30 CFR 250.1623 - Well-control fluids, equipment, and operations.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., (2) A well-control fluid-volume measuring device for determining fluid volumes when filling the hole on trips, and (3) A recording mud-pit-level indicator to determine mud-pit-volume gains and losses... the change in fluid level decreases the hydrostatic pressure 75 psi or every five stands of drill pipe...

Evolution of mud-capped dredge pits following excavation: sediment trapping and slope instability

NASA Astrophysics Data System (ADS)

Obelcz, J.; Xu, K.; Bentley, S. J.; Li, C.; Miner, M. D.; O'Connor, M. C.; Wang, J.

2016-02-01

Many fluvial channels incised the Northern Gulf of Mexico inner continental shelf during the late Quaternary. Mud-capped dredge pits (MCDPs), which are generally elongate and deep (8-10 m) excavations, target sandy fluvial channel deposits for coastal restoration projects. The morphological evolution of dredge excavations in noncohesive sandy substrate is well studied, but MCDPs have up to a several-meter-thick veneer of Holocene shelf mud overlying sandy channel deposits. This stratigraphy is hypothesized to result in more complex post-dredge morphology than pit walls simply slumping to the angle of repose shortly after excavation. Numerical modeling of MCDP post-dredge response conducted prior to excavation indicates pit walls may retrogressively fail, which is accounted for in pit design by assigning no-dredge setback buffers from pipelines or cultural and environmental resources. To validate model results and test effectiveness of setback buffers, a geophysical survey of the Sandy Point MCDP (20 km west of the Mississippi River Delta in 10m deep water), where 1.7 million m3 of sandy sediment was excavated in 2012, was conducted May 2015. A total of 84 line-km of high-resolution chirp subbottom and a 27 km2 grid of swath bathymetry and sidescan sonar were collected. The data indicate the dredge pit walls are differentially slumping, with the western pit wall in a more active state of failure than the eastern wall. The western failures morphologically resemble features observed along the muddy Mississippi River Delta Front at water depths of 20-100 m, including bowl-shaped collapse failures and retrogressive stair-stepped slumps; these failures may play a key role in evaluating the distance of setback buffer zone to pipelines. These features indicate the cohesive mud overlying the sandy infill has a prominent role in pit wall stability. A 0.5-1 m thick acoustically transparent package overlies the entire pit floor (interpreted as a possible fluid mud layer), overlying 1-3 m of post-dredge deposition that is concentrated along the western wall and center of the pit. The Sandy Point MCDP lies within a clockwise gyre, and its relief may serve as a significant trap of suspended sediment. These findings emphasize the role MCDPs play in sediment dynamics as well as their potential for submarine geohazards.

Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue.

PubMed

Kislinger, Thomas; Gramolini, Anthony O; MacLennan, David H; Emili, Andrew

2005-08-01

An optimized analytical expression profiling strategy based on gel-free multidimensional protein identification technology (MudPIT) is reported for the systematic investigation of biochemical (mal)-adaptations associated with healthy and diseased heart tissue. Enhanced shotgun proteomic detection coverage and improved biological inference is achieved by pre-fractionation of excised mouse cardiac muscle into subcellular components, with each organellar fraction investigated exhaustively using multiple repeat MudPIT analyses. Functional-enrichment, high-confidence identification, and relative quantification of hundreds of organelle- and tissue-specific proteins are achieved readily, including detection of low abundance transcriptional regulators, signaling factors, and proteins linked to cardiac disease. Important technical issues relating to data validation, including minimization of artifacts stemming from biased under-sampling and spurious false discovery, together with suggestions for further fine-tuning of sample preparation, are discussed. A framework for follow-up bioinformatic examination, pattern recognition, and data mining is also presented in the context of a stringent application of MudPIT for probing fundamental aspects of heart muscle physiology as well as the discovery of perturbations associated with heart failure.

Environmental dust effects on aluminum surfaces in humid air ambient.

PubMed

Yilbas, Bekir Sami; Hassan, Ghassan; Ali, Haider; Al-Aqeeli, Nasser

2017-04-05

Environmental dusts settle on surfaces and influence the performance of concentrated solar energy harvesting devices, such as aluminum troughs. The characteristics of environmental dust and the effects of mud formed from the dust particles as a result of water condensing in humid air conditions on an aluminum wafer surface are examined. The dissolution of alkaline and alkaline earth compounds in water condensate form a chemically active mud liquid with pH 8.2. Due to gravity, the mud liquid settles at the interface of the mud and the aluminum surface while forming locally scattered patches of liquid films. Once the mud liquid dries, adhesion work to remove the dry mud increases significantly. The mud liquid gives rise to the formation of pinholes and local pit sites on the aluminum surface. Morphological changes due to pit sites and residues of the dry mud on the aluminum surface lower the surface reflection after the removal of the dry mud from the surface. The characteristics of the aluminum surface can address the dust/mud-related limitations of reflective surfaces and may have implications for the reductions in the efficiencies of solar concentrated power systems.

Environmental dust effects on aluminum surfaces in humid air ambient

PubMed Central

Yilbas, Bekir Sami; Hassan, Ghassan; Ali, Haider; Al-Aqeeli, Nasser

2017-01-01

Environmental dusts settle on surfaces and influence the performance of concentrated solar energy harvesting devices, such as aluminum troughs. The characteristics of environmental dust and the effects of mud formed from the dust particles as a result of water condensing in humid air conditions on an aluminum wafer surface are examined. The dissolution of alkaline and alkaline earth compounds in water condensate form a chemically active mud liquid with pH 8.2. Due to gravity, the mud liquid settles at the interface of the mud and the aluminum surface while forming locally scattered patches of liquid films. Once the mud liquid dries, adhesion work to remove the dry mud increases significantly. The mud liquid gives rise to the formation of pinholes and local pit sites on the aluminum surface. Morphological changes due to pit sites and residues of the dry mud on the aluminum surface lower the surface reflection after the removal of the dry mud from the surface. The characteristics of the aluminum surface can address the dust/mud-related limitations of reflective surfaces and may have implications for the reductions in the efficiencies of solar concentrated power systems. PMID:28378798

Closure Report for Corrective Action Unit 356: Mud Pits and Disposal Sites, Nevada Test Site, Nevada with Errata Sheet

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

NNSA /NV

2002-11-12

This Closure Report (CR) has been prepared for Corrective Action Unit (CAU) 356, Mud Pits and Disposal Sites, in accordance with the Federal Facility Agreement and Consent Order. This CAU is located in Areas 3 and 20 of the Nevada Test Site (NTS) approximately 65 miles northwest of Las Vegas, Nevada. Corrective Action Unit 356 consists of seven Corrective Action Sites (CASs): 03-04-01, Area 3 Change House Septic System; 03-09-01, Mud Pit Spill Over; 03-09-03, Mud Pit; 03-09-04, Mud Pit; 03-09-05, Mud Pit; 20-16-01, Landfill; and 20-22-21, Drums. This CR identifies and rationalizes the U.S. Department of Energy (DOE), Nationalmore » Nuclear Security Administration Nevada Operations Office's (NNSA/NV's) recommendation that no further corrective action and closure in place is deemed necessary for CAU 356. This recommendation is based on the results of field investigation/closure activities conducted November 20, 2001, through January 3, 2002, and March 11 to 14, 2002. These activities were conducted in accordance with the Streamlined Approach for Environmental Restoration Plan (SAFER) for CAU 356. For CASs 03-09-01, 03-09-03, 20-16-01, and 22-20-21, analytes detected in soil during the corrective action investigation were evaluated against Preliminary Action Levels (PALs) and it was determined that no Contaminants of Concern (COCs) were present. Therefore, no further action is necessary for the soil at these CASs. For CASs 03-04-01, 03-09-04, and 03-09-05, analytes detected in soil during the corrective action investigation were evaluated against PALs and identifies total petroleum hydrocarbons (TPHs) and radionuclides (i.e., americium-241 and/or plutonium 239/240) as COCs. The nature, extent, and concentration of the TPH and radionuclide COCs were bounded by sampling and shown to be relatively immobile. Therefore, closure in place is recommended for these CASs in CAU 356. Further, use restrictions are not required at this CAU beyond the NTS use restrictions identified in the SAFER Plan. In addition, the septic tank associated with CAU 356 will be closed in accordance with applicable regulations.« less

Addendum 2 to the Closure Report for Corrective Action Unit 358: Areas 18, 19, 20 Cellars/Mud Pits, Nevada Test Site, Nevada, Revison 0

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

Grant Evenson

This document constitutes an addendum to the Closure Report for Corrective Action Unit 358: Areas 18, 19, 20 Cellars/Mud Pits, Nevada Test Site, Nevada, January 2004 as described in the document Supplemental Investigation Report for FFACO Use Restrictions, Nevada Test Site, Nevada (SIR) dated November 2008. The SIR document was approved by NDEP on December 5, 2008. The approval of the SIR document constituted approval of each of the recommended UR removals. In conformance with the SIR document, this addendum consists of: • This page that refers the reader to the SIR document for additional information • The cover, title,more » and signature pages of the SIR document • The NDEP approval letter • The corresponding section of the SIR document This addendum provides the documentation justifying the cancellation of the UR for CAS 19-09-05, Mud Pit. This UR was established as part of a Federal Facility Agreement and Consent Order (FFACO) corrective action and is based on the presence of contaminants at concentrations greater than the action levels established at the time of the initial investigation (FFACO, 1996). Since this UR was established, practices and procedures relating to the implementation of risk-based corrective actions (RBCA) have changed. Therefore, this UR was reevaluated against the current RBCA criteria as defined in the Industrial Sites Project Establishment of Final Action Levels (NNSA/NSO, 2006). This re-evaluation consisted of comparing the original data (used to define the need for the UR) to risk-based final action levels (FALs) developed using the current Industrial Sites RBCA process. The re-evaluation resulted in a recommendation to remove the UR because contamination is not present at the site above the risk-based FALs. Requirements for inspecting and maintaining this UR will be canceled, and the postings and signage at this site will be removed. Fencing and posting may be present at this site that are unrelated to the FFACO UR such as for radiological control purposes as required by the NV/YMP Radiological Control Manual (NNSA/NSO, 2004). This modification will not affect or modify any non-FFACO requirements for fencing, posting, or monitoring at this site.« less

Specific identification of Bacillus anthracis strains

NASA Astrophysics Data System (ADS)

Krishnamurthy, Thaiya; Deshpande, Samir; Hewel, Johannes; Liu, Hongbin; Wick, Charles H.; Yates, John R., III

2007-01-01

Accurate identification of human pathogens is the initial vital step in treating the civilian terrorism victims and military personnel afflicted in biological threat situations. We have applied a powerful multi-dimensional protein identification technology (MudPIT) along with newly generated software termed Profiler to identify the sequences of specific proteins observed for few strains of Bacillus anthracis, a human pathogen. Software termed Profiler was created to initially screen the MudPIT data of B. anthracis strains and establish the observed proteins specific for its strains. A database was also generated using Profiler containing marker proteins of B. anthracis and its strains, which in turn could be used for detecting the organism and its corresponding strains in samples. Analysis of the unknowns by our methodology, combining MudPIT and Profiler, led to the accurate identification of the anthracis strains present in samples. Thus, a new approach for the identification of B. anthracis strains in unknown samples, based on the molecular mass and sequences of marker proteins, has been ascertained.

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology.

PubMed

Zhang, L; Zhou, R; Niu, M; Zheng, J; Wu, C

2015-11-01

Artificial pit muds (APMs) is produced by peats, aged pit muds, yellow and black clays etc. and is one of essential factors for Luzhou-flavour liquor production. The microbial community of APMs significantly influence the quality of Luzhou-flavour liquor. The aim of this study was to investigate the differences in bacterial, archaeal and fungal community of APMs, starters and materials. Multiphase culture-independent technology were employed in this study, including nested PCR-denaturing gradient gel electrophoresis (nested PCR-DGGE), phospholipid fatty acid (PLFA), phospholipid ether lipids (PLEL) and fluorescence in situ hybridization (FISH) analysis. Results suggested that the microbial diversity significantly changed under environmental stress and different culture patterns during APMs cultivation. The dominant bacteria in APMs mainly fell into Clostridiales, Lactobacillales, Bacteroidales and Rhizobiales, Archaea affiliated with Methanomicrobiales and Methanosarcinales, and fungi belonged to Saccharomycetales and Eurotiales. Furthermore, the microbial community structures of APMs cultured by ground pile pattern were more similar with that of aged pit muds, meanwhile, the relative bands intensities of microbes, which are the main contributors for liquor brewing, increased with the culture times. Not only the niche selection and biogeochemical properties of APMs, but also the mutual collaboration and constraint between different microbes may result in enriching different liquor-brewing microbes into APMs. APM cultivation technology was necessary to promote enriching functional liquor-brewing microbes into APMs. These results may facilitate understanding the microbial succession during APMs manufacture. © 2015 The Society for Applied Microbiology.

Closure Report for Corrective Action Unit 139: Waste Disposal Sites, Nevada Test Site, Nevada

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

NSTec Environmental Restoration

2009-07-31

Corrective Action Unit (CAU) 139 is identified in the Federal Facility Agreement and Consent Order (FFACO) as 'Waste Disposal Sites' and consists of the following seven Corrective Action Sites (CASs), located in Areas 3, 4, 6, and 9 of the Nevada Test Site: CAS 03-35-01, Burn Pit; CAS 04-08-02, Waste Disposal Site; CAS 04-99-01, Contaminated Surface Debris; CAS 06-19-02, Waste Disposal Site/Burn Pit; CAS 06-19-03, Waste Disposal Trenches; CAS 09-23-01, Area 9 Gravel Gertie; and CAS 09-34-01, Underground Detection Station. Closure activities were conducted from December 2008 to April 2009 according to the FFACO (1996, as amended February 2008) andmore » the Corrective Action Plan for CAU 139 (U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office, 2007b). The corrective action alternatives included No Further Action, Clean Closure, and Closure in Place with Administrative Controls. Closure activities are summarized. CAU 139, 'Waste Disposal Sites,' consists of seven CASs in Areas 3, 4, 6, and 9 of the NTS. The closure alternatives included No Further Action, Clean Closure, and Closure in Place with Administrative Controls. This CR provides a summary of completed closure activities, documentation of waste disposal, and confirmation that remediation goals were met. The following site closure activities were performed at CAU 139 as documented in this CR: (1) At CAS 03-35-01, Burn Pit, soil and debris were removed and disposed as LLW, and debris was removed and disposed as sanitary waste. (2) At CAS 04-08-02, Waste Disposal Site, an administrative UR was implemented. No postings or post-closure monitoring are required. (3) At CAS 04-99-01, Contaminated Surface Debris, soil and debris were removed and disposed as LLW, and debris was removed and disposed as sanitary waste. (4) At CAS 06-19-02, Waste Disposal Site/Burn Pit, no work was performed. (5) At CAS 06-19-03, Waste Disposal Trenches, a native soil cover was installed, and a UR was implemented. (6) At CAS 09-23-01, Area 9 Gravel Gertie, a UR was implemented. (7) At CAS 09-34-01, Underground Detection Station, no work was performed.« less

Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC–MS/MS

PubMed Central

2015-01-01

Large-scale proteomics often employs two orthogonal separation methods to fractionate complex peptide mixtures. Fractionation can involve ion exchange separation coupled to reversed-phase separation or, more recently, two reversed-phase separations performed at different pH values. When multidimensional separations are combined with tandem mass spectrometry for protein identification, the strategy is often referred to as multidimensional protein identification technology (MudPIT). MudPIT has been used in either an automated (online) or manual (offline) format. In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging. Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms. When employing an off-line fractionation method with direct loading of samples onto the column from an eppendorf tube via a high-pressure device, a 5.3% loss in protein identifications is observed. When off-line fractionated samples are loaded via an autosampler, a 44.5% loss in protein identifications is observed compared with direct loading of samples onto a triphasic capillary column. Moreover, peptide recovery was significantly lower after offline fractionation than in online fractionation. Signal-to-noise (S/N) ratio, however, was not significantly altered between experimental groups. It is likely that offline sample collection results in stochastic peptide loss due to noncovalent adsorption to solid surfaces. Therefore, the use of the offline approaches should be considered carefully when processing minute quantities of valuable samples. PMID:25040086

Corrective Action Plan for Corrective Action Unit 562: Waste Systems, Nevada National Security Site, Nevada

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

NSTec Environmental Restoration

2011-04-30

This Corrective Action Plan has been prepared for Corrective Action Unit (CAU) 562, Waste Systems, in accordance with the Federal Facility Agreement and Consent Order (1996; as amended March 2010). CAU 562 consists of 13 Corrective Action Sites (CASs) located in Areas 2, 23, and 25 of the Nevada National Security Site. Site characterization activities were performed in 2009 and 2010, and the results are presented in Appendix A of the Corrective Action Decision Document for CAU 562. The scope of work required to implement the recommended closure alternatives is summarized. (1) CAS 02-26-11, Lead Shot, will be clean closedmore » by removing shot. (2) CAS 02-44-02, Paint Spills and French Drain, will be clean closed by removing paint and contaminated soil. As a best management practice (BMP), asbestos tile will be removed. (3) CAS 02-59-01, Septic System, will be clean closed by removing septic tank contents. As a BMP, the septic tank will be removed. (4) CAS 02-60-01, Concrete Drain, contains no contaminants of concern (COCs) above action levels. No further action is required; however, as a BMP, the concrete drain will be removed. (5) CAS 02-60-02, French Drain, was clean closed. Corrective actions were completed during corrective action investigation activities. As a BMP, the drain grates and drain pipe will be removed. (6) CAS 02-60-03, Steam Cleaning Drain, will be clean closed by removing contaminated soil. As a BMP, the steam cleaning sump grate and outfall pipe will be removed. (7) CAS 02-60-04, French Drain, was clean closed. Corrective actions were completed during corrective action investigation activities. (8) CAS 02-60-05, French Drain, will be clean closed by removing contaminated soil. (9) CAS 02-60-06, French Drain, contains no COCs above action levels. No further action is required. (10) CAS 02-60-07, French Drain, requires no further action. The french drain identified in historical documentation was not located during corrective action investigation activities. (11) CAS 23-60-01, Mud Trap Drain and Outfall, will be clean closed by removing sediment from the mud trap. As a BMP, the mud trap and outfall pipe will be removed. (12) CAS 23-99-06, Grease Trap, will be clean closed by removing sediment from the grease trap and backfilling the grease trap with grout. (13) CAS 25-60-04, Building 3123 Outfalls, will be clean closed by removing contaminated soil and the sludge-containing outfall pipe.« less

Sediment Transport and Slope Stability of Ship Shoal Borrow Areas for Coastal Restoration of Louisiana

NASA Astrophysics Data System (ADS)

Liu, H.; Xu, K.; Bentley, S. J.; Li, C.; Miner, M. D.; Wilson, C.; Xue, Z.

2017-12-01

Sandy barrier islands along Louisiana coast are degrading rapidly due to both natural and anthropogenic factors. Ship Shoal is one of the largest offshore sand resources, and has been used as a borrow area for Caminada Headland Restoration Project. Our knowledge of sediment transport and infilling processes in this new sandy and dynamic borrow area is rather limited. High resolution sub-bottom seismic data, side scan sonar images, multi-beam bathymetry and laser sediment grain size data were used to study seafloor morphological evolution and pit wall stability in response to both physical and geological processes. The multi-beam bathymetry and seismic profiling inside the pit showed that disequilibrium conditions led to rapid infilling in the pits at the beginning, but this process slowed down after the pit slope became stable and topography became smooth. We hypothesize that the erosion of the adjacent seabed sediment by energetic waves and longshore currents, the supply of suspended sediment from the rivers, and the erodible materials produced by local mass wasting on pit walls are three main types of infilling sediments. Compared with mud-capped dredge pits, this sandy dredge pit seems to have more gentle slopes on pit walls, which might be controlled by the angle of repose. Infilling sediment seems to be dominantly sandy, with some mud patches on bathymetric depressions. This study helps us better understand the impacts of mining sediment for coastal restoration and improves sand resource management efforts.

Morphological Response of a Mud Capped Dredge Pit in Western Louisiana After Sand Excavation for Barrier Island Restoration

NASA Astrophysics Data System (ADS)

Robichaux, P. A.; Xu, K.; Bentley, S. J.; Li, C.; Miner, M. D.

2017-12-01

Sand resources play a crucial role in supporting tourism, maintaining coastal ecosystems, and protecting property and infrastructure. Mud capped dredge pits (MCDPs) are created when paleochannel sand, covered by muddy shelf overburden, is excavated for restoration purposes; such paleochannels are one significant sand resource for coastal barrier protection. However, our knowledge of MCDPs is limited. To improve understanding of their morphological behavior, a dredge pit called Peveto Channel (PC) offshore of Holly Beach, LA, was studied in 2016. Our study consisted of a survey using multiple geophysical methods, including multibeam bathymetry, sidescan sonar, subbottom profiling, and magnetometry. Results indicate that PC has undergone 100% infilling since dredging occurred. Although the pit is filled up, analyses indicate the newly deposited material is unconsolidated and has yet to equilibrate to the ambient seafloor conditions. The surface of the pit area is pockmarked and uneven, likely caused by degassing processes and differential consolidation. Sidescan sonar images confirm that the pit walls have experienced little to no lateral erosion and are well preserved. The results from this survey and from historical surveys conducted in 2003 (a few months after dredging), 2004, 2006, and 2007 are compared to previously constructed numerical models used to predict the behavior of dredge pits. To our knowledge, PC is the only filled-up offshore dredge pit in coastal Louisiana. Thus the findings of this study provide new long-term information for regulatory policies and the feasibility of MCDPs as sand resources in the future.

