusions that can be drawn from the results of this study include: (1) The characteristics of the phreatomagmatic tephra indicate that at times the tuff cone crater was filled with water implying that the eruption site was submarine and most likely located in shallow coastal waters. The presence of reef-limestone fragments in the tephra supports this notion. On the other hand, the underlying and overlying lava flows, which do extend an unknown distance beyond the current shoreline, were clearly deposited on dry land. This implies that Kauai experienced significant changes in sea level in early to mid Pleistocene times. (2) The eruptions that produced the tuff cone and the overlying fountain-fed basanite lava are one million years apart, yet the dikes that fed these eruptions appear to have followed a similar path to the surface. This indicates that the magma is utilizing preexisting structural weaknesses to reach the surface.

Reprint of "Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi".

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-07-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Yellow Canary uranium deposits, Daggett County, Utah

USGS Publications Warehouse

Wilmarth, Verl Richard

1953-01-01

The Yellow Canary uranium deposit is on the west side of Red Creek Canyon in the northern part of the Uinta Mountains, Daggett County, Utah. Two claims have been developed by means of an adit, three opencuts, and several hundred feet of bulldozer trenches. No uranium ore has been produced from this deposit. The deposit is in the pre-Cambrian Red Creek quartzite. This formation is composed of intercalated beds of quartzite, hornblendite, garnet schist, staurolite schist, and quartz-mica schist and is intruded by dioritic dikes. A thick unit of highly fractured white quartzite near the top of the formation contains tyuyamunite as coatings on fracture surfaces. The tyuyamunite is associated with carnotite, volborthite, iron oxides, azurite, malachite, brochantite, and hyalite. The uranium and vanadium minerals are probably alteration products of primary minerals. The uranium content of 15 samples from this property ranged from 0.000 to 0.57 percent.

Exposure to an environment containing the aromatic red cedar, Juniperus virginiana: procarcinogenic, enzyme-inducing and insecticidal effects.

PubMed

Sabine, J R

1975-11-01

(1) Shavings from the Eastern Red Cedar (Juniperus virginiana) were examined for three diverse biological properties, i.e. enzyme induction, procarcinogenicity and insecticidal activity. (2) The ability of a cedar environment to stimulate liver drug-metabolizing enzymes in mice was confirmed by lowered values for barbiturate sleeping time. (3) In susceptible strains of mice (C3H-Avy, C3H-AvyfB and CBA/J) the use of cedar shavings as bedding increased significantly the incidence of spontaneous tumors of the liver and mammary gland, and also reduced the average time at which tumors appeared. (4) Cedar and some of its derivatives (Oil of Cedarwood, cedrene, cedrol) disrupted the reproductive and developmental cycle of a number of insects, including the Peanut Trash Bug (Elasmolomus sordidus), the Indian Meal Moth (Plodia interpunctella) and the Forage Mite (Tyrophagus putrescentiae).

Cellular aging (the Hayflick limit) and species longevity: a unification model based on clonal succession.

PubMed

Juckett, D A

1987-03-01

A model is presented which proposes a specific cause-and-effect relationship between a limited cell division potential and the maximum lifespan of humans and other mammals. It is based on the clonal succession hypothesis of Kay which states that continually replicating cell beds (e.g. bone marrow, intestinal crypts, epidermis) could be composed of cells with short, well-defined division potentials. In this model, the cells of these beds are proposed to exist in an ordered hierarchy which establishes a specific sequence for cell divisions throughout the organism's lifespan. The depletion of division potential at all hierarchical levels leads to a loss of bed function and sets an intrinsic limit to species longevity. A specific hierarchy for cell proliferation is defined which allows the calculation of time to bed depletion and, ultimately, to organism mortality. The model allows the existence of a small number (n) of critical cell beds within the organism and defines organism death as the inability of any one of these beds to produce cells. The model is consistent with all major observations related to cellular and organismic aging. In particular, it links the PDLs (population doubling limit) observed for various species to their mean lifespan; it explains the slow decline in PDL as a function of age of the donor; it establishes a thermodynamically stable maximum lifespan for a disease-free population; and it can explain why tissue transplants outlive donors or hosts.