Assessment of Mud-Capped Dredge Pit Evolution Offshore Louisiana: Implications to Sand Excavation and Coastal Restoration

NASA Astrophysics Data System (ADS)

Xu, K.; Miner, M. D.; Bentley, S. J.; Li, C.; Obelcz, J.; O'Connor, M. C.

2016-02-01

The shelf offshore Louisiana is characterized by a dominantly muddy seafloor with a paucity of restoration-quality sand proximal to shore. Discrete sand deposits associated with ancient rivers that incised the shelf during lower sea-level positions occur close to shore. These shelf channel sands have been targeted for coastal restoration projects resulting in significant cost savings over more distal deposits. Several recent projects targeted shelf paleo-fluvial deposits comprising relatively deep (10 m) channel sands underlying a muddy overburden. Because of contrasting characteristics of cohesive mud vs. non-cohesive sand and potential modern fluvial mud supply from the Mississippi and Atchafalaya Rivers, long term pit evolution is poorly understood relative to their more common sand-only counterparts. Alterations to seafloor topography from dredging shelf sediment resources can potentially affect oil and gas infrastructure or other resources of concern (i.e. historic shipwrecks) located proximal to dredge pits. Site-specific data required to make accurate predictions and empirical measurements to test and validate predictive models were only available for Peveto Channel offshore Holly Beach, Louisiana. Here we present new geophysical and geological data (bathymetry, sidescan, subbottom, and radionuclide of sediment cores) and physical oceanographic observations (hydrodynamics and sediment dynamics) collected at Raccoon Island (dredged in 2013) dredge pit in Louisiana. These field data collections along with pre-existing data provide a time-series to capture evolution at Raccoon Island post-excavation. Conceptual morphological models will be developed for dredge pit evolution and testing effectiveness of setback buffers protecting pipelines, habitats, and cultural resources. Our results will increase decision making ability regarding safety and protecting environmental and cultural resources, and better management of valuable sand resources.

Evidence for and implications of sedimentary diapirism and mud volcanism in the southern Utopia highland-lowland boundary plain, Mars

USGS Publications Warehouse

Skinner, J.A.; Tanaka, K.L.

2007-01-01

Several types of spatially associated landforms in the southern Utopia Planitia highland-lowland boundary (HLB) plain appear to have resulted from localized geologic activity, including (1) fractured rises, (2) elliptical mounds, (3) pitted cones with emanating lobate materials, and (4) isolated and coalesced cavi (depressions). Stratigraphic analysis indicates these features are Hesperian or younger and may be associated with resurfacing that preferentially destroyed smaller (< 8 ?? km diameter) impact craters. Based on landform geomorphologies and spatial distributions, the documented features do not appear to be specifically related to igneous or periglacial processes or the back-wasting and erosion of the HLB scarp. We propose that these features are genetically related to and formed by sedimentary (mud) diapirs that ascended from zones of regionally confined, poorly consolidated, and mechanically weak material. We note morphologic similarities between the mounds and pitted cones of the southern Utopia boundary plain and terrestrial mud volcanoes in the Absheron Peninsula, Azerbaijan. These analogs provide a context for understanding the geological environments and processes that supported mud diapir-related modification of the HLB. In southern Utopia, mud diapirs near the Elysium volcanic edifice may have resulted in laccolith-like intrusions that produced the fractured rises, while in the central boundary plain mud diapirs could have extruded to form pitted cones, mounds, and lobate flows, perhaps related to compressional stresses that account for wrinkle ridges. The removal of material a few kilometers deep by diapiric processes may have resulted in subsidence and deformation of surface materials to form widespread cavi. Collectively, these inferences suggest that sedimentary diapirism and mud volcanism as well as related surface deformations could have been the dominant Hesperian mechanisms that altered the regional boundary plain. We discuss a model in which detritus would have accumulated thickly in the annular spaces between impact-generated structural rings of Utopia basin. We envision that these materials, and perhaps buried ejecta of Utopia basin, contained volatile-rich, low-density material that could provide the source material for the postulated sedimentary diapirs. Thick, water-rich, low-density sediments buried elsewhere along the HLB and within the lowland plains may account for similar landforms and resurfacing histories. ?? 2006 Elsevier Inc. All rights reserved.

Record of Technical Change 2 for Closure Report for Corrective Action Unit 204: Storage Bunkers, Nevada Test Site, Nevada, Revision 0

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

Krauss, Mark J.; Birney, Cathleen

2006-04-01

CAS 05-33-01, Kay Blockhouse, consists of an area of approximately 11 acres and includes the Kay Blockhouse, two bum pits with steel frames, one bum pit with a soil berm, two open pits, two steel-lined subsurface pits, one berm with embedded piping, one berm with piping debris, a burn area with a large concrete block with an embedded steel prong, and one open pit with a concrete foundation at the north end. The Kay Blockhouse was constructed in 1951 and was used as an instrumentation bunker for Operation Ranger, a series of five atmospheric nuclear tests. The burn pits andmore » other surface features within the CAS boundary were not part of the nuclear testing. The Kay Blockhouse is constructed of concrete with a wooden entryway door. The details of the construction of the floor are unknown (NNSA/NSO, 2004b). During closure activities, lead- and radiologically impacted soil was removed, and verification samples were collected. Friable asbestos material was removed from the burn pits; the asbestos and steel frames from the bum pits were disposed of at the Area 23 Sanitary Landfill. In addition, the two steel-lined pits were filled with native soil and capped with 1.5 ft of concrete. The bunker was secured by installing security fencing and a gate around the entrance to the bunker. The RMA was reestablished and fenced with T-post and wire-rope fencing (NNSA/NSO, 2006a).« less

Availability of MudPIT data for classification of biological samples.

PubMed

Silvestre, Dario Di; Zoppis, Italo; Brambilla, Francesca; Bellettato, Valeria; Mauri, Giancarlo; Mauri, Pierluigi

2013-01-14

Mass spectrometry is an important analytical tool for clinical proteomics. Primarily employed for biomarker discovery, it is increasingly used for developing methods which may help to provide unambiguous diagnosis of biological samples. In this context, we investigated the classification of phenotypes by applying support vector machine (SVM) on experimental data obtained by MudPIT approach. In particular, we compared the performance capabilities of SVM by using two independent collection of complex samples and different data-types, such as mass spectra (m/z), peptides and proteins. Globally, protein and peptide data allowed a better discriminant informative content than experimental mass spectra (overall accuracy higher than 87% in both collection 1 and 2). These results indicate that sequencing of peptides and proteins reduces the experimental noise affecting the raw mass spectra, and allows the extraction of more informative features available for the effective classification of samples. In addition, proteins and peptides features selected by SVM matched for 80% with the differentially expressed proteins identified by the MAProMa software. These findings confirm the availability of the most label-free quantitative methods based on processing of spectral count and SEQUEST-based SCORE values. On the other hand, it stresses the usefulness of MudPIT data for a correct grouping of sample phenotypes, by applying both supervised and unsupervised learning algorithms. This capacity permit the evaluation of actual samples and it is a good starting point to translate proteomic methodology to clinical application.

A Modified MuDPIT Separation Identified 4,488 Proteins in a System Wide Analysis of Quiescence in Yeast

PubMed Central

Webb, Kristofor J.; Xu, Tao; Park, Sung Kyu; Yates, John R.

2013-01-01

A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near complete yeast proteome from a whole cell tryptic digest. This modified on-line two dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4,269 protein identifications were made from 4,189 distinguishable protein families from yeast during log phase growth. The “Micro” MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days’ time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations ‘oxidation reduction’, ‘catabolic processing’ and ‘cellular response to oxidative stress’ was seen in the quiescent cellular fraction, consistent with their long lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of ‘Ribosome’ and ‘Proteasome’, further defining the complex nature of yeast populations present during stationary phase growth. In total 4,488 distinguishable protein families were identified in all cellular conditions tested. PMID:23540446

Characterization of eubacterial and archaeal community diversity in the pit mud of Chinese Luzhou-flavor liquor by nested PCR-DGGE.

PubMed

Ding, Xiao-Fei; Wu, Chong-De; Zhang, Li-Qiang; Zheng, Jia; Zhou, Rong-Qing

2014-02-01

The aim of this study was to investigate and compare the microbial community structures of eubacteria and archaea in the pit mud of Chinese Luzhou-flavor liquor from the wall (C(w)) and bottom (C(b)) of cellar through nested PCR-denaturing gradient gel electrophoresis (DGGE). The Shannon-Wiener index (H) calculated from the DGGE profiles showed that the community diversities of eubacteria and archaea in samples from C(b) were almost higher than that from C(w). In addition, cluster analysis of the DGGE profiles revealed that some differences were found in the microbial community structure in samples from different locations. The closely relative microorganisms of all eubacterial 16S rRNA gene sequences fell into four phyla (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), including 12 genera and 2 uncultured eubacteria. Moreover, 37.1% eubacteria were affiliated with Clostridium. Particularly, genus Acinetobacter was absent in all samples from C(b) but present in all samples from C(w). The closely relative microorganisms of all archaeal 16S rRNA gene sequences fell into four genera, which included Methanobrevibacter, Methanoculleus, Methanobacterium and Methanosaeta, while the dominant archaea in samples from C(w) and C(b) were similar. Results presented in this study provide further understanding of the spatial differences in microbial community structure in the pit mud, and is of great importance for the production and quality improvement of Luzhou-flavor liquor.

Types and analysis of defects in welding junctions of the header to steam generator shells on power-generating units with VVER-1000

NASA Astrophysics Data System (ADS)

Ozhigov, L. S.; Voevodin, V. N.; Mitrofanov, A. S.; Vasilenko, R. L.

2016-10-01

Investigation objects were metal templates, which were cut during the repair of welding junction no. 111 (header to the steam generator shell) on a power-generating unit with VVER-1000 of the South-Ukraine NPP, and substances of mud depositions collected from walls of this junction. Investigations were carried out using metallography, optical microscopy, and scanning electron microscopy with energy dispersion microanalysis by an MMO-1600-AT metallurgical microscope and a JEOL JSM-7001F scanning electron microscope with the Shottky cathode. As a result of investigations in corrosion pits and mud depositions in the area of welding junction no. 111, iron and copper-enriched particles were revealed. It is shown that, when contacting with the steel header surface, these particles can form microgalvanic cells causing reactions of iron dissolution and the pit corrosion of metal. Nearby corrosion pits in metal are microcracks, which can be effect of the stress state of metal under corrosion pits along with revealed effects of twinning. The hypothesis is expressed that pitting corrosion of metal occurred during the first operation period of the power-generating unit in the ammonia water chemistry conditions (WCC). The formation of corrosion pits and nucleating cracks from them was stopped with the further operation under morpholine WCC. The absence of macrocracks in metal of templates verifies that, during operation, welding junction no. 111 operated under load conditions not exceeding the permissible ones by design requirements. The durability of the welding junction of the header to the steam generator shell significantly depends on the technological schedule of chemical cleaning and steam generator shut-down cooling.

46 CFR 108.173 - Class I, Division 2 locations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... locations. The following are Class I, Division 2 locations: (a) An enclosed space that has any open portion... mud pit. (b) A location in the weather that is— (1) Within the boundaries of the drilling derrick up...

Martian mud volcanism: Terrestrial analogs and implications for formational scenarios

USGS Publications Warehouse

Skinner, J.A.; Mazzini, A.

2009-01-01

The geology of Mars and the stratigraphic characteristics of its uppermost crust (mega-regolith) suggest that some of the pervasively-occurring pitted cones, mounds, and flows may have formed through processes akin to terrestrial mud volcanism. A comparison of terrestrial mud volcanism suggests that equivalent Martian processes likely required discrete sedimentary depocenters, volatile-enriched strata, buried rheological instabilities, and a mechanism of destabilization to initiate subsurface flow. We outline five formational scenarios whereby Martian mud volcanism might have occurred: (A) rapid deposition of sediments, (B) volcano-induced destabilization, (C) tectonic shortening, (D) long-term, load-induced subsidence, and (E) seismic shaking. We describe locations within and around the Martian northern plains that broadly fit the geological context of these scenarios and which contain mud volcano-like landforms. We compare terrestrial and Martian satellite images and examine the geological settings of mud volcano provinces on Earth in order to describe potential target areas for piercement structures on Mars. Our comparisons help to evaluate not only the role of water as a functional component of geological processes on Mars but also how Martian mud volcanoes could provide samples of otherwise inaccessible strata, some of which could contain astrobiological evidence.

New mud system produces solids-free, reusable water

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

NONE

1996-02-01

The Corpus Christi, Texas, based Cameron Equipment Co., Inc., has developed a closed-loop mud treating system that removes solids from water-based systems and leaves the separated fluid clean and chemical free enough to be re-used directly on the rig. The system has been successfully applied by a Gulf of Mexico operator in areas where zero discharge is required. The alternative mud conditions program offered by the developers is called the Cameron Fluid Recycling System. Designed for closed-loop water-based fluids, the system is a new method of removing solids from normally discharged fluids such as drilling mud, waste and wash water,more » or any other water-based fluid that contains undesirable solids. The patented method efficiently produces end products that are (1) dry solids; and (2) essentially 100% solids-free fluid that can be re-used in the same mud system. All excess drilling mud, and all wash water that would normally go to the reserve pit or a cuttings barge are collected in a tank. Recycled fluid is compatible with the mud system fluid, no harmful chemicals are used, and pH is not altered.« less

Characterization of factor VIII pharmaceutical preparations by means of MudPIT proteomic approach.

PubMed

Basilico, Fabrizio; Nardini, Ilaria; Mori, Filippo; Brambilla, Elena; Benazzi, Louise; De Palma, Antonella; Rosti, Enrico; Farina, Claudio; Mauri, PierLuigi

2010-09-21

For a good clinical outcome of Haemophilia A substitutive therapy a detailed characterization of factor VIII (FVIII) concentrates is required, in order to disclose the eventual relations between differently composed concentrates and their biological effects. This preliminary work could be a first step towards a deep structural characterization of FVIII concentrates, using the fast and simply manageable MudPIT technology, which enables the identification and characterization of protein mixtures taking advantage of both the high separation capacity of two-dimensional chromatography and the powerful peptide characterization ability of tandem mass spectrometry. The aim of this study was to evaluate the suitability of for the characterization of FVIII molecule in complex mixtures such its commercial concentrates, both plasma-derived and recombinant, and for the determination of the protein composition of different FVIII preparations. By means of Multidimensional Protein Identification Technology (MudPIT) it was possible to assess the presence of factor VIII in its preparations and to identify most of the contaminant proteins without gel separation. In particular, 125 and 42 proteins were identified in plasma-derived and recombinant concentrates, respectively. Concerning investigation of FVIII, 24 different peptides were identified in plasma-derived corresponding to 7, 29, 27, 19 and 67 of percentage coverage for A1, A2, A3, C1 and C2 domains, respectively. About its multimeric carrier von Willebrand factor (VWF), we have sequenced 42% of domain interacting with A3 and C2 domains of FVIII. Finally, it has been observed that normalized parameters, such as total peptide hits obtained by SEQUEST may be used for evaluation of the relative abundance of FVIII in different preparations. Copyright 2010 Elsevier B.V. All rights reserved.

Mixed-bed ion exchange chromatography employing a salt-free pH gradient for improved sensitivity and compatibility in MudPIT.

PubMed

Mommen, Geert P M; Meiring, Hugo D; Heck, Albert J R; de Jong, Ad P J M

2013-07-16

In proteomics, comprehensive analysis of peptides mixtures necessitates multiple dimensions of separation prior to mass spectrometry analysis to reduce sample complexity and increase the dynamic range of analysis. The main goal of this work was to improve the performance of (online) multidimensional protein identification technology (MudPIT) in terms of sensitivity, compatibility and recovery. The method employs weak anion and strong cation mixed-bed ion exchange chromatography (ACE) in the first separation dimension and reversed phase chromatography (RP) in the second separation dimension (Motoyama et.al. Anal. Chem 2007, 79, 3623-34.). We demonstrated that the chromatographic behavior of peptides in ACE chromatography depends on both the WAX/SCX mixing ratio as the ionic strength of the mobile phase system. This property allowed us to replace the conventional salt gradient by a (discontinuous) salt-free, pH gradient. First dimensional separation of peptides was accomplished with mixtures of aqueous formic acid and dimethylsulfoxide with increasing concentrations. The overall performance of this mobile phase system was found comparable to ammonium acetate buffers in application to ACE chromatography, but clearly outperformed strong cation exchange for use in first dimensional peptide separation. The dramatically improved compatibility between (salt-free) ion exchange chromatography and reversed phase chromatography-mass spectrometry allowed us to downscale the dimensions of the RP analytical column down to 25 μm i.d. for an additional 2- to 3-fold improvement in performance compared to current technology. The achieved levels of sensitivity, orthogonality, and compatibility demonstrates the potential of salt-free ACE MudPIT for the ultrasensitive, multidimensional analysis of very modest amounts of sample material.

Development, validation and application of specific primers for analyzing the clostridial diversity in dark fermentation pit mud by PCR-DGGE.

PubMed

Hu, Xiao-Long; Wang, Hai-Yan; Wu, Qun; Xu, Yan

2014-07-01

In this study, a Clostridia-specific primer set SJ-F and SJ-R, based on the available 16S rRNA genes sequences from database, was successfully designed and authenticated by theoretical and experimental evaluations. It targeted 19 clostridial families and unclassified_Clostridia with different coverage rates. The specificity and universality of novel primer set was tested again using the dark fermentation pit mud (FPM). It was demonstrated that a total of 13 closest relatives including 12 species were affiliated with 7 clostridial genera, respectively. Compared to the well-accepted bacterial universal primer pair P2/P3, five unexpected clostridial genera including Roseburia, Tissierella, Sporanaerobacter, Alkalibacter and Halothermothrix present in the FPM were also revealed. Therefore, this study could provide a good alternative to investigate the clostridial diversity and monitor their population dynamics rapidly and efficiently in various anaerobic environments and dark fermentation systems in future. Copyright © 2014 Elsevier Ltd. All rights reserved.

Corrective Action Decision Document/Closure Report for Corrective Action Unit 560: Septic Systems, Nevada Test Site, Nevada, Revision 0

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

Grant Evenson

2010-04-01

Corrective Action Unit 560 comprises seven corrective action sites (CASs): •03-51-01, Leach Pit •06-04-02, Septic Tank •06-05-03, Leach Pit •06-05-04, Leach Bed •06-59-03, Building CP-400 Septic System •06-59-04, Office Trailer Complex Sewage Pond •06-59-05, Control Point Septic System The purpose of this CADD/CR is to provide justification and documentation supporting the recommendation for closure of CAU 560 with no further corrective action. To achieve this, corrective action investigation (CAI) activities were performed from October 7, 2008, through February 24, 2010, as set forth in the Corrective Action Investigation Plan for Corrective Action Unit 560: Septic Systems, Nevada Test Site, Nevada, and Recordmore » of Technical Change No. 1. The purpose of the CAI was to fulfill the following data needs as defined during the data quality objective (DQO) process: •Determine whether contaminants of concern (COCs) are present. •If COCs are present, determine their nature and extent. •Provide sufficient information and data to complete appropriate corrective actions. The CAU 560 dataset from the investigation results was evaluated based on the data quality indicator parameters. This evaluation demonstrated the quality and acceptability of the dataset for use in fulfilling the DQO data needs. Analytes detected during the CAI were evaluated against final action levels (FALs) established in this document. The following contaminants were determined to be present at concentrations exceeding their corresponding FALs: •No contamination exceeding the FALs was identified at CASs 03-51-01, 06-04-02, and 06-59-04. •The soil at the base of the leach pit chamber at CAS 06-05-03 contains arsenic above the FAL of 23 milligrams per kilogram (mg/kg) and polychlorinated biphenyl (PCBs) above the FAL of 0.74 mg/kg, confined vertically from a depth of approximately 5 to 20 feet (ft) below ground surface. The contamination is confined laterally to the walls of the leach pit chamber and leach rock. The contamination present at CAS 06-05-03 within the leach pit was not feasible to remove. •The surface and subsurface soils within and surrounding the septic system at CAS 06-05-04 contained PCB concentrations above the FAL of 0.74 mg/kg. The lateral and vertical extent of COCs was determined for this CAS. Contaminated soils were removed up to within 18 ft of the building. The remaining contamination is confined to subsurface soils adjacent to and beneath Building CP-162 and was not feasible to remove. •The solid materials within the septic tank and soils immediately surrounding the inlet end of the tank at CAS 06-59-03 contained benzo(a)pyrene above the FAL of 0.21 mg/kg. The soils, tank contents, and tank were removed. Materials remaining at this CAS do not contain contamination exceeding FALs. •The solids contained within the septic tank and inlet pipe at CAS 06-59-05 contained the following contaminants above their respective FALs: PCBs, arsenic, lead, benzo(a)pyrene, and pesticides. The tank and inlet pipe contents were removed. Materials remaining at this CAS do not contain contamination exceeding FALs. Therefore, the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO) provides the following corrective action recommendations: •No further action for CASs 03-51-01, 06-04-02, and 06-59-04, as no contaminants of potential concern were present that exceed FALs. •Closure in place for CAS 06-05-03 under a corrective action with a use restriction (UR) for remaining PCB- and arsenic-impacted potential source material (PSM). The UR form and map have been filed in the NNSA/NSO Facility Information Management System, the FFACO database, and NNSA/NSO CAU/CAS files. •Closure in place for CAS 06-05-04 under a corrective action with a UR for remaining PCBs in soil adjacent to and beneath Building CP-162. The UR form and map have been filed in the NNSA/NSO Facility Information Management System, the FFACO database, and NNSA/NSO CAU/CAS files. •No further action for CAS 06-59-03, as the COC of benzo(a)pyrene in soil and PSM have been removed. •No further action for CAS 06-59-05, as the COCs in PSM within the septic tank and inlet piping have been removed and the tank was filled with concrete.« less

Installation Restoration Program Information Management System (IRPIMS) Data Loading Handbook. Version 2.1

DTIC Science & Technology

1989-09-01

STEEL STL STEEL TFL TEFLON TIL TILE WD WOOD WRI WROUGHT IRON Z OTHER A-14 coam Bc~ai=L a TEST PIT ois rn iEI AR AIR - ROTARY 8 BORED OR AUGERED C CABLE-TOOL...CO CORING Cs CHILLED SHOT D DUG DH DOWN THE HOLE HAMMER HA HAND AUGERED HS HOLLOW STEM AUGER J JETTED MR DIRECT CIRCULATION ROTARY , MUD p AIR ...INSTITUTE WARI WATER AND AIR RESEARCH. INC. WIL WILSON AND CO. A-18 M 0E 7 PIT E V/n.. CK: N’Y ESCI ENGINEERING -SCIENCE NA NOT APPLICABLE RB MR

Geophysical investigation, Salmon Site, Lamar County, Mississippi

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

NONE

Geophysical surveys were conducted in 1992 and 1993 on 21 sites at the Salmon Site (SS) located in Lamar County, Mississippi. The studies are part of the Remedial Investigation/Feasibility Study (RI/FS) being conducted by IT Corporation for the U.S. Department of Energy (DOE). During the 1960s, two nuclear devices and two chemical tests were detonated 826 meters (in) (2710 feet [ft]) below the ground surface in the salt dome underlying the SS. These tests were part of the Vela Uniform Program conducted to improve the United States capability to detect, identify, and locate underground nuclear detonations. The RI/FS is beingmore » conducted to determine if any contamination is migrating from the underground shot cavity in the salt dome and if there is any residual contamination in the near surface mud and debris disposal pits used during the testing activities. The objective of the surface geophysical surveys was to locate buried debris, disposal pits, and abandoned mud pits that may be present at the site. This information will then be used to identify the locations for test pits, cone penetrometer tests, and drill hole/monitor well installation. The disposal pits were used during the operation of the test site in the 1960s. Vertical magnetic gradient (magnetic gradient), electromagnetic (EM) conductivity, and ground-penetrating radar (GPR) surveys were used to accomplish these objectives. A description of the equipment used and a theoretical discussion of the geophysical methods are presented Appendix A. Because of the large number of figures relative to the number of pages of text, the geophysical grid-location maps, the contour maps of the magnetic-gradient data, the contour maps of the EM conductivity data, and the GPR traverse location maps are located in Appendix B, Tabs I through 22. In addition, selected GPR records are located in Appendix C.« less

Occupational exposure to airborne contaminants during offshore oil drilling.

PubMed

Kirkhus, Niels E; Thomassen, Yngvar; Ulvestad, Bente; Woldbæk, Torill; Ellingsen, Dag G

2015-07-01

The aim was to study exposure to airborne contaminants in oil drillers during ordinary work. Personal samples were collected among 65 drill floor workers on four stationary and six moveable rigs in the Norwegian offshore sector. Air concentrations of drilling mud were determined based on measurements of the non-volatile mud components Ca and Fe. The median air concentration of mud was 140 μg m(-3). Median air concentrations of oil mist (180 μg m(-3)), oil vapour (14 mg m(-3)) and organic carbon (46 μg m(-3)) were also measured. All contaminants were detected in all work areas (drill floor, shaker area, mud pits, pump room, other areas). The highest air concentrations were measured in the shaker area, but the differences in air concentrations between working areas were moderate. Oil mist and oil vapour concentrations were statistically higher on moveable rigs than on stationary rigs, but after adjusting for differences in mud temperature the differences between rig types were no longer of statistical significance. Statistically significant positive associations were found between mud temperature and the concentrations of oil mist (Spearman's R = 0.46) and oil vapour (0.39), and between viscosity of base oil and oil mist concentrations. Use of pressure washers was associated with higher air concentrations of mud. A series of 18 parallel stationary samples showed a high and statistically significant association between concentrations of organic carbon and oil mist (r = 0.98). This study shows that workers are exposed to airborne non-volatilized mud components. Air concentrations of volatile mud components like oil mist and oil vapour were low, but were present in all the studied working areas.

30 CFR 250.1623 - Well-control fluids, equipment, and operations.

Code of Federal Regulations, 2012 CFR

2012-07-01

... measuring device for determining fluid volumes when filling the hole on trips, and (3) A recording mud-pit... and an audible warning device. (c) When coming out of the hole with drill pipe or a workover string... that may be pulled prior to filling the hole and the equivalent well-control fluid volume shall be...

30 CFR 250.1623 - Well-control fluids, equipment, and operations.

Code of Federal Regulations, 2014 CFR

2014-07-01

... measuring device for determining fluid volumes when filling the hole on trips, and (3) A recording mud-pit... and an audible warning device. (c) When coming out of the hole with drill pipe or a workover string... that may be pulled prior to filling the hole and the equivalent well-control fluid volume shall be...

30 CFR 250.1623 - Well-control fluids, equipment, and operations.

Code of Federal Regulations, 2013 CFR

2013-07-01

... measuring device for determining fluid volumes when filling the hole on trips, and (3) A recording mud-pit... and an audible warning device. (c) When coming out of the hole with drill pipe or a workover string... that may be pulled prior to filling the hole and the equivalent well-control fluid volume shall be...

30 CFR 250.614 - Well-control fluids, equipment, and operations.

Code of Federal Regulations, 2012 CFR

2012-07-01

... well is shut in and secured. (b) When coming out of the hole with drill pipe or a workover string, the... string and drill collars that may be pulled prior to filling the hole and the equivalent well-control... fluid volumes when filling the hole on trips; and (3) A recording mud-pit-level indicator to determine...

Pitting Initiation and Propagation of X70 Pipeline Steel Exposed to Chloride-Containing Environments

PubMed Central

Yang, Zixuan; Kan, Bo; Li, Jinxu; Su, Yanjing; Qiao, Lijie; Volinsky, Alex A.

2017-01-01

Inclusion-induced pitting initiation mechanisms in X70 steel were investigated by scanning electron microscopy, scanning Kelvin probe force microscopy (SKPFM), immersion and electrochemical polarization tests in chloride-containing ion solutions. There are three inclusion types in the X70 steel. Corrosion test results indicated that pitting corrosion resistance of type A inclusion < type C inclusion < type B inclusion, i.e., (Mn, Ca)S < matrix < (Al, Ca)O. SKPFM test results show that the type A inclusion exhibited both lower and higher potentials than the matrix, while the type B inclusion exhibited higher potential than the matrix. The corrosion test and the SKPFM potential test results are consistent. Potentiodynamic polarization results indicate that the type A and C are active inclusions, while the type B is an inactive inclusion. Three kinds of possible mechanisms of inclusion-induced pitting corrosion are established for the X70 steel. PMID:28902156

Evidence of mud volcanism rooted in gas hydrate-rich cryosphere linking surface and subsurface for the search for life on Mars

NASA Astrophysics Data System (ADS)

De Toffoli, Barbara; Pozzobon, Riccardo; Mazzarini, Francesco; Massironi, Matteo; Cremonese, Gabriele

2017-04-01

We mapped around 6000 mounds in three different portions of the Martian surface on an average area of about 90.000 Km2 for each region. The study areas are located in Hellas basin, Utopia basin and a portion of the Northern Plains lying north of Arabia Terra, between Acidalia and Utopia Planitia. The aim of the study was to understand the nature of the observed features, particularly if they could be interpreted as mud volcanoes or not, and improve our knowledge about the Martian mound fields origin. The analysis of Context Camera (onboard Mars Reconnaissance Orbiter) images showed circular, elliptical and coalescent mounds with central and/or distal pits and flow features such as concentric annular lobes around the source pits and apron-like extensions. We produced DTMs and then high-to-diameter morphometric analysis on two groups of mounds located in Utopia and Hellas basins to enhance the geomorphological observations. We inferred, by means of cluster and fractal analyses, the thickness of the medium cracked by connected fractures and, consequently, the depths of reservoirs that fed the mounds. We found that the fields, which are seated at different latitudes, has been fed, at least partially, by reservoirs located at the base of the gas hydrate stability zone according to Clifford et al., 2010. This evidence produces a meaningful relationship between the clathrates distribution underneath the Martian surface and the occurrence of mound fields on the surface leading to the assumption that the involvement of water, ostensibly as a result of gas hydrate dissociation, plays a key role in the subsurface processes that potentially worked as triggers. These outcomes corroborate the hypothesis that the mapped mounds are actually mud volcanoes and make these structures outstanding targets for astrobiology and habitability studies. In fact, mud volcanoes, extruding material from depths that are still not affordable by our present-day instrumentations, could have sampled and brought to the surface with the sediments a putative extinct or extant deep biosphere. In conclusion, on the base of this study, emerged that: (i) mud volcanoes are the best terrestrial analogs for the considered Martian mounds, (ii) there is a recurrent specific subsurface environment where the phenomenon may be triggered and it is the base of gas hydrate-rich cryosphere for all the study areas and (iii) mud volcanism seems to be, at least partially, a geologically recent event in terms of planet thermal evolution timespan. In light of these results, the CaSSIS camera, onboard the Trace Gas Orbiter ExoMARS mission, will provide new images of these features to improve and widen the understanding of the mechanisms that lie behind this phenomenon.

Closure Report for Corrective Action Unit 562: Waste Systems, Nevada National Security Site, Nevada

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

NSTec Environmental Restoration

2012-08-15

This Closure Report (CR) presents information supporting closure of Corrective Action Unit (CAU) 562, Waste Systems, and provides documentation supporting the completed corrective actions and confirmation that closure objectives for CAU 562 were met. This CR complies with the requirements of the Federal Facility Agreement and Consent Order (FFACO) that was agreed to by the State of Nevada; the U.S. Department of Energy (DOE), Environmental Management; the U.S. Department of Defense; and DOE, Legacy Management (FFACO, 1996 as amended). CAU 562 consists of the following 13 Corrective Action Sites (CASs), located in Areas 2, 23, and 25 of the Nevadamore » National Security Site: · CAS 02-26-11, Lead Shot · CAS 02-44-02, Paint Spills and French Drain · CAS 02-59-01, Septic System · CAS 02-60-01, Concrete Drain · CAS 02-60-02, French Drain · CAS 02-60-03, Steam Cleaning Drain · CAS 02-60-04, French Drain · CAS 02-60-05, French Drain · CAS 02-60-06, French Drain · CAS 02-60-07, French Drain · CAS 23-60-01, Mud Trap Drain and Outfall · CAS 23-99-06, Grease Trap · CAS 25-60-04, Building 3123 Outfalls Closure activities began in October 2011 and were completed in April 2012. Activities were conducted according to the Corrective Action Plan for CAU 562 (U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office [NNSA/NSO], 2011). The corrective actions included No Further Action and Clean Closure. Closure activities generated sanitary waste and hazardous waste. Some wastes exceeded land disposal limits and required offsite treatment prior to disposal. Other wastes met land disposal restrictions and were disposed in appropriate onsite or offsite landfills. NNSA/NSO requests the following: · A Notice of Completion from the Nevada Division of Environmental Protection to NNSA/NSO for closure of CAU 562 · The transfer of CAU 562 from Appendix III to Appendix IV, Closed Corrective Action Units, of the FFACO« less

A novel multidimensional protein identification technology approach combining protein size exclusion prefractionation, peptide zwitterion-ion hydrophilic interaction chromatography, and nano-ultraperformance RP chromatography/nESI-MS2 for the in-depth analysis of the serum proteome and phosphoproteome: application to clinical sera derived from humans with benign prostate hyperplasia.

PubMed

Garbis, Spiros D; Roumeliotis, Theodoros I; Tyritzis, Stavros I; Zorpas, Kostas M; Pavlakis, Kitty; Constantinides, Constantinos A

2011-02-01

The current proof-of-principle study was aimed toward development of a novel multidimensional protein identification technology (MudPIT) approach for the in-depth proteome analysis of human serum derived from patients with benign prostate hyperplasia (BPH) using rational chromatographic design principles. This study constituted an extension of our published work relating to the identification and relative quantification of potential clinical biomarkers in BPH and prostate cancer (PCa) tissue specimens. The proposed MudPIT approach encompassed the use of three distinct yet complementary liquid chromatographic chemistries. High-pressure size-exclusion chromatography (SEC) was used for the prefractionation of serum proteins followed by their dialysis exchange and solution phase trypsin proteolysis. The tryptic peptides were then subjected to offline zwitterion-ion hydrophilic interaction chromatography (ZIC-HILIC) fractionation followed by their online analysis with reversed-phase nano-ultraperformance chromatography (RP-nUPLC) hyphenated to nanoelectrospray ionization-tandem mass spectrometry using an ion trap mass analyzer. For the spectral processing, the sequential use of the SpectrumMill, Scaffold, and InsPecT software tools was applied for the tryptic peptide product ion MS(2) spectral processing, false discovery rate (FDR) assessment, validation, and protein identification. This milestone serum analysis study allowed the confident identification of over 1955 proteins (p ≤ 0.05; FDR ≤ 5%) with a broad spectrum of biological and physicochemical properties including secreted, tissue-specific proteins spanning approximately 12 orders of magnitude as they occur in their native abundance levels in the serum matrix. Also encompassed in this proteome was the confident identification of 375 phosphoproteins (p ≤ 0.05; FDR ≤ 5%) with potential importance to cancer biology. To demonstrate the performance characteristics of this novel MudPIT approach, a comparison was made with the proteomes resulting from the immunodepletion of the high abundant albumin and IgG proteins with offline first dimensional tryptic peptide separation with both ZIC-HILIC and strong cation exchange (SCX) chromatography and their subsequent online RP-nUPLC-nESI-MS(2) analysis.

A Pre-Restoration Fishery Resource Utilization Assessment of an Estuarine Borrow Pit in Mobile Bay, Alabama

DTIC Science & Technology

2013-06-01

2 samples were characterized by juvenile drum (Sciaenidae spp.) and brown shrimp at Airport Hole, and white shrimp (Penaeus setiferus) and...and brown (n = 18, Penaeus aztecus) shrimp, blue (n = 1, Callinectes sapidus) and mud (n = 3, Rhithropanopeus harrisii) crabs, and oyster “clumps...macroinvertebrates ERDC TN-DOER-E37 June 2013 14 represented by 3 species of shellfish. Shellfish included white (n = 755) and brown (n=5) shrimp, blue crabs

Providing Boiler Inspections at US Army Installations: How to Perform Internal/Operational, Efficiency, and Emissions Testing

DTIC Science & Technology

2013-08-01

corrosion can be found on tubes , tubesheets, and in steam- drums, most often near the waterline in steam boilers . Oxygen pitting can also occur anywhere...components present in the feedwater onto wetted boiler surfaces including fire- tubes and water- tubes . Since scale is a good insulator, the thicker...steel surfaces of a steam boiler . However, heavier scale accumulates on the lower steel surfaces of the tubes , mud-drum, and boiler shell. SLUDGE

Sediment Transport over a Dredge Pit, Sandy Point Southeast, west flank of the Mississippi River during Summer Upcoast Currents: a Coupled Wave, Current and Sediment Numerical Model

NASA Astrophysics Data System (ADS)

Chaichitehrani, N.; Li, C.; Xu, K.; Bentley, S. J.; Miner, M. D.

2017-12-01

Sandy Point southeast, an elongated sand resource, was dredged in November 2012 to restore Pelican Island, Louisiana. Hydrodynamics and wave propagation patterns along with fluvial sediments from the Mississippi River influence the sediment and bottom boundary layer dynamics over Sandy Point. A state-of-the-art numerical model, Delft3D, was implemented to investigate current variations and wave transformation on Sandy Point as well as sediment transport pattern. Delft3d FLOW and WAVE modules were coupled and validated using WAVCIS and NDBC data. Sediment transport model was run by introducing both bed and river sediments, consisted of mainly mud and a small fraction of sand. A sediment transport model was evaluated for surface sediment concentration using data derived from satellite images. The model results were used to study sediment dynamics and bottom boundary layer characteristics focused on the Sandy Point area during summer. Two contrasting bathymetric configurations, with and without the Sandy Point dredge pit, were used to conduct an experiment on the sediment and bottom boundary layer dynamics. Preliminary model results showed that the presence of the Sandy Point pit has very limited effect on the hydrodynamics and wave pattern at the pit location. Sediments from the Mississippi River outlets, especially in the vicinity of the pit, get trapped in the pit under the easterly to the northeasterly upcoast current which prevails in August. We also examined the wave-induced sediment reworking and river-borne fluvial sediment over Sandy Point. The effect of wind induced orbital velocity increases the bottom shear stress compared to the time with no waves, relatively small wave heights (lower than 1.5 meters) along the deepest part of the pit (about 20 meters) causes little bottom sediment rework during this period. The results showed that in the summertime, river water is more likely the source of sedimentation in the pit.

Characterization of the human submandibular/sublingual saliva glycoproteome using lectin affinity chromatography coupled to Multidimensional Protein Identification Technology

PubMed Central

Gonzalez-Begne, Mireya; Lu, Bingwen; Liao, Lujian; Xu, Tao; Bedi, Gurrinder; Melvin, James E.; Yates, John R.

2011-01-01

In-depth analysis of the salivary proteome is fundamental to understanding the functions of salivary proteins in the oral cavity and to reveal disease biomarkers involved in different pathophysiological conditions, with the ultimate goal of improving patient diagnosis and prognosis. Submandibular and sublingual glands contribute saliva rich in glycoproteins to the total saliva output, making them valuable sources for glycoproteomic analysis. Lectin-affinity chromatography coupled to mass spectrometry-based shotgun proteomics was used to explore the submandibular/sublingual (SM/SL) saliva glycoproteome. A total of 262 N- and O-linked glycoproteins were identified by multidimensional protein identification technology (MudPIT). Only 38 were previously described in SM and SL salivas from the human salivary N-linked glycoproteome, while 224 were unique. Further comparison analysis with SM/SL saliva of the human saliva proteome, revealed 125 glycoproteins not formerly reported in this secretion. KEGG pathway analyses demonstrated that many of these glycoproteins are involved in processes such as complement and coagulation cascades, cell communication, glycosphingolipid biosynthesis neo-lactoseries, O-glycan biosynthesis, glycan structures-biosynthesis 2, starch and sucrose metabolism, peptidoglycan biosynthesis or others pathways. In summary, lectin-affinity chromatography coupled to MudPIT mass spectrometry identified many novel glycoproteins in SM/SL saliva. These new additions to the salivary proteome may prove to be a critical step for providing reliable biomarkers in the diagnosis of a myriad of oral and systemic diseases. PMID:21936497

Experimental study of hyperspectral responses of plants grown on mud pit soil

NASA Astrophysics Data System (ADS)

Credoz, Anthony; Hédacq, Rémy; Barreau, Christophe; Dubucq, Dominique

2016-10-01

On-shore, hyperspectral imagery is currently used to detect and measure remotely oil spill extension for environmental purpose and hydrocarbon seepage for petroleum exploration. In this study, variations of hyperspectral signatures of vegetal species have been analyzed at the laboratory scale to detect indirectly the potential impacts on the plants of crude oil seepage and spills in the soil. Experimental study has been performed under greenhouse to simulate the exposure of two species of plants to a co-contamination of hydrocarbons and heavy metals contained in sludge from mud pit. Maize and bramble have been selected for this study since they are cultivated and spontaneous species respectively located in the region of interest. Five levels of exposure were performed over a period of 100 days. Reflectance evolution of each plant was measured with a spectroradiometer from 350 nm to 2500 nm with a dedicated leaf clip. Net morphological impacts were observed for maize with a global reduction of plants and leaves sizes correlated to the level of cocontamination. Hyperspectral measurement on maize revealed a higher reflectance in the absorption wavelength of water at 1450 and 1900 nm due to contamination and water stress. Reflectance in the visible increased at 600 nm (red interval) for bramble plants exposed to co-contamination. Then, the level of reflectance in the NIR decreased between 700 and 800 nm (red-edge) and absorption of water also decreased at 1450 and 1900 nm as described previously for the maize.

Timing of fluid seepage on summits of Quaker and Conical serpentine mud volcanoes, Mariana forearc: Evidence from U/Th dating of carbonate chimneys

NASA Astrophysics Data System (ADS)

Tong, Hongpeng; Fryer, Patricia; Feng, Dong; Chen, Duofu

2017-04-01

Serpetinization of forearc mantle along deep faults in the Mariana convergent plate margin permits formation of large active serpentinite mud volcanoes on the overiding plate within 90 km of the trench. Fluid seepage on summits of the mud volcanoes lead to the formation of authigenic carbonate chimneys close to the seafloor. Such carbonate chimneys are unique archives of past fluid seepage and assciated envrionemtnal parameters. Here, we report U/Th dating and stable carbon and oxygen isotopes of the chimneys from Quaker and Conical serpentine mud volcanoes. The resulting U/Th ages of samples from Quaker Seamount show three time intervals of 11,081 to10,542 yBP, 5,857 to 5,583 yBP, and 781 to 164 yBP, respectively. By comparison, carbonates from Conical Seamount have U/Th ages between 3,070 yBP and 1,623 yBP. Our results suggest that fluid seepage on the summits of serpentine mud volcanoes are episodic and probably locally controlled. Samples from Quaker seamount show depletion of 13C (δ13C=-7.0-0.4‰ V-PDB), indicating contribution of carbon from anoxic oxidation of abiogenic methane. By contrast, samples from Conical seamount have positive δ18O values (0.6-6.3), suggesting enrichment of 18O in the seepage fluid. The data obtained provide time integrated variation of seepage fluids and seepage dynamics that are archived in authigenic carbonates. This finding adds to the ongoing multidisciplinary effort to better constrain the environment in the Mariana forearc region and to determine the locally dominant biogeochemical processes. Acknowlegment: This study was funded by the CAS (Grant No. XDB06030102).