Selective Preservation of Fossil Ghost Fish

NASA Astrophysics Data System (ADS)

Meacham, Amanda

2016-04-01

A unique type of fossil fish preservation has been discovered in the Angelo Member (Fossil Lake) of the Green River Formation. The Angelo Member is a predominately evaporative deposit dominated by dolomite, but contains facies of fossiliferous laminated calcimicrite. Fossil fish occurring in two beds conspicuously lack bones. Fish in the lower bed are only preserved as organic material, including skin, pigments, and eyes. Fish in the upper bed have three-dimensional etching where bones once existed but also contain skin, pigments, and eyes. The top third of the upper bed often contains calcite crystals that are pseudomorphs after trona and possibly halite. Preliminary mineralogical analysis and mapping of evaporate facies suggests that this unique preservation may be related to lake geochemical conditions, such as high pH and alkalinity. To our knowledge, this is the first time this type of preservation has been observed and studied. Fossils and sediments within these beds are being studied both vertically and laterally through the one-meter thick sequence containing the fossil fish using XRD, isotopic, SEM, thin section, and total organic carbon analysis. Nine quarries, 0.5-1 meter square, were excavated for both fossils and rock samples along with 17 additional rock sample locations across an approximately 25-kilometer square region. This investigation has the capability of reconstructing the paleoenvironment and lake chemistry of Fossil Lake during the deposition of the "ghost-fish" beds and solving the mystery of the "missing bones" and the unusual process of preservation.

Geology of deep-water sandstones in the Mississippi Stanley Shale at Cossatot Falls, Arkansas

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

Coleman, J.L. Jr.

1993-09-01

The Mississippian Stanley Shale crops out along the Cossatot River in the Ouachita Mountains of western Arkansas. Here, exposures of deep-water sandstones and shales, on recently established public lands, present a rare, three-dimensional look at sandstones of the usually obscured Stanley. Cossatot Falls, within the Cossatot River State Park Natural Area, is a series of class IV and V rapids developed on massive- to medium-bedded quartz sandstones on the northern flank of an asymmetric, thrust-faulted anticline. In western Arkansas, the Stanley Shale is a 10,000-ft (3200-m) succession of deep-water sandstone and shale. At Cossatot Falls, approximately 50 ft (155 m)more » of submarine-fan-channel sedimentary rocks are exposed during low-river stages. This section is composed primarily of sets of thinning-upward sandstone beds. With rare exceptions, the sandstones are turbidites, grading from massive, homogeneous, basal beds upward through festoon-cross-bedded thick beds, into rippled medium and thin beds. Sandstone sets are capped by thin shales and siltstones. Regional, north-northwestward paleocurrent indicators are substantiated by abundant, generally east-west ripple crests asymmetric to the north-northwest. Flute casts at the top of the sandstone sequence indicate an additional east-ward flow component. Based on regional, lithologic characteristics, the sandstones at Cossatot Falls appear to be within the Moyers Formation. The Moyers is the upper sandstone unit of the Stanley and is an oil and gas reservoir in the eastern Oklahoma Ouachita Mountains.« less

Identification of genotyping-by-sequencing sequence tags associated with milling performance and end-use quality traits in hard red spring wheat (Triticum aestivum L.)

USDA-ARS?s Scientific Manuscript database

Wheat quality is defined by culinary end-uses and processing characteristics. Wheat breeders are interested to identify quantitative trait loci for grain, milling, and end-use quality traits because it is imperative to understand the genetic complexity underlying quantitatively inherited traits to ...

In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus)

PubMed Central

Wang, Le; Yu, Cuiping; Guo, Liang; Lin, Haoran; Meng, Zining

2015-01-01

The common coral trout is one species of major importance in commercial fisheries and aquaculture. Recently, two different color morphs of Plectropomus leopardus were discovered and the biological importance of the color difference is unknown. Since coral trout species are poorly characterized at the molecular level, we undertook the transcriptomic characterization of the two color morphs, one black and one red coral trout, using Illumina next generation sequencing technologies. The study produced 55162966 and 54588952 paired-end reads, for black and red trout, respectively. De novo transcriptome assembly generated 95367 and 99424 unique sequences in black and red trout, respectively, with 88813 sequences shared between them. Approximately 50% of both trancriptomes were functionally annotated by BLAST searches against protein databases. The two trancriptomes were enriched into 25 functional categories and showed similar profiles of Gene Ontology category compositions. 34110 unigenes were grouped into 259 KEGG pathways. Moreover, we identified 14649 simple sequence repeats (SSRs) and designed primers for potential application. We also discovered 130524 putative single nucleotide polymorphisms (SNPs) in the two transcriptomes, supplying potential genomic resources for the coral trout species. In addition, we identified 936 fast-evolving genes and 165 candidate genes under positive selection between the two color morphs. Finally, 38 candidate genes underlying the mechanism of color and pigmentation were also isolated. This study presents the first transcriptome resources for the common coral trout and provides basic information for the development of genomic tools for the identification, conservation, and understanding of the speciation and local adaptation of coral reef fish species. PMID:26713756

Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data.