Pitted cones and domes on Mars: Observations in Acidalia Planitia and Cydonia Mensae using MOC, THEMIS, and TES data

USGS Publications Warehouse

Farrand, W. H.; Gaddis, L.R.; Keszthelyi, L.

2005-01-01

Domes and cones with summit pits located in Acidalia Planitia and Cydonia Mensae were studied using MOC and THEMIS images and a TES-derived thermal inertia map. North of 40.5??N latitude, the features have a dome-like morphology, and south of that latitude, the morphology is more cone-like. Layering is apparent in the summit craters of fresher looking southern cones, and asymmetric aprons were observed in some instances. Some of the northern domes also display layering in their summit craters, but asymmetric aprons were not observed. The northern domes can also display multiple summit pits or no summit pits at all and can occur in association with higher-albedo "pancake" features. The northern domes are higher in albedo but have apparent thermal inertias that are lower than the surrounding plains. The apparent thermal inertia values of the southern cones range from values comparable to the surrounding plains to slightly lower. From the TES thermal inertia map, we infer that the thermal inertia values of the pitted cones are between those of basaltic fine dust and sand, while those of the surrounding plains are closer to that of basaltic sand. While a unique interpretation of the origin of the pitted cones is not possible with the available data, we do not find compelling evidence to suggest an origin related to either basaltic volcanism or ground-ice. Instead, an origin for these features through some combination of mud volcanism and evaporite deposition around geysers and/or springs is most consistent with the observations. Copyright 2005 by the American Geophysical Union.

Prokaryotic diversity and biochemical properties in aging artificial pit mud used for the production of Chinese strong flavor liquor.

PubMed

Sun, Zhongke; Chen, Can; Hou, Xiaoge; Zhang, Jie; Tian, Fengshou; Li, Chengwei

2017-10-01

At present, artificial pit mud (APM) is widely used in Chinese liquor-making industry and plays a particular role in the production of Chinese strong flavor liquor (CSFL). However, APM frequently ages during fermentation, thus becoming unsuitable for sustainable use due to its low-quality. The reasons behind, and results of, APM aging during the production of CSFL are not yet understood. Sequencing the V4 region of the 16S rRNA gene shows that prokaryotic diversity is significantly decreased (Shannon's diversity index, P  < 0.01) and community composition is distinctly changed (from 1197 to 865 OTUs) in aging APM. On the phylum level, the increase of Firmicutes and decrease of Proteobacteria are the main consequences of APM aging during the production of CSFL. The counting of cultivatable bacteria confirmed that there was a large increase in Lactobacilli and aerobic spore-forming bacteria in aging low-quality APM (more than twofold). Unexpectedly, the total number of caproic acid-producing bacteria, mainly Clostridia , did not change significantly between the two kinds of APM. Furthermore, biochemical analysis indicates that the pH and the levels of NH 4 + and K + are decreased in aging low-quality APM ( P  < 0.01). The results obtained in this study support the possibility that environmental factors (pH, nutrients) induce the decrease of prokaryotic diversity, and the changed community composition influences the environmental properties. Therefore, through interfering with the cycle, APM aging can be controlled potentially by adjustment of environmental factors and/or supplementation of diminished or missed microorganisms.

No short-term cytogenetic consequences of Hungarian red mud catastrophe.

PubMed

Gundy, Sarolta; Farkas, Gyöngyi; Székely, Gábor; Kásler, Miklós

2013-01-01

Red mud is an industrial waste produced in the process of alumina extraction from bauxite with concentrated NaOH. When the red mud-containing reservoir collapsed in Ajka Alumina Plant Hungary in October 2010, the most serious immediate effects were caused by the high alkalinity (pH ≥ 13) of the flood. Many persons suffered burn-like damage to tissues and contact with caustic desiccated ultra-fine dust with traces of toxic metals also caused irritation of upper respiratory tract and eyes. This catastrophe was unique from the point of view of genotoxic effects as well. Therefore cytogenetic examinations were carried out on inhabitants, either with burns (17 persons) or on those inhaling desiccated caustic dust (42 persons). Chromosomal aberration (CA) analysis and bleomycin (BLM)-sensitivity assays, as possible markers of effects, were studied in peripheral blood lymphocytes of persons within 4-6 weeks following the catastrophe. Controls were matched for age, sex and smoking habits, and also places of residence with different constituents of air pollution either from rural (59 persons), or from urban environments (59 persons). Neither spontaneous rate of CAs (1.47% vs. 1.69%) nor BLM-induced in vitro chromosomal breakage (0.79 vs. 0.83 break/cell) showed elevated rates when cytogenetic biomarkers of genotoxicity were compared between controls and exposed persons. Time spent in cleaning did not affect cytogenetic changes either (R(2) = 0.04). BLM-induced mutagen sensitivity was similar in exposed and control persons (27.1% vs. 30.5%). It seems that the red mud exposure does not appear to pose an immediate genotoxic hazard on residents when measured with cytogenetic methods. We recommend, however, that those involved in clean-up activities should be followed closely not only for overall health, but also for further genotoxic risk assessment, because the long-term hazards of ultra-fine fugitive dust particles with alkalinity of residual NaOH in red mud are still unknown.

Seabed texture and composition changes offshore of Port Royal Sound, South Carolina before and after the dredging for beach nourishment

NASA Astrophysics Data System (ADS)

Xu, Kehui; Sanger, Denise; Riekerk, George; Crowe, Stacie; Van Dolah, Robert F.; Wren, P. Ansley; Ma, Yanxia

2014-08-01

Beach nourishment has been a strategy widely used to slow down coastal erosion in many beaches around the world. The dredging of sand at the borrow site, however, can have complicated physical, geological and ecological impacts. Our current knowledge is insufficient to make accurate predictions of sediment infilling in many dredging pits due to lack of detailed sediment data. Two sites in the sandy shoal southeast of Port Royal Sound (PRS) of South Carolina, USA, were sampled 8 times from April 2010 to March 2013; one site (defined as 'borrow site') was 2 km offshore and used as the dredging site for beach nourishment of nearby Hilton Head Island in Beaufort County, South Carolina, and the other site (defined as 'reference site') was 10 km offshore and not directly impacted by the dredging. A total of 184 surficial sediment samples were collected randomly at two sites during 8 sampling periods. Most sediments were fine sand, with an average grain size of 2.3 phi and an organic matter content less than 2%. After the dredging in December 2011-January 2012, sediments at the borrow site became finer, changing from 1.0 phi to 2.3 phi, and carbonate content decreased from 10% to 4%; changes in mud content and organic matter were small. Compared with the reference site, the borrow site experienced larger variations in mud and carbonate content. An additional 228 sub-samples were gathered from small cores collected at 5 fixed stations in the borrow site and 1 fixed station at the reference site 0, 3, 6, 9, and 12 months after the dredging; these down-core sub-samples were divided into 1-cm slices and analyzed using a laser diffraction particle size analyzer. Most cores were uniform vertically and consisted of fine sand with well to moderately well sorting and nearly symmetrical averaged skewness. Based on the analysis of grain size populations, 2 phi- and 3 phi-sized sediments were the most dynamic sand fractions in PRS. Mud deposition on shoals offshore of PRS presumably happens when offshore mud transport is prevalent and there is a following rapid sand accumulation to bury the mud. However, in this borrow site there was very little accumulation of mud. This will allow the site to be used in future nourishment projects presuming no accumulation of mud occurs in the future.

JOINTS AND SYN-SEDIMENTARY FAULTS NETWORKS IN MARINE CLAYS AND MUDSTONES. Importance for Radwaste storage

NASA Astrophysics Data System (ADS)

Arnould, M.

2009-12-01

There is a number of marine clays, mudstones, marls, 100 to 200 m thick, showing smectites, mixed layers illite/smectite, with a small percentage of organic matter and sulphides with a variable clay, silt, and carbonate content. I published (Arnould , 2006) examples from Lower Cambrian to Miocene in age and from the Baltic shore to Spain in Europe. Observations were made mostly in quarries and pits down to more than 40 m and in underground research laboratories (URL). Only visible on fresh cuts amongst a variety of fissures there is always a network of joints. Schematically one family is the bedding (horizontal) the two others are normal to the bedding and orthogonal between them. The orientations of vertical joints are different from the orientations of pits and quarries’s walls. The networks are intrinsic. It was first well described by Skempton & al (1969) in Eocene London Clay. Joints are matt in texture, clean, without filling or cement. The order of magnitude of their linear dimensions is decimeter to meter. It is necessary to start from the original sediment: mud. Deposited in flakes mud has a bee’s nest microscopic structure. Each nest is full of water. Hence mud may have a water content up to 300%, reported to its dry weight. Paradoxically mud is impervious. As proposed by Cosgrove (2001) progressive but discontinuous hydraulic fracturing could be the origin of vertical joints, with drainage upwards and compaction of the sediment. Geological observations show that ioints are formed during the sedimentation process. There is also a world literature concluding at the necessary early fracturing of mudstones and marls hosts of sand dykes. Very few faults are identified in field observations and on exploration logs. But it is obvious that drainage and compaction of mud over thousands square kilometers induced differential settlements with many syn-sedimentary non tectonic faults constituting another discontinuity network. These faults inside the same material with rather small throws are difficult to identify. Their number increases wifh accuracy of geophysical research. Conclusions for underground storage of radioactive waste . There are four underground laboratories on duty in mudstones and clays in Western Europe. No natural discontinuities, joints or faults have been observed during their excavation rapidly followed by lining.This draw some people to the imprudent conclusion that there were no natural discontinuities. In accordance to the very low permeabilities measured by in situ tests all natural discontinuities are closed up at depth by the stresss field. They are sealed but not healed because the temperature of diagenesis remained below 50°C. They can reopen by relaxation of stresses and by desiccation, as in Tournemire tunnel /URL in toarcian mudstones and at Mont Terri URL in Opalinus Clay. Open fissures visible in non lined parts of galleries appear weeks or months after the excavation. After the change of concept from burial to storage and retrievability the problem should not be underestimated. References : Arnould M (2006) Discontinuity networks in mudstones : a geological approach. Bull Eng Geol Environ. Springer ed 65:413-422 Skempton & al (1969) Joints and fissures in the London Clay at Wraysbury and Edgware Geotechnique 19 : 205-217.

Large-scale identification of c-MYC-associated proteins using a combined TAP/MudPIT approach.

PubMed

Koch, Heike B; Zhang, Ru; Verdoodt, Berlinda; Bailey, Aaron; Zhang, Chang-Dong; Yates, John R; Menssen, Antje; Hermeking, Heiko

2007-01-15

The c-MYC oncogene encodes a transcription factor, which is sufficient and necessary for the induction of cellular proliferation. However, the c-MYC protein is a relatively weak transactivator suggesting that it may have other functions. To identify protein interactors which may reveal new functions or represent regulators of c-MYC we systematically identified proteins associated with c-MYC in vivo using a proteomic approach. We combined tandem affinity purification (TAP) with the mass spectral multidimensional protein identification technology (MudPIT). Thereby, 221 c-MYC-associated proteins were identified. Among them were 17 previously known c-MYC-interactors. Selected new c-MYC-associated proteins (DBC-1, FBX29, KU70, MCM7, Mi2-beta/CHD4, RNA Pol II, RFC2, RFC3, SV40 Large T Antigen, TCP1alpha, U5-116kD, ZNF281) were confirmed independently. For association with MCM7, SV40 Large T Antigen and DBC-1 the functionally important MYC-box II region was required, whereas FBX29 and Mi2-beta interacted via MYC-box II and the BR-HLH-LZ motif. In addition, regulators of c-MYC activity were identified: ectopic expression of FBX29, an E3 ubiquitin ligase, decreased c-MYC protein levels and inhibited c-MYC transactivation, whereas knock-down of FBX29 elevated the concentration of c-MYC. Furthermore, sucrose gradient analysis demonstrated that c-MYC is present in numerous complexes with varying size and composition, which may accommodate the large number of new c-MYC-associated proteins identified here and mediate the diverse functions of c-MYC. Our results suggest that c-MYC, besides acting as a mitogenic transcription factor, regulates cellular proliferation by direct association with protein complexes involved in multiple synthetic processes required for cell division, as for example DNA-replication/repair and RNA-processing. Furthermore, this first comprehensive description of the c-MYC-associated sub-proteome will facilitate further studies aimed to elucidate the biology of c-MYC.

Proteomic Analysis of Fusarium solani Isolated from the Asian Longhorned Beetle, Anoplophora glabripennis

PubMed Central

Scully, Erin D.; Hoover, Kelli; Carlson, John; Tien, Ming; Geib, Scott M.

2012-01-01

Wood is a highly intractable food source, yet many insects successfully colonize and thrive in this challenging niche. Overcoming the lignin barrier of wood is a key challenge in nutrient acquisition, but full depolymerization of intact lignin polymers has only been conclusively demonstrated in fungi and is not known to occur by enzymes produced by insects or bacteria. Previous research validated that lignocellulose and hemicellulose degradation occur within the gut of the wood boring insect, Anoplophora glabripennis (Asian longhorned beetle), and that a fungal species, Fusarium solani (ATCC MYA 4552), is consistently associated with the larval stage. While the nature of this relationship is unresolved, we sought to assess this fungal isolate's ability to degrade lignocellulose and cell wall polysaccharides and to extract nutrients from woody tissue. This gut-derived fungal isolate was inoculated onto a wood-based substrate and shotgun proteomics using Multidimensional Protein Identification Technology (MudPIT) was employed to identify 400 expressed proteins. Through this approach, we detected proteins responsible for plant cell wall polysaccharide degradation, including proteins belonging to 28 glycosyl hydrolase families and several cutinases, esterases, lipases, pectate lyases, and polysaccharide deacetylases. Proteinases with broad substrate specificities and ureases were observed, indicating that this isolate has the capability to digest plant cell wall proteins and recycle nitrogenous waste under periods of nutrient limitation. Additionally, several laccases, peroxidases, and enzymes involved in extracellular hydrogen peroxide production previously implicated in lignin depolymerization were detected. In vitro biochemical assays were conducted to corroborate MudPIT results and confirmed that cellulases, glycosyl hydrolases, xylanases, laccases, and Mn- independent peroxidases were active in culture; however, lignin- and Mn- dependent peroxidase activities were not detected While little is known about the role of filamentous fungi and their associations with insects, these findings suggest that this isolate has the endogenous potential to degrade lignocellulose and extract nutrients from woody tissue. PMID:22496740

CRISPR, a Crossroads in Genetic Intervention: Pitting the Right to Health against the Right to Disability

PubMed Central

Benston, Shawna

2016-01-01

Reproductive genetic technologies (RGTs), including gene-editing technology, are being discovered and refined at an exponential pace. One gene-editing innovation that demands our swift attention is CRISPR/Cas9, a system of clustered regularly interspaced short palindromic repeats and a protein called Cas9. As CRISPR and other RGTs continue being developed, we must remain vigilant concerning the potential implications of genetic-engineering technology on our interpersonal and legal relationships. In the face of increasingly numerous and refined RGTs, we must maintain the rights of everyone: potential parents, prospective children, and individuals (both living and prospective) with disabilities. For those who wish to become parents, how should procreation be regulated in light of developing RGTs, especially gene-editing technology? What duties do parents owe their children, and when does such a duty attach? What role should RGTs play in parents’ fulfillment of their duties to their children? This article will contextualize the right to health and what I will term the “right to disability” in the CRISPR/Cas9 landscape. The article will then explore these rights in reference to the “subjunctive-threshold” interpretation of harm. Finally, I will argue that RGTs must be thoughtfully regulated, with such regulations taking into account the opinions of geneticists, bioethicists, and lay people concerning both the right to health and the right to disability. PMID:27688903

CRISPR, a Crossroads in Genetic Intervention: Pitting the Right to Health against the Right to Disability.

PubMed

Benston, Shawna

2016-03-01

Reproductive genetic technologies (RGTs), including gene-editing technology, are being discovered and refined at an exponential pace. One gene-editing innovation that demands our swift attention is CRISPR/Cas9, a system of clustered regularly interspaced short palindromic repeats and a protein called Cas9. As CRISPR and other RGTs continue being developed, we must remain vigilant concerning the potential implications of genetic-engineering technology on our interpersonal and legal relationships. In the face of increasingly numerous and refined RGTs, we must maintain the rights of everyone: potential parents, prospective children, and individuals (both living and prospective) with disabilities. For those who wish to become parents, how should procreation be regulated in light of developing RGTs, especially gene-editing technology? What duties do parents owe their children, and when does such a duty attach? What role should RGTs play in parents' fulfillment of their duties to their children? This article will contextualize the right to health and what I will term the "right to disability" in the CRISPR/Cas9 landscape. The article will then explore these rights in reference to the "subjunctive-threshold" interpretation of harm. Finally, I will argue that RGTs must be thoughtfully regulated, with such regulations taking into account the opinions of geneticists, bioethicists, and lay people concerning both the right to health and the right to disability.

Impact to Underground Sources of Drinking Water and Domestic Wells from Production Well Stimulation and Completion Practices in the Pavillion, Wyoming, Field.

PubMed

DiGiulio, Dominic C; Jackson, Robert B

2016-04-19

A comprehensive analysis of all publicly available data and reports was conducted to evaluate impact to Underground Sources of Drinking Water (USDWs) as a result of acid stimulation and hydraulic fracturing in the Pavillion, WY, Field. Although injection of stimulation fluids into USDWs in the Pavillion Field was documented by EPA, potential impact to USDWs at the depths of stimulation as a result of this activity was not previously evaluated. Concentrations of major ions in produced water samples outside expected levels in the Wind River Formation, leakoff of stimulation fluids into formation media, and likely loss of zonal isolation during stimulation at several production wells, indicates that impact to USDWs has occurred. Detection of organic compounds used for well stimulation in samples from two monitoring wells installed by EPA, plus anomalies in major ion concentrations in water from one of these monitoring wells, provide additional evidence of impact to USDWs and indicate upward solute migration to depths of current groundwater use. Detections of diesel range organics and other organic compounds in domestic wells <600 m from unlined pits used prior to the mid-1990s to dispose diesel-fuel based drilling mud and production fluids suggest impact to domestic wells as a result of legacy pit disposal practices.