PubMed

Mao, X; Sahana, G; De Koning, D-J; Guldbrandtsen, B

2016-04-01

Male calves and culled cows of dairy cattle are used for beef production. However, unlike beef breeds, the genetics of growth performance traits in dairy breeds have not been extensively studied. Here, we performed a genome-wide association study (GWAS) on Holsteins ( = 5,519), Jerseys ( = 1,231), and Red Dairy Cattle ( = 4,410) to identify QTL for growth traits. First, a GWAS was performed within breeds using whole-genome sequence variants. Later, a meta-analysis was performed to combine information across the 3 breeds. We have identified several QTL that have large effects on growth traits in Holsteins and Red Dairy Cattle but with little overlap across breeds. Only 1 QTL located on chromosome 10 was shared between Holsteins and Red Dairy Cattle. The most significant variant (BTA10:59,164,533, rs43636323; -value = 2.8 × 10) in this QTL explained 2.4% of the total additive genetic variance in Red Dairy Cattle. The gene is a strong candidate for the underlying gene of this QTL. In Red Dairy Cattle, a QTL near 25 Mb on chromosome 14 was very significantly associated with growth traits, consistent with the previously reported gene , which affects growth in beef cattle and humans. No QTL for growth performance was statistically significant in Jerseys, possibly due to the low power of detection with the small sample size. The meta-analysis of the 3 breeds increased the power to detect QTL.

Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters.

PubMed

Thimmaiah, Tim; Voje, William E; Carothers, James M

2015-01-01

With progress toward inexpensive, large-scale DNA assembly, the demand for simulation tools that allow the rapid construction of synthetic biological devices with predictable behaviors continues to increase. By combining engineered transcript components, such as ribosome binding sites, transcriptional terminators, ligand-binding aptamers, catalytic ribozymes, and aptamer-controlled ribozymes (aptazymes), gene expression in bacteria can be fine-tuned, with many corollaries and applications in yeast and mammalian cells. The successful design of genetic constructs that implement these kinds of RNA-based control mechanisms requires modeling and analyzing kinetically determined co-transcriptional folding pathways. Transcript design methods using stochastic kinetic folding simulations to search spacer sequence libraries for motifs enabling the assembly of RNA component parts into static ribozyme- and dynamic aptazyme-regulated expression devices with quantitatively predictable functions (rREDs and aREDs, respectively) have been described (Carothers et al., Science 334:1716-1719, 2011). Here, we provide a detailed practical procedure for computational transcript design by illustrating a high throughput, multiprocessor approach for evaluating spacer sequences and generating functional rREDs. This chapter is written as a tutorial, complete with pseudo-code and step-by-step instructions for setting up a computational cluster with an Amazon, Inc. web server and performing the large numbers of kinefold-based stochastic kinetic co-transcriptional folding simulations needed to design functional rREDs and aREDs. The method described here should be broadly applicable for designing and analyzing a variety of synthetic RNA parts, devices and transcripts.

Causative Role of Grapevine Red Blotch Virus in Red Blotch Disease.

PubMed

Yepes, Luz Marcela; Cieniewicz, Elizabeth; Krenz, Björn; McLane, Heather; Thompson, Jeremy R; Perry, Keith Lloyd; Fuchs, Marc

2018-05-17

Grapevine red blotch virus (GRBV) has a monopartite single-stranded DNA genome and is the type species of the genus Grablovirus in the family Geminiviridae. To address the etiological role of GRBV in the recently recognized red blotch disease of grapevine, infectious GRBV clones were engineered from the genome of each of the two previously identified phylogenetic clades for Agrobacterium tumefaciens-mediated inoculations of tissue culture-grown Vitis spp. plants. Following agroinoculation and one or two dormancy cycles, systemic GRBV infection was detected by multiplex polymerase chain reaction (PCR) in Vitis vinifera exhibiting foliar disease symptoms but not in asymptomatic vines. Infected rootstock genotype SO4 (V. berlandieri × V. riparia) exhibited leaf chlorosis and cupping, while infection was asymptomatic in agroinoculated 110R (V. berlandieri × V. rupestris), 3309C (V. riparia × V. rupestris), and V. rupestris. Spliced GRBV transcripts of the replicase-associated protein coding region accumulated in leaves of agroinfected vines, as shown by reverse-transcription PCR; this was consistent with systemic infection resulting from virus replication. Additionally, a virus progeny identical in nucleotide sequence to the infectious GRBV clones was recovered from agroinfected vines by rolling circle amplification, cloning, and sequencing. Concomitantly, subjecting naturally infected grapevines to microshoot tip culture resulted in an asymptomatic plant progeny that tested negative for GRBV in multiplex PCR. Altogether, our agroinoculation and therapeutic experiments fulfilled Koch's postulates and revealed the causative role of GRBV in red blotch disease.

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

PubMed Central

Röthig, Till; Yum, Lauren K.; Kremb, Stephan G.; Roik, Anna; Voolstra, Christian R.

2017-01-01

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment. PMID:28303925

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment.

PubMed

Röthig, Till; Yum, Lauren K; Kremb, Stephan G; Roik, Anna; Voolstra, Christian R

2017-03-17

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L -1 ) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.

Molecular delineation of the Agave Red Worm Comadia redtenbacheri  (Lepidoptera: Cossidae).

PubMed

CÁrdenas-Aquino, MarÍa Del Rosario; AlarcÓn-rodrÍguez, Norma Marina; Rivas-Medrano, Mario; GonzÁlez-hernÁndez, HÉctor; Vargas-hernÁndez, Mateo; SÁnchez-Arroyo, Hussein; Llanderal-cÁzares, Celina

2018-01-25

Comadia redtenbacheri (Hammerschmidt) (Agave Red Worm) is the only member of the family Cossidae that has been described as a phytophagous specialist of the plant genus Agave, which is mainly distributed in México. A new extraction protocol adapted from Stewart Via (1993) has been implemented for sequencing the COI gene from samples collected in five states of the North Central (Querétaro and Zacatecas), South Central (Estado de México) and East Central (Hidalgo and Tlaxcala) regions of México with the purpose of contributing to delineation of the species. A Maximum Likelihood (ML) tree based on these COI sequences as well as COI sequences from other Cossinae species was developed to complement the existing morphological and taxonomic approaches to delineation of this species. As expected, our Comadia samples cluster together within a monophyletic clade that includes four C. redtenbacheri sequences previously reported. This group seems to be consistent with our reconstruction, which is supported by a bootstrap value of over 99%. The closely related branches associated with the latter group include organisms known to be the plant and tree borers of the Cossinae subfamily. The COI sequences from our samples were analyzed to determine the percentage of identity among the C. redtenbacheri in a first attempt to detect differences in the sequence that matches a particular region of México.

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.

Influence of Flow Sequencing Attributed to Climate Change and Climate Variability on the Assessment of Water-dependent Ecosystem Outcomes

NASA Astrophysics Data System (ADS)

Wang, J.; Nathan, R.; Horne, A.

2017-12-01

Traditional approaches to characterize water-dependent ecosystem outcomes in response to flow have been based on time-averaged hydrological indicators, however there is increasing recognition for the need to characterize ecological processes that are highly dependent on the sequencing of flow conditions (i.e. floods and droughts). This study considers the representation of flow regimes when considering assessment of ecological outcomes, and in particular, the need to account for sequencing and variability of flow. We conducted two case studies - one in the largely unregulated Ovens River catchment and one in the highly regulated Murray River catchment (both located in south-eastern Australia) - to explore the importance of flow sequencing to the condition of a typical long-lived ecological asset in Australia, the River Red Gum forests. In the first, the Ovens River case study, the implications of representing climate change using different downscaling methods (annual scaling, monthly scaling, quantile mapping, and weather generator method) on the sequencing of flows and resulting ecological outcomes were considered. In the second, the Murray River catchment, sequencing within a historic drought period was considered by systematically making modest adjustments on an annual basis to the hydrological records. In both cases, the condition of River Red Gum forests was assessed using an ecological model that incorporates transitions between ecological conditions in response to sequences of required flow components. The results of both studies show the importance of considering how hydrological alterations are represented when assessing ecological outcomes. The Ovens case study showed that there is significant variation in the predicted ecological outcomes when different downscaling techniques are applied. Similarly, the analysis in the Murray case study showed that the drought as it historically occurred provided one of the best possible outcomes for River Red Gum forests when compared to other re-arrangements of flow within the same drought. These results have implications for the way we represent climate change impacts and drought risk assessments where ecological outcomes are a key management objective.