Corrective Action Investigation Plan for Corrective Action Unit 139: Waste Disposal Sites, Nevada Test Site, Nevada, Rev. No.: 0

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

Grant Evenson

2006-04-01

Corrective Action Unit (CAU) 139 is located in Areas 3, 4, 6, and 9 of the Nevada Test Site, which is 65 miles northwest of Las Vegas, Nevada. Corrective Action Unit 139 is comprised of the seven corrective action sites (CASs) listed below: (1) 03-35-01, Burn Pit; (2) 04-08-02, Waste Disposal Site; (3) 04-99-01, Contaminated Surface Debris; (4) 06-19-02, Waste Disposal Site/Burn Pit; (5) 06-19-03, Waste Disposal Trenches; (6) 09-23-01, Area 9 Gravel Gertie; and (7) 09-34-01, Underground Detection Station. These sites are being investigated because existing information on the nature and extent of potential contamination is insufficient to evaluatemore » and recommend corrective action alternatives with the exception of CASs 09-23-01 and 09-34-01. Regarding these two CASs, CAS 09-23-01 is a gravel gertie where a zero-yield test was conducted with all contamination confined to below ground within the area of the structure, and CAS 09-34-01 is an underground detection station where no contaminants are present. Additional information will be obtained by conducting a corrective action investigation (CAI) before evaluating corrective action alternatives and selecting the appropriate corrective action for the other five CASs where information is insufficient. The results of the field investigation will support a defensible evaluation of viable corrective action alternatives that will be presented in the Corrective Action Decision Document. The sites will be investigated based on the data quality objectives (DQOs) developed on January 4, 2006, by representatives of the Nevada Division of Environmental Protection; U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office; Stoller-Navarro Joint Venture; and Bechtel Nevada. The DQO process was used to identify and define the type, amount, and quality of data needed to develop and evaluate appropriate corrective actions for CAU 139.« less

Addendum to the Closure Report for Corrective Action Unit 335: Area 6 Injection Well and Drain Pit Nevada Test Site, Nevada, Revison 0

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

Lynn Kidman

This document constitutes an addendum to the June 2003, Closure Report for Corrective Action Unit 335: Area 6 Injection Well and Drain Pit as described in the document Recommendations and Justifications for Modifications for Use Restrictions Established under the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office Federal Facility Agreement and Consent Order (UR Modification document) dated February 2008. The UR Modification document was approved by NDEP on February 26, 2008. The approval of the UR Modification document constituted approval of each of the recommended UR modifications. In conformance with the UR Modification document, this addendum consistsmore » of: • This cover page that refers the reader to the UR Modification document for additional information • The cover and signature pages of the UR Modification document • The NDEP approval letter • The corresponding section of the UR Modification document This addendum provides the documentation justifying the cancellation of the URs for: • CAS 06-20-02, 20-inch Cased Hole • CAS 06-23-03, Drain Pit These URs were established as part of Federal Facility Agreement and Consent Order (FFACO) corrective actions and were based on the presence of contaminants at concentrations greater than the action levels established at the time of the initial investigation (FFACO, 1996; as amended August 2006). Since these URs were established, practices and procedures relating to the implementation of risk-based corrective actions (RBCA) have changed. Therefore, these URs were re-evaluated against the current RBCA criteria as defined in the Industrial Sites Project Establishment of Final Action Levels (NNSA/NSO, 2006c). This re-evaluation consisted of comparing the original data (used to define the need for the URs) to risk-based final action levels (FALs) developed using the current Industrial Sites RBCA process. The re-evaluation resulted in a recommendation to remove these URs because contamination is not present at these sites above the risk-based FALs. Requirements for inspecting and maintaining these URs will be canceled, and the postings and signage at each site will be removed. Fencing and posting may be present at these sites that are unrelated to the FFACO URs such as for radiological control purposes as required by the NV/YMP Radiological Control Manual (NNSA/NSO, 2004f). This modification will not affect or modify any non-FFACO requirements for fencing, posting, or monitoring at these sites.« less

Corrective Action Decision Document/Closure Report for Corrective Action Unit 274: Septic Systems, Nevada Test Site, Nevada, Rev. No.: 0

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

Grant Evenson

2006-09-01

This Corrective Action Decision Document/Closure Report has been prepared for Corrective Action Unit 274, Septic Systems, Nevada Test Site (NTS), Nevada in accordance with the ''Federal Facility Agreement and Consent Order'' (1996). Corrective Action Unit (CAU) 274 is comprised of five corrective action sites (CASs): (1) CAS 03-02-01, WX-6 ETS Building Septic System; (2) CAS 06-02-01, Cesspool; (3) CAS 09-01-01, Spill Site; (4) CAS 09-05-01, Leaching Pit; and (5) CAS 20-05-01, Septic System. The purpose of this Corrective Action Decision Document/Closure Report is to provide justification and documentation supporting the closure of CAU 274 with no further corrective action. Tomore » achieve this, corrective action investigation (CAI) activities were performed from November 14 through December 17, 2005 as set forth in the CAU 274 Corrective Action Investigation Plan. The purpose of the CAI was to fulfill the following data needs as defined during the data quality objective (DQO) process: (1) Determine whether contaminants of concern (COCs) are present. (2) If contaminants of concern are present, determine their nature and extent. (3) Provide sufficient information and data to complete appropriate corrective actions. The CAU 274 dataset from the investigation results was evaluated based on the data quality indicator parameters. This evaluation demonstrated the quality and acceptability of the dataset for use in fulfilling the DQO data needs. Analytes detected during the CAI were evaluated against final action levels (FALs) established in this document. No analytes were detected at concentrations exceeding the FALs. No COCs have been released to the soil at CAU 274, and corrective action is not required. Therefore, the DQO data needs were met, and it was determined that no corrective action based on risk to human receptors is necessary for the site. All FALs were calculated using the industrial site worker scenario except for benzo(a)pyrene, which was calculated based on the occasional use scenario. Benzo(a)pyrene was detected above the preliminary action level at CAS 20-05-01; however, it was not identified as a COC because the concentration was below the FAL. As a best management practice and to ensure that future site workers are not exposed to this site contaminant for more than this decision-basis exposure duration, an administrative use restriction was established around the leachfield at CAS 20-05-01. In addition, the removal of the septic tanks and septic tank contents at CASs 03-02-01, 06-02-01, and 20-05-01 was performed.« less

Atteinte cardiaque au cours de la dystrophie myotonique de Steinert: expérience marocaine, à propos de 18 cas

PubMed Central

Saghi, Ghita; Bouhouch, Rachida; Salaheddine, Loubna; Birouk, Nezha; Nadifi, Salama; Fellat, Ibtissam; Cherti, Mohamed

2015-01-01

La maladie de Steinert ou dystrophie myotonique de type 1 (DM1) est une maladie génétique à transmission autosomique dominante caractérisée par une myotonie et une atteinte de plusieurs organes dont le cœur. L'atteinte cardiaque est la plus grave des atteintes systémiques puisqu'elle conditionne le pronostic vital. Ce travail a pour but de déterminer les anomalies cardiaques rencontrées au cours de la DM1 et de mettre en exergue l'intérêt d'un examen cardiaque rigoureux et régulier, indépendamment de la sévérité de l'atteinte neuromusculaire, ainsi que l'apport des examens cardiaques complémentaires et notamment l'exploration électrophysiologique. 18 patients atteints de DM1 ont bénéficiés d'une exploration cardiaque systématique. Il s'agit de 9 hommes et de 9 femmes, d’âge moyen de 41,8 +/- 16,2 ans. 66 p.100 des patients sont symptomatiques sur le plan cardiovasculaire. Les anomalies électrocardiographiques sont dominées par un trouble de la conduction intra-ventriculaire dans 16 p.100 des cas et un BAV de 1er degré dans 16 p.100 des cas. L'Holter ECG objective une hyperexcitabilité à l’étage atrial et/ou ventriculaire dans 50p.100 des cas. L'ETT est normale chez 95 p.100 des patients. L'exploration électrophysiologique, réalisée chez 4 patients symptomatiques, a objectivé un bloc tronculaire dans un cas ayant conduit à l'implantation d'un PM double chambre. Un seul patient est décédé suite à une détresse respiratoire. Enfin, on n'a pas noté de corrélation entre l'atteinte cardiaque et neuromusculaire. Une exploration cardiaque est indispensable chez tout patient atteint de DM1, en dépit de l'absence de symptômes, et un bilan annuel minimal s'impose pour guetter un éventuel trouble rythmique et/ou conductif, fatal en l'absence de traitement adéquat. PMID:26097635

Physical and Chemical Properties of Sintering Red Mud and Bayer Red Mud and the Implications for Beneficial Utilization

PubMed Central

Wang, Ping; Liu, Dong-Yan

2012-01-01

Performances of two common types of red mud, Bayer red mud and Sintering red mud, were investigated in this research. Their compositions, mechanical properties and microstructure characterization were measured through XRD, TG and SEM analysis. Their shear strength, particle size, density and hydraulic characteristics also had been performed. Huge differences between the basic mineral types of these two kinds of red mud also can be found. The comparison of compositions shows that CaCO3 content in Sintering red mud is higher, Bayer red mud has more hazardous elements such as As, Pb and Hg and both have a high concentration of radioactivity. The micro particle of Bayer red mud is finer and more disperse, but the Sintering red mud has higher shear strength. Combining the TG and hydraulic characteristics analysis, it can be shown that Bayer red mud has higher value of water content and Sintering red mud has higher hydraulic conductivity. The paper then illustrates that Sintering red mud can become the main filling material of supporting structure of red mud stocking yard. Bayer red mud has a high reuse value and also can be used as a mixing material of masonry mortar.

Sedimentology of gravelly Lake Lahontan highstand shoreline deposits, Churchill Butte, Nevada, USA

NASA Astrophysics Data System (ADS)

Blair, Terence C.

1999-02-01

Gravelly shoreline deposits of the latest Pleistocene highstand of Lake Lahontan occur in pristine depositional morphology, and are exposed in gravel pits along Churchill Butte in west-central Nevada. Four environments differentiated at this site are alluvial fan/colluvium, lakeshore barrier spit, lake lower-shoreface spit platform, and lake bottom. Lakeshore deposits abut, along erosional wave headcuts, either unsorted muddy to bouldery colluvium fringing Churchill Butte bedrock, or matrix-supported, cobbly and pebbly debris-flow deposits of the Silver Springs fan. The lakeshore barrier spit is dominated by granule pebble gravel concentrated by wave erosion of the colluvial and alluvial-fan facies. The lakeward side of the barrier consists of beachface deposits of well-sorted granules or pebbles in broad, planar beds 1-10 cm thick and sloping 10-15°. They interfinger downslope with thicker (10-25 cm) and less steep (5-10°) lakeward-dipping beds of fine to medium pebble gravel of the lake upper shoreface. Interstratified with the latter are 10-40-cm-thick sets of high-angle cross-beds that dip southward, alongshore. Higher-angle (15-20°), landward-dipping foresets of similar texture but poorer sorting comprise the proximal backshore on the landward side of the barrier. They were deposited during storm surges that overtopped the barrier berm. Gastropod-rich sand and mud, also deposited by storm-induced washover, are found landward of the gravel foresets in a 15-m-wide backshore pond. Algal stromatolites, ostracodes, and diatoms accumulated in this pond between storm events. The lake lower shoreface, extending from water depths of 2 to 8 m, consists of a southward-prograding spit platform built by longshore drift. The key component of this platform is large-scale sandy pebble gravel in 16° southward-dipping `Gilbert' foresets that grade at a water depth of about 6-7 m to 4°-dipping sandy toesets. A shift from bioturbated lower-shoreface sand and silt, to flat and laminated lake-bottom silt and mud, occurs between water depths of 10-40 m and over a shore-normal distance of ≥250 m. This lake-bottom mud facies, unlike the others, is areally expansive.

Ascent velocity and dynamics of the Fiumicino mud eruption, Rome, Italy

NASA Astrophysics Data System (ADS)

Vona, A.; Giordano, G.; De Benedetti, A. A.; D'Ambrosio, R.; Romano, C.; Manga, M.

2015-08-01

In August 2013 drilling triggered the eruption of mud near the international airport of Fiumicino (Rome, Italy). We monitored the evolution of the eruption and collected samples for laboratory characterization of physicochemical and rheological properties. Over time, muds show a progressive dilution with water; the rheology is typical of pseudoplastic fluids, with a small yield stress that decreases as mud density decreases. The eruption, while not naturally triggered, shares several similarities with natural mud volcanoes, including mud componentry, grain-size distribution, gas discharge, and mud rheology. We use the size of large ballistic fragments ejected from the vent along with mud rheology to compute a minimum ascent velocity of the mud. Computed values are consistent with in situ measurements of gas phase velocities, confirming that the stratigraphic record of mud eruptions can be quantitatively used to infer eruption history and ascent rates and hence to assess (or reassess) mud eruption hazards.

A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom

PubMed Central

Trevisan-Silva, Dilza; Bednaski, Aline V.; Fischer, Juliana S.G.; Veiga, Silvio S.; Bandeira, Nuno; Guthals, Adrian; Marchini, Fabricio K.; Leprevost, Felipe V.; Barbosa, Valmir C.; Senff-Ribeiro, Andrea; Carvalho, Paulo C.

2017-01-01

Venoms are a rich source for the discovery of molecules with biotechnological applications, but their analysis is challenging even for state-of-the-art proteomics. Here we report on a large-scale proteomic assessment of the venom of Loxosceles intermedia, the so-called brown spider. Venom was extracted from 200 spiders and fractioned into two aliquots relative to a 10 kDa cutoff mass. Each of these was further fractioned and digested with trypsin (4 h), trypsin (18 h), pepsin (18 h), and chymotrypsin (18 h), then analyzed by MudPIT on an LTQ-Orbitrap XL ETD mass spectrometer fragmenting precursors by CID, HCD, and ETD. Aliquots of undigested samples were also analyzed. Our experimental design allowed us to apply spectral networks, thus enabling us to obtain meta-contig assemblies, and consequently de novo sequencing of practically complete proteins, culminating in a deep proteome assessment of the venom. Data are available via ProteomeXchange, with identifier PXD005523. PMID:28696408

Isoform-specific functions of Mud/NuMA mediate binucleation of Drosophila male accessory gland cells.

PubMed

Taniguchi, Kiichiro; Kokuryo, Akihiko; Imano, Takao; Minami, Ryunosuke; Nakagoshi, Hideki; Adachi-Yamada, Takashi

2014-12-20

In standard cell division, the cells undergo karyokinesis and then cytokinesis. Some cells, however, such as cardiomyocytes and hepatocytes, can produce binucleate cells by going through mitosis without cytokinesis. This cytokinesis skipping is thought to be due to the inhibition of cytokinesis machinery such as the central spindle or the contractile ring, but the mechanisms regulating it are unclear. We investigated them by characterizing the binucleation event during development of the Drosophila male accessory gland, in which all cells are binucleate. The accessory gland cells arrested the cell cycle at 50 hours after puparium formation (APF) and in the middle of the pupal stage stopped proliferating for 5 hours. They then restarted the cell cycle and at 55 hours APF entered the M-phase synchronously. At this stage, accessory gland cells binucleated by mitosis without cytokinesis. Binucleating cells displayed the standard karyokinesis progression but also showed unusual features such as a non-round shape, spindle orientation along the apico-basal axis, and poor assembly of the central spindle. Mud, a Drosophila homolog of NuMA, regulated the processes responsible for these three features, the classical isoform Mud(PBD) and the two newly characterized isoforms Mud(L) and Mud(S) regulated them differently: Mud(L) repressed cell rounding, Mud(PBD) and Mud(S) oriented the spindle along the apico-basal axis, and Mud(S) and Mud(L) repressed central spindle assembly. Importantly, overexpression of Mud(S) induced binucleation even in standard proliferating cells such as those in imaginal discs. We characterized the binucleation in the Drosophila male accessory gland and examined mechanisms that regulated unusual morphologies of binucleating cells. We demonstrated that Mud, a microtubule binding protein regulating spindle orientation, was involved in this binucleation. We suggest that atypical functions exerted by three structurally different isoforms of Mud regulate cell rounding, spindle orientation and central spindle assembly in binucleation. We also propose that Mud(S) is a key regulator triggering cytokinesis skipping in binucleation processes.

Chemo-Mechanical Characteristics of Mud Formed from Environmental Dust Particles in Humid Ambient Air

PubMed Central

Hassan, Ghassan; Yilbas, B. S.; Said, Syed A. M.; Al-Aqeeli, N.; Matin, Asif

2016-01-01

Mud formed from environmental dust particles in humid ambient air significantly influences the performance of solar harvesting devices. This study examines the characterization of environmental dust particles and the chemo-mechanics of dry mud formed from dust particles. Analytical tools, including scanning electron microscopy, atomic force microscopy, energy dispersive spectroscopy, particle sizing, and X-ray diffraction, are used to characterize dry mud and dust particles. A micro/nano tribometer is used to measure the tangential force and friction coefficient while tensile tests are carried out to assess the binding forces of dry mud pellets. After dry mud is removed, mud residuals on the glass surface are examined and the optical transmittance of the glass is measured. Dust particles include alkaline compounds, which dissolve in water condensate and form a mud solution with high pH (pH = 7.5). The mud solution forms a thin liquid film at the interface of dust particles and surface. Crystals form as the mud solution dries, thus, increasing the adhesion work required to remove dry mud from the surface. Optical transmittance of the glass is reduced after dry mud is removed due to the dry mud residue on the surface. PMID:27445272

Chemo-Mechanical Characteristics of Mud Formed from Environmental Dust Particles in Humid Ambient Air.

PubMed

Hassan, Ghassan; Yilbas, B S; Said, Syed A M; Al-Aqeeli, N; Matin, Asif

2016-07-22

Mud formed from environmental dust particles in humid ambient air significantly influences the performance of solar harvesting devices. This study examines the characterization of environmental dust particles and the chemo-mechanics of dry mud formed from dust particles. Analytical tools, including scanning electron microscopy, atomic force microscopy, energy dispersive spectroscopy, particle sizing, and X-ray diffraction, are used to characterize dry mud and dust particles. A micro/nano tribometer is used to measure the tangential force and friction coefficient while tensile tests are carried out to assess the binding forces of dry mud pellets. After dry mud is removed, mud residuals on the glass surface are examined and the optical transmittance of the glass is measured. Dust particles include alkaline compounds, which dissolve in water condensate and form a mud solution with high pH (pH = 7.5). The mud solution forms a thin liquid film at the interface of dust particles and surface. Crystals form as the mud solution dries, thus, increasing the adhesion work required to remove dry mud from the surface. Optical transmittance of the glass is reduced after dry mud is removed due to the dry mud residue on the surface.

Maladie thromboembolique veineuse dans la région de Sidi Bel Abbes, Algérie: fréquence et facteurs de risque

PubMed Central

Chalal, Nourelhouda; Demmouche, Abbassia

2013-01-01

Introduction La maladie thromboembolique veineuse (MTEV) présente par ses deux entités cliniques: thrombose veineuse profonde (TVP) et embolie pulmonaire (EP), est une pathologie fréquente ayant une forte morbi-mortalité. En Algérie, cette pathologie prend de plus en plus de l'ampleur, en l'absence de toute publication révélant sa fréquence et le pouvoir thrombogène des facteurs de risque qui lui sont corrélés. Notre étude a pour objectif de déterminer la fréquence et les facteurs de risque de ce type d'affection dans la région de Sidi Bel Abbes, Algérie. Méthodes Il s'agit d'une étude rétrospective allant du 1er janvier 2006 au 10 juin 2012 ciblant les patients hospitalisés pour TVP et /ou EP au sein du service de cardiologie du CHU de Sidi Bel Abbes. Résultats 183 patients atteints de la MTEV dont 112 femmes (61.2%) d’âge moyen 46.4 ± 17.9 et 71 hommes (38.7%) d’âge moyen 51.5 ± 17.7 ont été notés. 146 cas parmi eux (79.7%) présentaient une TVP isolée, alors que 37 autres (20.2%) étaient atteints d'EP, dont 16 cas de TVP associée. Les facteurs de risque les plus fréquents enregistrés en cas de TVP sont surtout: l'immobilité, l'hypertension, la chirurgie, et la contraception orale, tandis que: l'immobilité, la chirurgie, l'hypertension et les fractures sont les facteurs de risques les plus incriminés en cas d'EP. 24.7% des patients présentaient plusieurs facteurs de risque. L'antécédent personnel de la MTEV, était présent dans 12.02% des cas. 97.5% des TVP ont touché les membres inférieurs mais seulement 2.5% des TVP étaient localisés au niveau des membres supérieurs. Conclusion Au terme de notre étude, et en dépit de sa fréquence non alarmante, il serait indispensable d'envisager l'adoption d'une stratégie prophylactique adéquate afin de lutter contre le développement redoutable de ce genre d'affection dans la région de Sidi Bel Abbes. PMID:24648858

Factors controlling mud accumulation in the Heuksan mud belt off southwestern Korea

NASA Astrophysics Data System (ADS)

Chang, Tae Soo; Ha, Hun Jun; Chun, Seung Soo

2015-12-01

The Heuksan mud belt (hereafter HMB) is 20~50 km wide, ~200 km long, and ~50 m thick, having accumulated in the course of the Holocene transgression on the tide-dominated epicontinental shelf southwest of Korea. The internal architecture of the HMB is characterized by offshore prograding clinoforms. Of particular interest are the depositional processes responsible for this anomalously thick mud accumulation within a relatively short period of time. Tidal currents are important in the dispersal of mud in the HMB, although these alone cannot explain such an enormous mud deposit. In order to understand the formative processes of the HMB, a detailed sedimentary facies analysis, including high-resolution grain-size measurements, has been conducted on more than 30 short cores and three long drill cores recovered from the mud belt. Five major mud facies were identified. Of these, mud sequences showing a thickening-thinning trend of alternating silt and clay laminae suggestive of a tidal origin occur dominantly at inner to mid shelf locations. By contrast, internally structureless muds with sharp bases and no bioturbation, which are interpreted of representing fluid-mud deposits, are widespread at mid to outer shelf locations. Wave-generated mud ripples and storm beds on the inner shelf suggest that storm waves in winter resuspend previously deposited mud to form near-bed fluid-mud suspensions with resulting gravity-driven mud transport across the low-gradient outer shelf. This previously not recognized process is probably a major factor controlling depositional processes on the giant mud belt, enabling rapid accumulation and offshore progradation even during transgression, i.e., at times of sea-level rise.

Stockpiling and Comprehensive Utilization of Red Mud Research Progress

PubMed Central

Liu, Dong-Yan; Wu, Chuan-Sheng

2012-01-01

With increasing production of red mud, the environmental problems caused by it are increasingly serious, and thus the integrated treatment of red mud is imminent. This article provides an overview of the composition and the basic characteristics of red mud. The research progress of safe stockpiling and comprehensive utilization of red mud is summarized. The safe stockpiling of red mud can be divided into two aspects: the design and safe operation of the stocking yard. The comprehensive utilization of red mud can be further divided into three aspects: the effective recycling of components, resource utilization and application in the field of environmental protection. This paper points out that the main focus of previous studies on red mud stockpiling is cost reproduction and land tenure. The recovery of resources from red mud has a high value-added, but low level industrialization. The use of red mud as a building material and filler material is the most effective way to reduce the stockpiling of red mud. Red mud used for environmental remediation materials is a new hotspot and worth promoting for its simple processing and low cost.

Pozzolanic Activity Assessment of LUSI (LUmpur SIdoarjo) Mud in Semi High Volume Pozzolanic Mortar

PubMed Central

Hardjito, Djwantoro; Antoni; Wibowo, Gunadi M.; Christianto, Danny

2012-01-01

LUSI mud obtained from the mud volcano in Sidoarjo, Indonesia, is a viable aluminosilicate material to be utilized as pozzolanic material. LUSI is an abbreviation of the local name of the mud, i.e., Lumpur Sidoarjo, meaning Sidoarjo mud. This paper reports the results of an investigation to assess the pozzolanic activity of LUSI mud, especially in semi high volume pozzolanic mortar. In this case, the amount of mud incorporated is between 30% to 40% of total cementitious material, by mass. The content of SiO2 in the mud is about 30%, whilst the total content of SiO2, Fe2O3 and Al2O3 is more than 70%. Particle size and degree of partial cement replacement by treated LUSI mud affect the compressive strength, the strength activity index (SAI), the rate of pozzolanic activity development, and the workability of mortar incorporating LUSI mud. Manufacturing semi high volume LUSI mud mortar, up to at least 40% cement replacement, is a possibility, especially with a smaller particle size of LUSI mud, less than 63 μm. The use of a larger percentage of cement replacement by LUSI mud does not show any adverse effect on the water demand, as the flow of the fresh mortar increased with the increase of percentage of LUSI mud usage.