Dinoflagellate cysts and pollen from the Tjörnes / Breidavik section: a biostratigraphical and palaeoclimatological study of Plio-Pleistocene sediments from northern Iceland.

NASA Astrophysics Data System (ADS)

Verhoeven, Koen; Louwye, Stephen; Eiríksson, Jon

2010-05-01

On the Tjörnes peninsula in northern Iceland, a unique sequence of Plio-Pleistocene shallow marine, continental and glacial sediments is exposed in cliffs near the Tjörnes Fracture Zone. The lowest part of the sequence consists of the more than 500 m thick Tjörnes beds of Pliocene age. In the overlying Breidavik Group, marine interglacial sediments are present together with lava flows and glacial deposits. In this unit, cycles 3, 4, 5 and 7 of the 14 glacial/interglacial cycles were examined for palynomorphs. Sixty eight samples from the sedimentary succession of the Tjörnes beds and 20 samples from the overlying Breidavik Group were palynologicaly investigated for dinoflagellate cysts, pollen and spores. Despite the fact that half of the samples were barren or yielded a very low dinoflagellate cyst concentration (<25 cysts/g), the recovered assemblage holds valuable palaeoecological and biostratigraphical information. The dinoflagellate cyst assemblage from the Tjörnes section reflects a Pliocene flora. Typical Miocene species disappearing at the Miocene - Pliocene boundary (5.33 Ma) such as Selenopemphix armageddonensis are not observed. The combination of the Pliocene record and the lack of typical Miocene species sets a maximum age for the base of the Tjörnes Beds at 5.33 Ma. The nearly continuous occurrence of Batiacasphaera minuta (highest occurrence at 3.8 Ma) and Operculodinium tegillatum (HO at 3.7 Ma) in the upper part of the Tjörnes beds (the Serripes mollusc zone) gives a minimum age of about 3.7 Ma for the top of this zone. These results indicate that the sediments of the Tjörnes beds are older and were deposited faster than previously thought, based on a K/Ar dating of the overlying basalt flows (Albertsson, 1976). In the Serripes zone, the new species Selenopemphix islandicus was recorded. Observations of fragile heterotrophic cysts such as Barssidinium pliocenicum (HO at 2.66 Ma), Echinidinium euaxum (HO at 2.66 Ma), Selenopemphix dionaeacysta (HO at 2.4 to 2.6 Ma) and Trinovantedinium glorianum (HO 2.4 to 2.6 Ma) in the Hörgi Formation sets a minimum age of 2.7 Ma for the third glacial/interglacial cycle. In accordance to the age of the upper Tjörnes beds, this formation has to be older than thought in the present age model of the outcrop. (Símonarson and Eiríksson, 2008). The biostratigraphical analysis indicates an upper Piacenzian age for the Hörgi Formation, instead of the previous Gelasian age. The K/Ar dates of the Höskuldsvik lavas between the Tjörnes beds and the Breidavik Group (2.55+/-0.27Ma; 2.36+/-0.16Ma) appears to be too young. Sea surface temperature reconstruction of the ocean water based on the warm/cold ratio of dinoflagellate cysts indicates higher values for the Tjörnes beds and the Hörgi Formation (3), compared to the colder water of the Svarthamar (5) and Torfhóll (7) Members. The appearance of pollen of temperate plants such as Ilex, Juglans and Tilia in the Tjörnes beds ánd the Hörgi Formation confirms the Pliocene age, and is in agreement with the dinoflagellate cyst biostratigraphy. References: Albertsson, K.J. 1976: K/Ar ages of Pliocene-Pleistocene glaciations in Iceland with special reference to the Tjörnes sequence, northern Iceland. PhD thesis University of Cambridge, 268pp. Símonarson, L.A. and Eiríksson, J. 2008: Tjörnes - Pliocene and Pleistocene sediments and fauna. Jökull 58, 331-342.