Numerical simulation of mud erosion rate in sand-mud alternate layer and comparison with experiment

NASA Astrophysics Data System (ADS)

Yoshida, T.; Yamaguchi, T.; Oyama, H.; Sato, T.

2015-12-01

For gas production from methane hydrates in sand-mud alternate layers, depressurization method is expected as feasible. After methane hydrate is dissociated, gas and water flow in pore space. There is a concern about the erosion of mud surface and it may result in flow blockage that disturbs the gas production. As a part of a Japanese National hydrate research program (MH21, funded by METI), we developed a numerical simulation of water-induced mud erosion in pore-scale sand-mud domains to model such mud erosion. The size of which is of the order of 100 micro meter. Water flow is simulated using a lattice Boltzmann method (LBM) and mud surface is treated as solid boundary with arbitrary shape, which changes with time. Periodic boundary condition is adopted at the domain boundaries, except for the surface of mud layers and the upper side. Shear stress acting on the mud surface is calculated using a momentum-exchange method. Mud layer is eroded when the shear stress exceeds a threshold coined a critical shear stress. In this study, we compared the simulated mud erosion rate with experimental data acquired from an experiment using artificial sand-mud core. As a result, the simulated erosion rate agrees well with that of the experiment.

Mud volcanoes on Mars?

NASA Technical Reports Server (NTRS)

Komar, Paul D.

1991-01-01

The term mud volcano is applied to a variety of landforms having in common a formation by extrusion of mud from beneath the ground. Although mud is the principal solid material that issues from a mud volcano, there are many examples where clasts up to boulder size are found, sometimes thrown high into the air during an eruption. Other characteristics of mud volcanoes (on Earth) are discussed. The possible presence of mud volcanoes, which are common and widespread on Earth, on Mars is considered.

Linked halokinesis and mud volcanism at the Mercator mud volcano, Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Perez-Garcia, Carolina; Berndt, Christian; Klaeschen, Dirk; Mienert, Jürgen; Haffert, Laura; Depreiter, Davy; Haeckel, Matthias

2011-05-01

Mud volcanoes are seafloor expressions of focused fluid flow that are common in compressional tectonic settings. New high-resolution 3-D seismic data from the Mercator mud volcano (MMV) and an adjacent buried mud volcano (BMV) image the internal structure of the top 800 m of sediment at both mud volcanoes, revealing that both are linked and have been active episodically. The total volumes of extruded mud range between 0.15 and 0.35 km3 and 0.02-0.05 km3 for the MMV and the BMV, respectively. The pore water composition of surface sediment samples suggests that halokinesis has played an important role in the evolution of the mud volcanoes. We propose that erosion of the top of the Vernadsky Ridge that underlies the mud volcanoes activated salt movement, triggering deep migration of fluids, dissolution of salt, and sediment liquefaction and mobilization since the end of the Pliocene. Since beginning of mud volcanism in this area, the mud volcanoes erupted four times while there was only one reactivation of salt tectonics. This implies that there are other mechanisms that trigger mud eruptions. The stratigraphic relationship of mudflows from the MMV and BMV indicates that the BMV was triggered by the MMV eruptions. This may either be caused by loading-induced hydrofracturing within the BMV or due to a common feeder system for both mud volcanoes. This study shows that the mud volcanoes in the El Arraiche mud volcano field are long-lived features that erupt with intervals of several tens of thousands of years.

Anatahan, Northern Mariana Islands: Reconnaissance geological observations during and after the volcanic crisis of spring 1990, and monitoring prior to the May 2003 eruption

USGS Publications Warehouse

Rowland, S.K.; Lockwood, J.P.; Trusdell, F.A.; Moore, R.B.; Sako, M.K.; Koyanagi, R.Y.; Kojima, G.

2005-01-01

Anatahan island is 9.5 km east-west by 3.5 km north-south and truncated by an elongate caldera 5 km east-west by 2.5 km north-south. A steep-walled pit crater ???1 km across and ???200 m deep occupies the eastern part of the caldera. The island is the summit region of a mostly submarine stratovolcano. The oldest subaerial rocks (stage 1) are exposed low on the outer flanks and in the caldera walls. These include thick (???10 m) and thin (2-3 m) lava flows, well-indurated tuffs, and scoria units that make up the bulk of the island. Rock compositions range from basaltic andesite to dacite, and most are plagioclase-phyric. On the steep north and south flanks of the volcano, these rocks are cut by numerous east-west-oriented, few-hundred-m-long lineaments of undetermined origin. Indurated breccias unconformably overlie scarps cut into stage 1 units low on the south flank. Intermediate-age eruptive units (stage 2) include caldera-filling lava flows and pyroclastic deposits and, on the outer flanks, vents and valley-filling lava flows. The youngest pre-2003 volcanic unit on Anatahan (stage 3) is a hydromagmatic surge and fall deposit rich in accretionary lapilli. Prior to 2003, this unit was found over almost the entire island, and in many places original depositional surfaces and outcrops could be found in high-energy environments along the coast, indicating a young (but undetermined) age. During reconnaissance visits in 1990, 1992, 1994, and 2001, geothermal activity (fumaroles as well as pits with boiling, sediment-laden pools) was observed in the southern part of the pit crater. In March and April 1990, increased local seismicity, a large regional earthquake, and reported increased fumarolic activity in the pit crater prompted evacuation of Anatahan village, at the west end of the island. Our first field investigation took place in late April 1990 to assess the level of volcanic unrest, conduct reconnaissance geological observations, collect rock and geothermal water samples, and set up a geophysical monitoring network. Results at this time were inconclusive with respect to determining whether the activity was anomalous. Water in some of the geothermal pits within the pit crater was boiling, and pH values as low as 0.7 were recorded in the field. An electronic distance measurement (EDM) network was installed, and over a ???1-week period, up to 9 cm of extension occurred across some lines but not others. Seismicity was characterized by intermittent local earthquakes but no sustained swarms or tremor. A brief visit in June 1990 revealed that the shallow lake near the boiling pits was gone, but activity in the pits themselves was similar to that of April 1990. Only minor extension had occurred along a single EDM line since the previous visit, and no earthquakes >M2.5 occurred during the visit. Subsequent 1- to 2-day visits occurred in October 1990, May 1992, May 1994, and June 2001. Activity within the geothermal pits was relatively constant during every visit, although during this 11-year period the level of the water in each pit decreased. In June 2001, a ???50-m-wide region of mud pots and steaming ground in the central part of the geothermal area had developed. No geologic evidence, however, suggested that an eruption would occur <2 years afterward. Most of the EDM lines showed slight extension between late 1990 and 1992, followed by very gradual contraction from 1992 to 2001. A more extensive seismic-monitoring system was installed on the Northern Mariana Islands during these visits, and it recorded a small seismic swarm at Anatahan from May to July 1993. The telemetry component of the seismic equipment broke prior to 2001 and had not been repaired by the time of the May 2003 eruption, so no precursory seismic data were recorded to indicate pre-eruption unrest. ?? 2005 Elsevier B.V. All rights reserved.

Mud volcanoes of the Orinoco Delta, Eastern Venezuela

USGS Publications Warehouse

Aslan, A.; Warne, A.G.; White, W.A.; Guevara, E.H.; Smyth, R.C.; Raney, J.A.; Gibeaut, J.C.

2001-01-01

Mud volcanoes along the northwest margin of the Orinoco Delta are part of a regional belt of soft sediment deformation and diapirism that formed in response to rapid foredeep sedimentation and subsequent tectonic compression along the Caribbean-South American plate boundary. Field studies of five mud volcanoes show that such structures consist of a central mound covered by active and inactive vents. Inactive vents and mud flows are densely vegetated, whereas active vents are sparsely vegetated. Four out of the five mud volcanoes studied are currently active. Orinoco mud flows consist of mud and clayey silt matrix surrounding lithic clasts of varying composition. Preliminary analysis suggests that the mud volcano sediment is derived from underlying Miocene and Pliocene strata. Hydrocarbon seeps are associated with several of the active mud volcanoes. Orinoco mud volcanoes overlie the crest of a mud-diapir-cored anticline located along the axis of the Eastern Venezuelan Basin. Faulting along the flank of the Pedernales mud volcano suggests that fluidized sediment and hydrocarbons migrate to the surface along faults produced by tensional stresses along the crest of the anticline. Orinoco mud volcanoes highlight the proximity of this major delta to an active plate margin and the importance of tectonic influences on its development. Evaluation of the Orinoco Delta mud volcanoes and those elsewhere indicates that these features are important indicators of compressional tectonism along deformation fronts of plate margins. ?? 2001 Elsevier Science B.V. All rights reserved.

Walking through volcanic mud: the 2,100 year-old Acahualinca footprints (Nicaragua) II: the Acahualinca people, environmental conditions and motivation

NASA Astrophysics Data System (ADS)

Schmincke, Hans-Ulrich; Rausch, Juanita; Kutterolf, Steffen; Freundt, Armin

2010-10-01

We analyzed bare human footprints in Holocene tuff preserved in two pits in the Acahualinca barrio in the northern outskirts of Managua (Nicaragua). Lithology, volcanology, and age of the deposits are discussed in a companion paper (Schmincke et al. Bull Volcanol doi: 10.1007/s00445-008-0235-9 , 2008). The footprint layer occurs within a series of rapidly accumulated basaltic-andesitic tephra that is regionally correlated to the Masaya Triple Layer Tephra. The people were probably trying to escape from a powerful volcanic eruption at Masaya Caldera 20 km farther south that occurred at 2.1 ka BP. We subdivided the swath of footprints, up to 5.6 m wide, in the northern pit (Pit I) into (1) a central group of footprints made by about six individuals, the total number being difficult to determine because people walked in each other’s footsteps one behind the other and (2) two marginal groups on either side of the central group with more widely spaced tracks. The western band comprises tracks of three adjacent individuals and an isolated single footprint farther out. The eastern marginal area comprises an inner band of deep footprints made by three individuals and, farther out, three clearly separated individuals. We estimate the total number of people as 15-16. In the southern narrow and smaller pit (Pit II), we recognize tracks of ca. 12 individuals, no doubt made by the same group. The group represented in both pits probably comprised male and female adults, teenagers and children based on differences in length of footprints and of strides and depth of footprints made in the soft wet ash. The smallest footprints (probably made by children) occur in the central group, where protection was most effective. The footprint layer is composed of a lower 5-15-cm thick, coarse-grained vesicle tuff capped by a medium to fine-grained tuff up to 3 cm thick. The surface on which the people walked was muddy, and the soft ash was squeezed up on the sides of the foot imprints and between toes. Especially, deep footprints are mainly due to local thickening of the water-rich ash, multiple track use, and differences in weight of individuals. The excellent preservation of the footprints, ubiquitous mudcracks, sharp and well-preserved squeeze-ups along the margins of the tracks and toe imprints, and the absence of raindrop impressions all suggest that the eruption occurred during the dry season. The people walked at a brisk pace, as judged from the tight orientation of the swath and the length of the strides. The directions of a major erosional channel in the overlying deposits that probably debouched into Lake Managua and the band of footprints are strictly parallel, indicating that people walked together in stride along the eastern margin of a channel straight toward the lake shore, possibly a site with huts and/or boats for protection and/or escape.

Cyclic Activity of Mud Volcanoes: Evidences from Trinidad (SE Caribbean)

NASA Astrophysics Data System (ADS)

Deville, E.

2007-12-01

Fluid and solid transfer in mud volcanoes show different phases of activity, including catastrophic events followed by periods of relative quiescence characterized by moderate activity. This can be notably shown by historical data onshore Trinidad. Several authors have evoked a possible link between the frequencies of eruption of some mud volcanoes and seismic activity, but in Trinidad there is no direct correlation between mud eruptions and seisms. It appears that each eruptive mud volcano has its own period of catastrophic activity, and this period is highly variable from one volcano to another. The frequency of activity of mud volcanoes seems essentially controlled by local pressure regime within the sedimentary pile. At the most, a seism can, in some cases, activate an eruption close to its term. The dynamics of expulsion of the mud volcanoes during the quiescence phases has been studied notably from temperature measurements within the mud conduits. The mud temperature is concurrently controlled by, either, the gas flux (endothermic gas depressurizing induces a cooling effect), or by the mud flux (mud is a vector for convective heat transfer). Complex temperature distribution was observed in large conduits and pools. Indeed, especially in the bigger pools, the temperature distribution characterizes convective cells with an upward displacement of mud above the deep outlet, and ring-shaped rolls associated with the burial of the mud on the flanks of the pools. In simple, tube-like shaped, narrow conduits, the temperature is more regular, but we observed different types of profiles, with either downward increasing or decreasing temperatures. If the upward flow of mud would be regular, we should expect increasing temperatures and progressively decreasing gradient with depth within the conduits. However, the variable measured profiles from one place to another, as well as time-variable measured temperatures within the conduits and especially, at the base of the conduits, shows that the fluid flow expelled by the studied mud volcanoes is not constant but highly variable through short time-periods. We notably observed very short time-period cyclic variations with a frequency of about 10 minutes. These high frequencies temperature changes could be related to the dynamics of two-phase flows (gas and mud) through the mud volcano conduits. We also observed locally a significant daily changes of the temperature of the expelled mud which shows also that the mud flux is changing very rapidly from one day to another.

Preliminary analytical results for a mud sample collected from the LUSI Mud Volcano, Sidoarjo, East Java, Indonesia

USGS Publications Warehouse

Plumlee, Geoffrey S.; Casadevall, Thomas J.; Wibowo, Handoko T.; Rosenbauer, Robert J.; Johnson, Craig A.; Breit, George N.; Lowers, Heather; Wolf, Ruth E.; Hageman, Philip L.; Goldstein, Harland L.; Anthony, Michael W.; Berry, Cyrus J.; Fey, David L.; Meeker, Gregory P.; Morman, Suzette A.

2008-01-01

On May 29, 2006, mud and gases began erupting unexpectedly from a vent 150 meters away from a hydrocarbon exploration well near Sidoarjo, East Java, Indonesia. The eruption, called the LUSI (Lumpur 'mud'-Sidoarjo) mud volcano, has continued since then at rates as high as 160,000 m3 per day. At the request of the United States Department of State, the U.S. Geological Survey (USGS) has been providing technical assistance to the Indonesian Government on the geological and geochemical aspects of the mud eruption. This report presents initial characterization results of a sample of the mud collected on September 22, 2007, as well as inerpretive findings based on the analytical results. The focus is on characteristics of the mud sample (including the solid and water components of the mud) that may be of potential environmental or human health concern. Characteristics that provide insights into the possible origins of the mud and its contained solids and waters have also been evaluated.

30 CFR 250.1614 - Mud program.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 2 2014-07-01 2014-07-01 false Mud program. 250.1614 Section 250.1614 Mineral Resources BUREAU OF SAFETY AND ENVIRONMENTAL ENFORCEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS... requirements concerning mud control, mud test and monitoring equipment, mud quantities, and safety precautions...

30 CFR 250.1614 - Mud program.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 2 2013-07-01 2013-07-01 false Mud program. 250.1614 Section 250.1614 Mineral Resources BUREAU OF SAFETY AND ENVIRONMENTAL ENFORCEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS... requirements concerning mud control, mud test and monitoring equipment, mud quantities, and safety precautions...

30 CFR 250.1614 - Mud program.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 2 2012-07-01 2012-07-01 false Mud program. 250.1614 Section 250.1614 Mineral Resources BUREAU OF SAFETY AND ENVIRONMENTAL ENFORCEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS... requirements concerning mud control, mud test and monitoring equipment, mud quantities, and safety precautions...

Chemical Speciation of Chromium in Drilling Muds

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

Taguchi, Takeyoshi; Yoshii, Mitsuru; Shinoda, Kohzo

2007-02-02

Drilling muds are made of bentonite and other clays, and/or polymers, mixed with water to the desired viscosity. Without the drilling muds, corporations could not drill for oil and gas and we would have hardly any of the fuels and lubricants considered essential for modern industrial civilization. There are hundreds of drilling muds used and some kinds of drilling muds contain chromium. The chemical states of chromium in muds have been studied carefully due to concerns about the environmental influence. However it is difficult to determine the chemical state of chromium in drilling muds directly by conventional analytical methods. Wemore » have studied the chemical form of chromium in drilling muds by using a laboratory XAFS system and a synchrotron facility.« less

Chemical, mineralogical, and isotopic characteristics of mud from the LUSI mud volcano, Sidoarjo, East Java, Indonesia: implications for the environment, public health, and eruption processes

NASA Astrophysics Data System (ADS)

Plumlee, G. S.; Casadevall, T. J.; Wibowo, H. T.; Rosenbauer, R. J.; Johnson, C. A.; Breit, G. N.; Hageman, P. L.; Wolf, R. E.; Morman, S. A.

2009-12-01

On May 29, 2006, mud and gases began erupting from a vent 150 meters away from a gas exploration well near Sidoarjo, East Java, Indonesia. The eruption, called the LUSI mud volcano, has continued at rates as high as 160,000 m3 per day. At the request of the United States Department of State, the U.S. Geological Survey (USGS) has been providing technical assistance to the Indonesian Government on the geological and geochemical aspects of the mud eruption. This paper will present analytical results of mud samples collected in Sept. 2007 and Nov. 2008, and interpretive findings based on the analytical results. The 2007 mud sample contains high proportions of particles that could be ingestible by hand-mouth transmission (~98 vol % <250 microns,), inhalable into the upper respiratory tract (~80 vol % <10 microns), and respirable into the lung alveoli (~ 40 vol % <2.5 microns), so the mud and dust from the dried mud could be readily taken up by exposed individuals. Our results confirm those of a previous study that the levels of potentially toxic heavy metals or metalloids in the mud are low. A complex mixture of organic compounds in the mud is likely derived from petroleum source rocks. Although the 2007 mud sample contains several percent iron sulfides, net acid production tests indicate that enough carbonate material is also present to prevent the mud from becoming acid-generating due to weathering and sulfide oxidation in the near-surface environment. Water derived from settling mud deposits may have the potential to adversely affect the quality of surface- or groundwater sources for drinking water, due to high levels of fluoride, nitrate, iron, manganese, aluminum, sulfate, chloride, and total dissolved solids. The very high nitrate levels in the waters contained within the mud may present a source of nutrients that could enhance algal blooms and resulting adverse impacts such as hypoxia in fresh-water and marine ecosystems into which some of the mud is being discharged. In agreement with previous studies, water separated from the 2007 mud sample is compositionally and isotopically compatible with an origin as sedimentary formation water. The iron disulfide fraction of the mud sample is isotopically light, and likely formed by bacterial sulfate reduction during diagenesis of clay-rich rocks from which the mud was derived. A smaller, isotopically heavy monosulfide fraction likely formed later by thermogenic reduction of formation-water sulfate to sulfide and reaction of the resulting sulfide with reactive iron in the mud. Additional linked earth science and public health studies are needed to more fully understand eruption processes, and the potential environmental and health consequences of the erupting mud, waters, and gases, and of the accumulating mud deposits.

Geoacoustic Characterization of the Mud Drape at the New England Mud Patch

NASA Astrophysics Data System (ADS)

Reed, A. H.

2016-02-01

The New England Mud Patch is an extensive deposit of fine-grained sediments that extends from an area south of Cape Cod, MA to south of Montauk Point Long Island, NY out on the continental shelf in water depths of 60 to 90 meters. The mud patch has a remarkable accumulation of up to a 13 meter thick sequence of mud that overlays a transgressive surface of Pleistocene Age and then thins out on the periphery where surficial sediments convert from mud to sand and sand/gravel. The deposit likely accumulated in this region due to the coalescing of shelf currents that had oppositional flow. This work focuses on a section of the mud patch that is centered over the thickest portion of mud and extends east-west for 30 km and north south for 10 km. Gravity cores were collected throughout this region and the cores penetrated the upper 2-4 m of mud at 28 different sites with multiple cores collected in several locations. The mud thickness in these regions exceeded the core barrel length, therefore the cores did not penetrate into the basal sand sediment layer, a relict transgressional horizon, which displays prominently in the acoustic data for this selected region. These cores were evaluated for compressional sound speed (averaging 1480 m/s) and density (1580 kg/m3) and found to be largely homogeneous and similar throughout the study area. The largest source of inhomogeneity was due to dispersed shell hash and disarticulated bivalves, but these inclusions represent minor components in the total sediment volume. The overlying sediment that characterizes the New England Mud Patch can be readily classified as mud, silty mud, or sandy-silty mud. This fine-grained sediment deposit reflects upon the low-energy nature of the hydrodynamics within this region.

Red mud as a carbon sink: variability, affecting factors and environmental significance.

PubMed

Si, Chunhua; Ma, Yingqun; Lin, Chuxia

2013-01-15

The capacity of red mud to sequester CO(2) varied markedly due to differences in bauxite type, processing and disposal methods. Calcium carbonates were the dominant mineral phases responsible for the carbon sequestration in the investigated red mud types. The carbon sequestration capacity of red mud was not fully exploited due to shortages of soluble divalent cations for formation of stable carbonate minerals. Titanate and silicate ions were the two major oxyanions that appeared to strongly compete with carbonate ions for the available soluble Ca. Supply of additional soluble Ca and Mg could be a viable pathway for maximizing carbon sequestration in red mud and simultaneously reducing the causticity of red mud. It is roughly estimated that over 100 million tonnes of CO(2) have been unintentionally sequestered in red mud around the world to date through the natural weathering of historically produced red mud. Based on the current production rate of red mud, it is likely that some 6 million tonnes of CO(2) will be sequestered annually through atmospheric carbonation. If appropriate technologies are in place for incorporating binding cations into red mud, approximately 6 million tonnes of additional CO(2) can be captured and stored in the red mud while the hazardousness of red mud is simultaneously reduced. Copyright © 2012 Elsevier B.V. All rights reserved.