LIVING WITH A RED DWARF: ROTATION AND X-RAY AND ULTRAVIOLET PROPERTIES OF THE HALO POPULATION KAPTEYN’S STAR

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

Guinan, Edward F.; Engle, Scott G.; Durbin, Allyn, E-mail: scott.engle@villanova.edu

As part of Villanova’s Living with a Red Dwarf program, we have obtained UV, X-ray, and optical data of the Population II red dwarf—Kapteyn’s Star. Kapteyn’s Star is noteworthy for its large proper motions and high radial velocity of ∼+245 km s{sup −1}. As the nearest Pop II red dwarf, it serves as an old age anchor for calibrating activity/irradiance–rotation–age relations, and an important test bed for stellar dynamos and the resulting X-ray–UV emissions of slowly rotating, near-fully convective red dwarf stars. Adding to the notoriety, Kapteyn’s Star has recently been reported to host two super-Earth candidates, one of whichmore » (Kapteyn b) is orbiting within the habitable zone. However, Robertson et al. questioned the planet’s existence since its orbital period may be an artifact of activity, related to the star’s rotation period. Because of its large Doppler-shift, measures of the important, chromospheric H i Lyα 1215.67 Å emission line can be reliably made, because it is mostly displaced from ISM and geo-coronal sources. Lyα emission dominates the FUV region of cool stars. Our measures can help determine the X-ray–UV effects on planets hosted by Kapteyn’s Star, and planets hosted by other old red dwarfs. Stellar X-ray and Lyα emissions have strong influences on the heating and ionization of upper planetary atmospheres and can (with stellar winds and flares) erode or even eliminate planetary atmospheres. Using our program stars, we have reconstructed the past exposures of Kapteyn’s Star's planets to coronal—chromospheric XUV emissions over time.« less

Kinderhookian (Lower Mississippian) calcareous rocks of the Howard Pass quadrangle, western Brooks Range: A section in Geologic studies in Alaska by the U.S. Geological Survey, 1995

USGS Publications Warehouse

Dumoulin, Julie A.; Harris, Anita G.

1997-01-01

Calcareous rocks of Kinderhookian (early Early Mississippian) age are widely distributed across the Howard Pass quadrangle in the western Brooks Range. Most occur in the lower part of the Lisburne Group (herein called the Rough Mountain Creek unit) and the upper part of the Endicott Group (Kayak Shale) in two sequences (Key Creek and Aniuk River) of the Endicott Mountains allochthon. Kinderhookian strata are also found in the Kelly River allochthon (Utukok Formation?) and in sections of uncertain stratigraphic affinity and structural level spatially associated with mafic volcanic rocks.Predominant Kinderhookian lithologies in the Lisburne Group are skeletal supportstone (rich in pelmatozoans, bryozoans, and brachiopods) and lesser spiculite; skeletal supportstone and calcarenite are the chief calcareous rock types in the Kayak Shale. Conodont and brachiopod faunas indicate that all of the Rough Mountain Creek unit and much of the Kayak Shale in the study area are of late Kinderhookian age. Lithologic and paleontologic data suggest that Kinderhookian strata in the Howard Pass quadrangle were deposited largely in inner- and middle-shelf settings with normal marine salinity and locally high energy. Overall, calcareous beds in the Rough Mountain Creek unit accumulated in a wider range of environments, less subject to siliciclastic input, than did calcareous beds in the Kayak, and Kinderhookian beds of both units in the Key Creek sequence formed in less diverse, somewhat shallower environments than correlative rocks in the Aniuk River sequence. Lithofacies patterns and contact relations imply that decreased siliciclastic influx, perhaps accompanied by relative sea-level rise, initiated deposition of the Rough Mountain Creek unit; relative sea-level rise and concurrent circulatory restriction most likely ended its deposition.Kinderhookian calcareous rocks in the Howard Pass quadrangle have several implications for middle Paleozoic paleogeography of the western Brooks Range. First, sequences of the Endicott Mountains allochthon that contain the Rough Mountain Creek unit contrast sharply with other sequences included in this allochthon that contain thicker and younger Carboniferous platform carbonate successions. These differences in stratigraphic succession suggest significant shortening within the Endicott Mountains allochthon. Second, Kinderhookian calcareous rocks in the Howard Pass quadrangle may have been a secondary source for carbonate turbidites of the Rim Butte unit (Ipnavik allochthon).

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

PubMed

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.