Shallow-Water Mud Acoustics

DTIC Science & Technology

2015-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Shallow- Water Mud Acoustics William L. Siegmann...shallow water over mud sediments and of acoustic detection, localization, and classification of objects buried in mud. OBJECTIVES • Develop...including long-range conveyance of information; detection, localization, and classification of objects buried in mud; and improvement of shallow water

46 CFR 128.450 - Liquid-mud systems.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Liquid-mud systems. 128.450 Section 128.450 Shipping...: EQUIPMENT AND SYSTEMS Design Requirements for Specific Systems § 128.450 Liquid-mud systems. (a) Liquid-mud... this chapter. (b) Tanks for oil-based liquid mud must be fitted with tank vents equipped with flame...

Binding of Vapour-Phase Mercury (Hg0) on Chemically Treated Bauxite Residues (Red Mud)

EPA Science Inventory

In this study, Hg capture using red mud, seawater-neutralized red mud, and acid-treated red mud is evaluated and compared to other, more conventional sorbent materials. Red mud (also known as bauxite residue) is a by-product of extracting alumina from ground bauxite ore by treati...

30 CFR 250.1614 - Mud program.

Code of Federal Regulations, 2011 CFR

2011-07-01

... OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Sulphur Operations § 250.1614... shall comply with requirements concerning mud control, mud test and monitoring equipment, mud quantities...

Recycling red mud from the production of aluminium as a red cement-based mortar.

PubMed

Yang, Xiaojie; Zhao, Jianfeng; Li, Haoxin; Zhao, Piqi; Chen, Qin

2017-05-01

Current management for red mud is insufficient and a new method is needed. A series of experiments have been carried out to develop a new approach for effective management of red mud. Mortars without or with 3%, 6% and 9% red mud were prepared and their fresh and hardened properties were measured to access the possibility of recycling the red mud in the production of red cement-based mortar. The mechanisms corresponding to their mechanical performance variations were explored by X-ray powder diffraction and scanning electron microscopy. The results show that the fresh mortars with red mud present an increase of viscosity as compared with the control. However, little difference is found when the content of red mud is altered. It also can be seen that red mud increases flow time and reduces the slump flow of the mortar. Meanwhile, it is found that mortar with red mud is provided with higher air content. Red mud is eligible to adjust the decorative mortar colour. Compressive strength of mortar is improved when less than 6% red mud is added. However, overall it has a slightly negative effect on tensile bond strength. It decreases the Ca(OH) 2 content and densifies the microstructure of hardened paste. The heavy metal concentrations in leachates of mortars with red mud are much lower than the values required in the standard, and it will not do harm to people's health and the environment. These results are important to recycle and effectively manage red mud via the production of red cement-based mortar.

Hidden values in bauxite residue (red mud): Recovery of metals

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

Liu, Yanju; Naidu, Ravi, E-mail: ravi.naidu@unisa.edu.au

Highlights: • Current iron recovery techniques using red mud are depicted. • Advantages and disadvantages exist in different recovering processes. • Economic and environmental friendly integrated usage of red mud is promising. - Abstract: Bauxite residue (red mud) is a hazardous waste generated from alumina refining industries. Unless managed properly, red mud poses significant risks to the local environment due to its extreme alkalinity and its potential impacts on surface and ground water quality. The ever-increasing generation of red mud poses significant challenges to the aluminium industries from management perspectives given the low proportion that are currently being utilized beneficially.more » Red mud, in most cases, contains elevated concentrations of iron in addition to aluminium, titanium, sodium and valuable rare earth elements. Given the scarcity of iron supply globally, the iron content of red mud has attracted increasing research interest. This paper presents a critical overview of the current techniques employed for iron recovery from red mud. Information on the recovery of other valuable metals is also reviewed to provide an insight into the full potential usage of red mud as an economic resource rather than a waste. Traditional hydrometallurgy and pyrometallurgy are being investigated continuously. However, in this review several new techniques are introduced that consider the process of iron recovery from red mud. An integrated process which can achieve multiple additional values from red mud is much preferred over the single process methods. The information provided here should help to improve the future management and utilization of red mud.« less

Linking geochemical processes in mud volcanoes with arsenic mobilization driven by organic matter.

PubMed

Liu, Chia-Chuan; Kar, Sandeep; Jean, Jiin-Shuh; Wang, Chung-Ho; Lee, Yao-Chang; Sracek, Ondra; Li, Zhaohui; Bundschuh, Jochen; Yang, Huai-Jen; Chen, Chien-Yen

2013-11-15

The present study deals with geochemical characterization of mud fluids and sediments collected from Kunshuiping (KSP), Liyushan (LYS), Wushanting (WST), Sinyangnyuhu (SYNH), Hsiaokunshui (HKS) and Yenshuikeng (YSK) mud volcanoes in southwestern Taiwan. Chemical constituents (cations, anions, trace elements, organic carbon, humic acid, and stable isotopes) in both fluids and mud were analyzed to investigate the geochemical processes and spatial variability among the mud volcanoes under consideration. Analytical results suggested that the anoxic mud volcanic fluids are highly saline, implying connate water as the probable source. The isotopic signature indicated that δ(18)O-rich fluids may be associated with silicate and carbonate mineral released through water-rock interaction, along with dehydration of clay minerals. Considerable amounts of arsenic in mud irrespective of fluid composition suggested possible release through biogeochemical processes in the subsurface environment. Sequential extraction of As from the mud indicated that As was mostly present in organic and sulphidic phases, and adsorbed on amorphous Mn oxyhydroxides. Volcanic mud and fluids are rich in organic matter (in terms of organic carbon), and the presence of humic acid in mud has implications for the binding of arsenic. Functional groups of humic acid also showed variable sources of organic matter among the mud volcanoes being examined. Because arsenate concentration in the mud fluids was found to be independent from geochemical factors, it was considered that organic matter may induce arsenic mobilization through an adsorption/desorption mechanism with humic substances under reducing conditions. Organic matter therefore plays a significant role in the mobility of arsenic in mud volcanoes. Copyright © 2012 Elsevier B.V. All rights reserved.

Study on dealkalization and settling performance of red mud.

PubMed

Luo, Muxi; Qi, Xuejiao; Zhang, Yurui; Ren, Yufei; Tong, Jiacheng; Chen, Zining; Hou, Yiming; Yeerkebai, Nuerxiate; Wang, Hongtao; Feng, Shijin; Li, Fengting

2017-01-01

At present, the dealkalization and comprehensive utilization of red mud is a worldwide problem. Studies on the settling performance and phase transformation of red mud by HCl, CaO, and H 2 O leaching are limited. In this study, the characteristics of red mud were systematically analyzed. The average sizes of graded and initial red mud were 4.11 and 9.20 μm, respectively. X-ray diffraction (XRD), X-ray fluorescence spectra (XRF), and thermogravimetry-differential scanning calorimetry (TG-DSC) results indicated the different mineralogical phases, composition, and thermal behavior. The addition of HCl could neutralize the alkalization in the red mud slurry, and CaO could replace the Na and K. Notably, the pH of the red mud slurry had no obvious change with the increase in water washing times in a certain pH. Interestingly, soluble Al and Fe were not detected in the HCl-red mud and CaO-red mud. In addition, the settling ratio was used to express the settling performance of the red mud slurry. Their interaction mechanisms were proposed, which may include phase transformation and the changing of the size and surface area. The research provided a better understanding of the phase transformation and settling performance in the treatment of red mud by HCl, CaO, and H 2 O leaching.

The use of red mud as an immobiliser for metal/metalloid-contaminated soil: A review.

PubMed

Hua, Yumei; Heal, Kate V; Friesl-Hanl, Wolfgang

2017-03-05

This review focuses on the applicability of red mud as an amendment for metal/metalloid-contaminated soil. The varying properties of red muds from different sources are presented as they influence the potentially toxic element (PTE) concentration in amended soil. Experiments conducted worldwide from the laboratory to the field scale are screened and the influencing parameters and processes in soils are highlighted. Overall red mud amendment is likely to contribute to lowering the PTE availability in contaminated soil. This is attributed to the high pH, Fe and Al oxide/oxyhydroxide content of red mud, especially hematite, boehmite, gibbsite and cancrinite phases involved in immobilising metals/metalloids. In most cases red mud amendment resulted in a lowering of metal concentrations in plants. Bacterial activity was intensified in red mud-amended contaminated soil, suggesting the toxicity from PTEs was reduced by red mud, as well as indirect effects due to changes in soil properties. Besides positive effects of red mud amendment, negative effects may also appear (e.g. increased mobility of As, Cu) which require site-specific risk assessments. Red mud remediation of metal/metalloid contaminated sites has the potential benefit of reducing red mud storage and associated problems. Copyright © 2016 Elsevier B.V. All rights reserved.

Data on cost analysis of drilling mud displacement during drilling operation.

PubMed

Okoro, Emeka Emmanuel; Dosunmu, Adewale; Iyuke, Sunny E

2018-08-01

The focus of this research was to present a data article for analyzing the cost of displacing a drilling fluid during the drilling operation. The cost of conventional Spud, KCl and Pseudo Oil base (POBM) muds used in drilling oil and gas wells are compared with that of a Reversible Invert Emulsion Mud. The cost analysis is limited to three sections for optimum and effective Comparison. To optimize drilling operations, it is important that we specify the yardstick by which drilling performance is measured. The most relevant yardstick is the cost per foot drilled. The data have shown that the prices for drilling mud systems are a function of the mud system formulation cost for that particular mud weight and maintenance per day. These costs for different mud systems and depend on the base fluid. The Reversible invert emulsion drilling fluid, eliminates the cost acquired in displacing Pseudo Oil Based mud (POBM) from the well, possible formation damage (permeability impairment) resulting from the use of viscous pill in displacing the POBM from the wellbore, and also eliminates the risk of taking a kick during mud change-over. With this reversible mud system, the costs of special fluids that are rarely applied for the well-completion purpose (cleaning of thick mud filter cake) may be reduced to the barest minimum.

Legacy of the California Gold Rush: Environmental geochemistry of arsenic in the southern Mother Lode Gold District

USGS Publications Warehouse

Savage, K.S.; Bird, D.K.; Ashley, R.P.

2000-01-01

Gold mining activity in the Sierra Nevada foothills, both recently and during the California Gold Rush, has exposed arsenic-rich pyritic rocks to weathering and erosion. This study describes arsenic concentration and speciation in three hydrogeologic settings in the southern Mother Lode Gold District: mineralized outcrops and mine waste rock (overburden); mill tailings submerged in a water reservoir; and lake waters in this monomictic reservoir and in a monomictic lake developing within a recent open-pit mine. These environments are characterized by distinct modes of rock-water interaction that influence the local transport and fate of arsenic. Arsenic in outcrops and waste rock occurs in arsenian pyrite containing an average of 2 wt% arsenic. Arsenic is concentrated up to 1300 ppm in fine-grained, friable iron-rich weathering products of the arsenian pyrite (goethite, jarosite, copiapite), which develop as efflorescences and crusts on weathering outcrops. Arsenic is sorbed as a bidentate complex on goethite, and substitutes for sulfate in jarosite. Submerged mill tailings obtained by gravity core at Don Pedro Reservoir contain arsenic up to 300 ppm in coarse sand layers. Overlying surface muds have less arsenic in the solid fraction but higher concentrations in porewaters (up to 500 ??g/L) than the sands. Fine quartz tailings also contain up to 3.5 ppm mercury related to the ore processing. The pH values in sediment porewaters range from 3.7 in buried gypsum-bearing sands and tailings to 7 in the overlying lake sediments. Reservoir waters immediately above the cores contain up to 3.5 ??g/L arsenic; lake waters away from the submerged tailings typically contain less than 1 ??g/L arsenic. Dewatering during excavation of the Harvard open-pit mine produced a hydrologic cone of depression that has been recovering toward the pre-mining groundwater configuration since mining ended in 1994. Aqueous arsenic concentrations in the 80 m deep pit lake are up to 1000 ??g/L. Redistribution of the arsenic occurs during summer stratification, with highest concentrations at middle depths. The total mass of arsenic in the pit lake increases coinciding with early winter rains that erode, partially dissolve, and transport arsenic-bearing salts into the pit lake. Arsenic concentration, speciation, and distribution in the Sierra Nevada foothills depend on many factors, including the lithologic sources of arsenic, climatic influences on weathering of host minerals, and geochemical characteristics of waters with which source and secondary minerals react. Oxidation of arsenian pyrite to goethite, jarosite, and copiapite causes temporary attenuation of arsenic during summer, when these secondary minerals accumulate; subsequent rapid dissemination of arsenic into the aqueous environment is caused by annual winter storms. As the population of the Mother Lode area grows, it is increasingly important to consider these effects during planning and development of land and groundwater resources.

Visible and Near-Infrared Spectroscopy of Hephaestus Fossae Cratered Cones, Mars

NASA Astrophysics Data System (ADS)

Dapremont, A.; Wray, J. J.

2017-12-01

Hephaestus Fossae are a system of sub-parallel fractures on Mars (> 500 km long) interpreted as near-surface tensional cracks [1]. Images of the Martian surface from the High Resolution Imaging Science Experiment have revealed cratered cones within the Hephaestus Fossae region. A volcanic origin (cinder/tuff cones) has been proposed for these features based on morphometric measurements and fine-scale surface characteristics [2]. In an effort to further constrain the origin of these cones as the products of igneous or sedimentary volcanism, we use data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM). We take advantage of CRISM's S (0.4 - 1.0 microns) and L (1.0 - 3.9 microns) detector wavelength ranges to investigate the presence or absence of spectral signatures consistent with previous identifications of igneous and mud volcanism products on Mars [3,4]. Hephaestus Fossae cratered cone rims exhibit a consistent nanophase ferric oxide signature. We also identify ferrous phases and 3-micron absorptions (attributed to fundamental vibrational stretch frequencies in H2O) on the crater rims of several cones. Mafic signatures on cratered cone rims support an igneous provenance for these features. The 3-micron absorptions are consistent with the presence of structurally bound or adsorbed water. Our CRISM observations are similar to those of small edifice features in Chryse Planitia, which were interpreted as mud volcanism products based on their enrichment of nanophase ferric minerals and 3-micron absorptions on summit crater rims [3]. Hydrothermal activity was invoked for a Coprates Chasma pitted cone (scoria/tuff cone) based on CRISM identification of partially dehydrated opaline silica, which we do not observe in Hephaestus Fossae [4]. Our spectral observations are more consistent with mud volcanism, but we do not definitively rule out an igneous volcanic origin for the cones in our study region. We demonstrate that VNIR spectroscopy is a valuable tool in developing criteria to determine the origin (igneous/sedimentary/periglacial) of cone features on Mars. [1] Skinner and Tanaka (2007) Icarus 186: 41-59. [2] Dundas et al (2007) LPSC XXXVIII Abs #2116. [3] Komatsu et al (2016) Icarus 268: 56-75. [4] Brož et al (2017) Earth and Planetary Sci Letters 473: 122-130.

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies.

PubMed

Feigl, Viktória; Ujaczki, Éva; Vaszita, Emese; Molnár, Mónika

2017-10-01

Red mud can be applied as soil ameliorant to acidic, sandy and micronutrient deficient soils. There are still knowledge gaps regarding the effects of red mud on the soil microbial community. The Biolog EcoPlate technique is a promising tool for community level physiological profiling. This study presents a detailed evaluation of Biolog EcoPlate data from two case studies. In experiment "A" red mud from Ajka (Hungary) was mixed into acidic sandy soil in soil microcosms at 5-50 w/w%. In experiement "B" red mud soil mixture was mixed into low quality subsoil in a field experiment at 5-50 w/w%. According to average well color development, substrate average well color development and substrate richness 5-20% red mud increased the microbial activity of the acidic sandy soil over the short term, but the effect did not last for 10months. Shannon diversity index showed that red mud at up to 20% did not change microbial diversity over the short term, but the diversity decreased by the 10th month. 30-50% red mud had deteriorating effect on the soil microflora. 5-20% red mud soil mixture in the low quality subsoil had a long lasting enhancing effect on the microbial community based on all Biolog EcoPlate parameters. However, 50% red mud soil mixture caused a decrease in diversity and substrate richness. With the Biolog EcoPlate we were able to monitor the changes of the microbial community in red mud affected soils and to assess the amount of red mud and red mud soil mixture applicable for soil treatment in these cases. Copyright © 2017 Elsevier B.V. All rights reserved.

Hidden values in bauxite residue (red mud): recovery of metals.

PubMed

Liu, Yanju; Naidu, Ravi

2014-12-01

Bauxite residue (red mud) is a hazardous waste generated from alumina refining industries. Unless managed properly, red mud poses significant risks to the local environment due to its extreme alkalinity and its potential impacts on surface and ground water quality. The ever-increasing generation of red mud poses significant challenges to the aluminium industries from management perspectives given the low proportion that are currently being utilized beneficially. Red mud, in most cases, contains elevated concentrations of iron in addition to aluminium, titanium, sodium and valuable rare earth elements. Given the scarcity of iron supply globally, the iron content of red mud has attracted increasing research interest. This paper presents a critical overview of the current techniques employed for iron recovery from red mud. Information on the recovery of other valuable metals is also reviewed to provide an insight into the full potential usage of red mud as an economic resource rather than a waste. Traditional hydrometallurgy and pyrometallurgy are being investigated continuously. However, in this review several new techniques are introduced that consider the process of iron recovery from red mud. An integrated process which can achieve multiple additional values from red mud is much preferred over the single process methods. The information provided here should help to improve the future management and utilization of red mud. Copyright © 2014 Elsevier Ltd. All rights reserved.

Experimental Study on Application of Boron Mud Secondary Resource to Oxidized Pellets Production

NASA Astrophysics Data System (ADS)

Fu, Xiao-Jiao; Chu, Man-Sheng; Zhao, Jia-Qi; Chen, Shuang-Yin; Liu, Zheng-Gen; Wang, Si-Yuan

2017-07-01

In order to realize comprehensive and massive treatment of boron mud secondary resource, fundamental study on boron mud applied to oxidized pellets production as additive was carried out in the paper under laboratory conditions. The effects of boron mud on the performance of oxidized pellets were investigated systemically, and boron mud was combined with other boron-rich material innovatively. The results showed that, within certain limits, boron mud can improve properties of oxidized pellets. The bentonite content decreased to 0.3 % when adding 1.0 % boron mud additive and the pellets met blast furnace requirements. With the combination additive content 0.8 %, bentonite content can be further decreased to 0.2 %, and the pellets properties were better than base pellet. Therefore, it was an effective way to reduce environmental pollution and optimize blast furnace operation by developing boron mud secondary resource as pellets additive.

Acoustical Properties of Mud Sediments

DTIC Science & Technology

2015-09-30

Acoustical Properties of Mud Sediments Allan D. Pierce Boston University 399 Quaker Meeting House Road P. O. Box 339 East Sandwich, MA 03537...shallow-ocean mud sediments. Other goals are to assess prior data relating to the acoustic properties of mud and to provide guidance in the...development and interpretation of experiments. A related goal is to construct models that will guide inversion techniques for inferring properties of mud

Warts phosphorylates Mud to promote Pins-mediated mitotic spindle orientation in Drosophila independent of Yorkie

PubMed Central

Dewey, Evan B.; Sanchez, Desiree; Johnston, Christopher A.

2015-01-01

SUMMARY Multicellular animals have evolved conserved signaling pathways that translate cell polarity cues into mitotic spindle positioning to control the orientation of cell division within complex tissue structures. These oriented cell divisions are essential for the development of cell diversity and the maintenance of tissue homeostasis. Despite intense efforts, the molecular mechanisms that control spindle orientation remain incompletely defined. Here we describe a role for the Hippo (Hpo) kinase complex in promoting Partner of Inscuteable (Pins)-mediated spindle orientation. Knockdown of Hpo, Salvador (Sav), or Warts (Wts) each result in a partial loss of spindle orientation, a phenotype previously described following loss of the Pins-binding protein Mushroom body defect (Mud). Similar to orthologs spanning yeast to mammals, Wts kinase localizes to mitotic spindle poles, a prominent site of Mud localization. Wts directly phosphorylates Mud in vitro within its C-terminal coiled-coil domain. This Mud coiled-coil domain directly binds the adjacent Pins-binding domain to dampen the Pins/Mud interaction, and Wts-mediated phosphorylation uncouples this intramolecular Mud interaction. Loss of Wts prevents cortical Pins/Mud association without affecting Mud accumulation at spindle poles, suggesting phosphorylation acts as a molecular switch to specifically activate cortical Mud function. Finally, loss of Wts in Drosophila imaginal disc epithelial cells results in diminished cortical Mud and defective planar spindle orientation. Our results provide new insights into the molecular basis for dynamic regulation of the cortical Pins/Mud spindle positioning complex and highlight a novel link with an essential, evolutionarily-conserved cell proliferation pathway. PMID:26592339

Warts phosphorylates mud to promote pins-mediated mitotic spindle orientation in Drosophila, independent of Yorkie.

PubMed

Dewey, Evan B; Sanchez, Desiree; Johnston, Christopher A

2015-11-02

Multicellular animals have evolved conserved signaling pathways that translate cell polarity cues into mitotic spindle positioning to control the orientation of cell division within complex tissue structures. These oriented cell divisions are essential for the development of cell diversity and the maintenance of tissue homeostasis. Despite intense efforts, the molecular mechanisms that control spindle orientation remain incompletely defined. Here, we describe a role for the Hippo (Hpo) kinase complex in promoting Partner of Inscuteable (Pins)-mediated spindle orientation. Knockdown of Hpo, Salvador (Sav), or Warts (Wts) each result in a partial loss of spindle orientation, a phenotype previously described following loss of the Pins-binding protein Mushroom body defect (Mud). Similar to orthologs spanning yeast to mammals, Wts kinase localizes to mitotic spindle poles, a prominent site of Mud localization. Wts directly phosphorylates Mud in vitro within its C-terminal coiled-coil domain. This Mud coiled-coil domain directly binds the adjacent Pins-binding domain to dampen the Pins/Mud interaction, and Wts-mediated phosphorylation uncouples this intramolecular Mud interaction. Loss of Wts prevents cortical Pins/Mud association without affecting Mud accumulation at spindle poles, suggesting phosphorylation acts as a molecular switch to specifically activate cortical Mud function. Finally, loss of Wts in Drosophila imaginal disc epithelial cells results in diminished cortical Mud and defective planar spindle orientation. Our results provide new insights into the molecular basis for dynamic regulation of the cortical Pins/Mud spindle positioning complex and highlight a novel link with an essential, evolutionarily conserved cell proliferation pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Onset of Channelling in a Fluidized Mud Layer

NASA Astrophysics Data System (ADS)

Papanicolaou, T.; Tsakiris, A. G.; Billing, B. M.

2012-12-01

Fluidization of a soil occurs when the drag force exerted on the soil grains by upwelling water equals the submerged weight of the soil grains, hence reducing the effective (or contact) stress between the soil grains to zero. In nature, fluidization is commonly encountered in localized portions of highly saturated mud layers found in tidal flats, estuaries and lakes, where upward flow is initiated by significant pore water pressure gradients triggered by wave or tidal action. The water propagates through the fluidized mud layer by forming channels (or vents), carrying the fluidized mud to the surface and forming mud volcano structures. The presence of these fluidization channels alters the mud layer structure with implications on its hydraulic and geotechnical properties, such as the hydraulic conductivity. Despite the importance of these channels, the conditions that lead to their formation and their effects on the mud layer structure still remain poorly documented. The present study couples experimental and theoretical methods aimed at quantifying the conditions, under which fluidization of a saturated mud layer is accompanied by the formation of channels, and assessing the effects of channeling on the mud layer structure. Fluidization and channel formation in a mud layer were reproduced in the laboratory using a carefully designed fluidization column attached to a pressurized vessel (plenum). To eliminate any effects of the material, the mud was produced from pure kaolin clay and deionized water. Local porosity measurements along the mud layer prior, during and after fluidization were conducted using an Americium-241 gamma source placed on a fully automated carriage. Different water inflow rates, q, were applied to the base of the mud layer and the plenum pressure was monitored throughout the experiment. These experiments revealed that for high q values, a single vertical channel formed and erupted at the center of the fluidization column. Instead for low q values, the experiments suggested that a channel network formed within the mud layer leading to the eruption of multiple channels on the mud layer surface. The gamma source measurements captured quantitatively the porosity increase as the channel formed. The experiments were complemented with a theoretical analysis using the two-phase, flow mass and momentum governing equations. This analysis aims to establish a relation between the applied pressure, the fluid velocity and the local porosity of mud during the formation of the channels.

Acute and physical effects of water-based drilling mud in the marine copepod Calanus finmarchicus.

PubMed

Farkas, Julia; Yvonne Bådsvik, Camilla; Altin, Dag; Nordtug, Trond; Olsen, Anders Johny; Hansen, Bjørn Henrik

2017-01-01

The aim of this study was to investigate impacts of fine particulate fraction of a commonly used barite-containing drilling mud on the pelagic filter feeding copepod Calanus finmarchicus. The results show that the tested drilling mud had a low acute toxicity on C. finmarchicus (LC50 > 320 mg/L) and that the observed toxicity was likely caused by dissolved constituents in the mud and not the particle phase containing the weighting agent barite. Further, animals were exposed to drilling mud at a concentration of 10 mg/L for 168 hr followed by a 100 hr recovery phase. A rapid uptake of drilling mud particles was observed, while the excretion was slow and incomplete even after 100 hr recovery in clean seawater. The uptake of drilling mud particles caused a significant increase in sinking velocity of copepods, indicating that uptake of drilling mud particles affected their buoyancy. Long-term exposure to low concentrations of drilling mud could therefore cause physical effects such as impacts on the animal's buoyancy which may affect the energy budget of the copepods.

Comparison of Copper Scavenging Capacity between Two Different Red Mud Types

PubMed Central

Ma, Yingqun; Si, Chunhua; Lin, Chuxia

2012-01-01

A batch experiment was conducted to compare the Cu scavenging capacity between two different red mud types: the first one was a highly basic red mud derived from a combined sintering and Bayer process, and the second one was a seawater-neutralized red mud derived from the Bayer process. The first red mud contained substantial amounts of CaCO3, which, in combination with the high OH− activity, favored the immobilization of water-borne Cu through massive formation of atacamite. In comparison, the seawater-neutralized red mud had a lower pH and was dominated by boehmite, which was likely to play a significant role in Cu adsorption. Overall, it appears that Cu was more tightly retained by the CaCO3-dominated red mud than the boehmite-dominated red mud. It is concluded that the heterogeneity of red mud has marked influences on its capacity to immobilize water-borne Cu and maintain the long-term stability of the immobilized Cu species. The research findings obtained from this study have implications for the development of Cu immobilization technology by using appropriate waste materials generated from the aluminium industry.

The effects of drilling muds on marine invertebrate larvae and adults

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

Raimondi, P.T.; Barnett, A.M.; Krause, P.R.

1997-06-01

A series of laboratory experiments tested the effects of drilling muds from an active platform off southern California on larvae and adults of marine invertebrates. Red abalone (Haliotis rufescens) were used to determine effects of drilling muds on fertilization, early development, survivorship, and settlement, and experiments on adult brown cup corals (Paracyathus stearnsii) tested effects on adult survivorship, viability, and tissue loss. Exposures to drilling muds did not have an effect on abalone fertilization or early development. However, several exposures to drilling muds resulted in weak, but significant, positive effects of drilling muds on settlement of competent larvae. In contrast,more » settlement of red abalone larvae on natural coralline algal crusts decreased with increasing concentrations of drilling muds. This suggests that drilling muds affect either the abalone`s ability to detect natural settlement inducers, or they affect the inducer itself. Exposure of brown cup corals to concentrations of drilling muds adversely impacted their survivorship and viability. These effects were likely caused by increased tissue mortality of the coral polyps.« less

Numerical investigation of fluid mud motion using a three-dimensional hydrodynamic and two-dimensional fluid mud coupling model

NASA Astrophysics Data System (ADS)

Yang, Xiaochen; Zhang, Qinghe; Hao, Linnan

2015-03-01

A water-fluid mud coupling model is developed based on the unstructured grid finite volume coastal ocean model (FVCOM) to investigate the fluid mud motion. The hydrodynamics and sediment transport of the overlying water column are solved using the original three-dimensional ocean model. A horizontal two-dimensional fluid mud model is integrated into the FVCOM model to simulate the underlying fluid mud flow. The fluid mud interacts with the water column through the sediment flux, current, and shear stress. The friction factor between the fluid mud and the bed, which is traditionally determined empirically, is derived with the assumption that the vertical distribution of shear stress below the yield surface of fluid mud is identical to that of uniform laminar flow of Newtonian fluid in the open channel. The model is validated by experimental data and reasonable agreement is found. Compared with numerical cases with fixed friction factors, the results simulated with the derived friction factor exhibit the best agreement with the experiment, which demonstrates the necessity of the derivation of the friction factor.

The diversity of mud volcanoes in the landscape of Azerbaijan

NASA Astrophysics Data System (ADS)

Rashidov, Tofig

2014-05-01

As the natural phenomenon the mud volcanism (mud volcanoes) of Azerbaijan are known from the ancient times. The historical records describing them are since V century. More detail study of this natural phenomenon had started in the second half of XIX century. The term "mud volcano" (or "mud hill") had been given by academician H.W. Abich (1863), more exactly defining this natural phenomenon. All the previous definitions did not give such clear and capacious explanation of it. In comparison with magmatic volcanoes, globally the mud ones are restricted in distribution; they mainly locate within the Alpine-Himalayan, Pacific and Central Asian mobile belts, in more than 30 countries (Columbia, Trinidad Island, Italy, Romania, Ukraine, Georgia, Azerbaijan, Turkmenistan, Iran, Pakistan, Indonesia, Burma, Malaysia, etc.). Besides it, the zones of mud volcanoes development are corresponded to zones of marine accretionary prisms' development. For example, the South-Caspian depression, Barbados Island, Cascadia (N.America), Costa-Rica, Panama, Japan trench. Onshore it is Indonesia, Japan, and Trinidad, Taiwan. The mud volcanism with non-accretionary conditions includes the areas of Black Sea, Alboran Sea, the Gulf of Mexico (Louisiana coast), Salton Sea. But new investigations reveal more new mud volcanoes and in places which were not considered earlier as the traditional places of mud volcanoes development (e.g. West Nile Rive delta). Azerbaijan is the classic region of mud volcanoes development. From over 800 world mud volcanoes there are about 400 onshore and within the South-Caspian basin, which includes the territory of East Azerbaijan (the regions of Shemakha-Gobustan and Low-Kura River, Absheron peninsula), adjacent water area of South Caspian (Baku and Absheron archipelagoes) and SW Turkmenistan and represents an area of great downwarping with thick (over 25 km) sedimentary series. Generally, in the modern relief the mud volcanoes represent more or less large uplifts on surface, often of plane-conical shape, rising for 5 to 400 m and more over the country (for example, mud volcano Toragay, 400 m height). The base diameter is from 100 m to 3-4 km and more. Like the magmatic ones, the mud volcanoes are crowned with crater of convex-plane or deeply-seated shape. In Azerbaijan there are all types of mud volcanoes: active, extinct, buried, submarine, island, abundantly oil seeping. According to their morphology they are defined into cone-shaped, dome-shaped, ridge-shaped, plateau-shaped. The crater shapes are also various: conical, convex-plane, shield-shaped, deeply-seated, caldera-like. The most complete morphological classification was given in "Atlas of mud volcanoes of Azerbaijan" (Yakubov et al., 1971). Recently (Aliyev Ad. et al., 2003) it was proposed a quite new morphological classification of mud volcanoes of Azerbaijan. For the first time the mud volcanic manifestations had been defined. Volcanoes are ranged according to morphological signs, crater shape and type of activity.

Feasibility of Using Dredged Mud for Prepared the Permeable Brick

NASA Astrophysics Data System (ADS)

Zhou, Chaoqun; Cheng, Xiaosu; Zeng, Lingke; Wang, Hui; Chen, Jing

2017-10-01

Through experimental analysis found that the chemical composition of the dredged mud is similar to clay and the dredged mud does not leach heavy metals. Using the dredged mud in the preparation of permeable bricks reduced the quantity of incineration dredged mud buried in landfills, and the exploitation and consumption of natural sandstone. The dredged mud needs to be checked by the validation criteria when the second use, so we used the TCLP test to identify hazardous materials. Its leaching of heavy metals was in line with industry standard. And the basic formula of permeable brick were prepared, its performance was in line with national standards. The use of dredged mud preparing eco-friendly permeable bricks, not only solves the problem of environmental pollution, but also gets some economic and social profit.

Paraformaldehyde-Resistant Starch-Fermenting Bacteria in “Starch-Base” Drilling Mud

PubMed Central

Myers, G. E.

1962-01-01

Starch-fermenting bacteria were found in each of 12 samples of nonfermenting starch-base drilling mud examined. Of the 12 samples, 3 contained very active starch-fermenting gram-positive spore-bearing bacilli closely resembling Bacillus subtilis. Similar active starch-fermenting bacteria were found in fermenting starch-base drilling mud and in corn starch and slough water used to prepare such mud. The active starch-fermenting microorganisms completely hydrolyzed 1% (w/v) corn starch within 24 hr at 37.5 C. The active starch-fermenting bacteria isolated from fermenting drilling mud were capable of surviving 12 hr of continuous exposure to 0.1% (w/w) paraformaldehyde or 1 hr of continuous exposure to 0.5% (w/w) paraformaldehyde, with no diminution in starch-fermenting ability. The same organisms fermented starch after 3 hr of continuous exposure to 0.5% (w/w) paraformaldehyde, but not after 4 hr of exposure. The phenomenon of rapid disappearance of paraformaldehyde from fermenting drilling mud was observed in the laboratory using a modified sodium sulfite test. Paraformaldehyde, initially present in a concentration of 0.192 lb per barrel of mud, completely disappeared in 9 hr at 22 to 23 C. A significant decrease in paraformaldehyde concentration was detected 0.5 hr after preparation of the mud. It is suggested that the presence of relatively high concentrations of ammonia and chloride in the mud may facilitate the disappearance of paraformaldehyde. The failure of 0.1% (w/w) paraformaldehyde to inhibit the strong starch-fermenting microorganisms isolated from fermenting drilling mud, and the rapid disappearance of paraformaldehyde from the mud, explains the fermentation of starch which occurred in this mud, despite the addition of paraformaldehyde. PMID:13936949

Clostridium botulinum in Scottish fish farms and farmed trout.

PubMed

Burns, G F; Williams, H

1975-02-01

Rainbow trout and specimens of pond mud were collected from three fish farms and examined for the presence of Clostridium botulinum. Two of the farms were constructed with concrete channels and one was mud-bottomed. Cl. botulinum was isolated only from the mud-bottomed farm (24% of muds), and the isolates were all non-proteolytic type B. The implications of the presence of Cl. botulinum spores in the mud of fish farms is discussed.

Biogeochemical interactions among the arsenic, iron, humic substances, and microbes in mud volcanoes in southern Taiwan.

PubMed

Liu, Chia-Chuan; Maity, Jyoti Prakash; Jean, Jiin-Shuh; Sracek, Ondra; Kar, Sandeep; Li, Zhaohui; Bundschuh, Jochen; Chen, Chien-Yen; Lu, Hsueh-Yu

2011-01-01

Fluid and mud samples collected from Hsiaokunshui (HKS), Wushanting (WST), Yenshuikeng (YSK), Kunshuiping (KSP), Liyushan (LYS), and Sinyangnyuhu (SYNH) mud volcanoes of southwestern Taiwan were characterized for major ions, humic substances (HS) and trace elements concentrations. The relationship between the release of arsenic (As) and activities of sulfate-reducing bacteria has been assessed to understand relevant geochemical processes in the mud volcanoes. Arsenic (0.02-0.06 mg/L) and humic substances (4.13 × 10(-4) to 1.64 × 10(-3) mM) in the fluids of mud volcanoes showed a positive correlation (r = 0.99, p < 0.05) except in Liyushan mud volcano. Arsenic and iron in mud sediments formed two separate groups i) high As, but low Fe in HKS, WST, and SYNH; and ii) low As, but high Fe in the YSK, KSP, and LYS mud volcanoes. The Eh(S.H.E.) values of the mud volcano liquids were characterized by mild to strongly reducing conditions. The HKS, SYNH, and WST mud volcanoes (near the Chishan Fault) belongs to strong reducing environment (-33 to -116 mV), whereas the LYS, YSK, and KSP mud volcanoes located near the coastal plain are under mild reducing environment (-11 to 172 mV). At low Eh values mud volcanoes, saturation index (SI) values of poorly crystalline phases such as amorphous ferric hydroxide indicate understaturation, whereas saturation is reached in relatively high Eh(S.H.E.) values mud volcanoes. Arsenic contents in sediments are low, presumably due to its release to fluids (As/Fe ratio in YSK, KSP, and LYS sediment: 4.86 × 10(-4)-6.20 × 10(-4)). At low Eh(S.H.E.) values (mild to strong reducing environment), arsenic may co-precipitate with sulfides as a consequence of sulfate reduction (As/Fe ratios in WST, HKS, and SYNH sediments: 0.42-0.69).

Valorisation of waste ilmenite mud in the manufacture of sulphur polymer cement.

PubMed

Contreras, Manuel; Gázquez, Manuel Jesús; García-Díaz, Irene; Alguacil, Francisco J; López, Félix A; Bolívar, Juan Pedro

2013-10-15

This paper reports the preparation of sulphur polymer cements (SPCs) incorporating waste ilmenite mud for use in concrete construction works. The ilmenite mud raw material and the mud-containing SPCs (IMC-SPCs) were characterised physico-chemically and radiologically. The optimal IMC-SPC mixture had a sulphur/mud ratio (w/w) of 1.05 (mud dose 20 wt%); this cement showed the greatest compressive strength (64 MPa) and the lowest water absorption coefficient (0.4 g cm(-2) at 28 days). Since ilmenite mud is enriched in natural radionuclides, such as radium isotopes (2.0·10(3) Bq kg(-1)(228)Ra and 5.0·10(2) Bq kg(-1)(226)Ra), the IMC-SPCs were subjected to leaching experiments, which showed their environmental impact to be negligible. The activity concentration indices for the different radionuclides in the IMC-SPCs containing 10% and 20% ilmenite mud met the demands of international standards for materials used in the construction of non-residential buildings. Copyright © 2013 Elsevier Ltd. All rights reserved.

Suspended sediment concentration in the Lower Sea Scheldt (Belgium): long term trends and relation to mud disposal

NASA Astrophysics Data System (ADS)

Depreiter, Davy; van Holland, Gijsbert; Lanckriet, Thijs; Beirinckx, Kirsten; Vanlede, Joris; Maris, Tom

2015-04-01

In this presentation, results from different monitoring and research projects (OMES, MONEOS, Flexible Disposal and Marine-Fluvial mud ratio) will be integrated to increase the insight in the trends and relation between mud disposal and the increasing sediment concentrations (SSC) in the Lower Sea Scheldt. In the Scheldt Estuary, major projects have been carried out in the past decade, among which the third deepening of the navigation channel and the opening of the Deurganck dock. Maintenance dredging is carried out to guarantee a minimum navigation depth. A rising trend in the volume of mud dredged in the Lower Sea Scheldt is observed since 2006, the year after the opening of the Deurganck Dock. The trend is explained by increasing mud volumes dredged in this dock and on a nearby sill. This volume culminated in 2011 (4.8 million m³) when the depth of this dock was increased to its design depth. The dredged mud is disposed upstream, quickly to be resuspended. Near the mud disposal location, yearly averaged SSC (measured at 4.5 m above bed) tripled between 2005 and 2011 (108 to 348 mg/L), and SSC peaks increased even stronger. A multivariate regression model indicated a strong correlation between mud disposal volumes and timing and observed SSC. Mud disposal volumes and SSC where somewhat lower again after 2011. The SSC increase raises an alert with regard to the risk for a regime shift towards a hyperturbid system. Increasing SSC may indeed decrease the hydraulic resistance initiating a feedback mechanism that results in further increasing SSC values. It thus appears that more mud is being circulated: the Deurganck dock acts as mud sink, from which the mud is - after dredging and disposal - resuspended. The mud may have different sources: fluvial or marine influx. The increasing SSC might not only be related to the mud disposal, but also to changing tidal characteristics that enhance the influx of marine suspended sediments. To elucidate this, an analysis of the marine fraction in soil and suspended sediments has also been performed.

[Observation on eggs of Oncomelania hupensis hupensis with scanning electron microscope].

PubMed

Xia, Q B; Yuan, Y B; Liu, B; Tan, P P

2001-01-01

To observe the structure of the mud hull packed Oncomelania eggs and the surface structure of colloid membrane called the third grade membrane of eggs. Scanning electron microscopy was used to observe Oncomelania snail eggs with integral mud hull collected from eastern Dongting Lake. The mud hull of eggs was made of unshapen small humification combined with earth granules with a diameter of 2.6-9.2 microns. The mud hull in 60 um thickness was honeycomb-like in shape with many small holes and small folds on the wall. There were many round or irregularly round hollownesses on the inner layer of mud hull that contacts colloid membrane but no hole through mud hull. There were some protein fiber networks covering on the colloid membrane and apophysis. The structure of the mud hull showed that the exchange of matter was maintained between eggs and outside, and the mud hull is of great importance to regulating temperature and moisture for the growth of eggs by preventing hydrosoluble substances from penetrating into eggs. The protein fiber networks act on gluing mud hull and buffering outside power. The dense glue membrane might be a main barricade to prevent pharmaceutical molecules from penetrating into eggs.

Effect of graft source on unrelated donor hemopoietic stem cell transplantation in adults with acute myeloid leukemia after reduced-intensity or nonmyeloablative conditioning: a study from the Société Francaise de Greffe de Moelle et de Thérapie Cellulaire.

PubMed

Malard, Florent; Milpied, Noel; Blaise, Didier; Chevallier, Patrice; Michallet, Mauricette; Lioure, Bruno; Clément, Laurence; Hicheri, Yosr; Cordonnier, Catherine; Huynh, Anne; Yakoub-Agha, Ibrahim; Peffault de Latour, Regis; Mohty, Mohamad

2015-06-01

This retrospective report compared the 4-year outcomes of allogeneic stem cell transplantation (allo-SCT) in 651 adult patients with acute myeloid leukemia receiving a reduced-intensity (RIC) or nonmyeloablative conditioning (NMA) regimen according to the type of unrelated donors. These were either umbilical cord blood (UCB, n = 205), a 9/10 mismatched unrelated donor (MisMUD, n = 99), or a 10/10 matched unrelated donor (MUD, n = 347) graft. Neutrophil recovery was slower in UCB (74.5% by day 42) compared with MisMUD (94.8%) and MUD (95.6%) (P < .001). There was no significant difference in nonrelapse mortality between UCB and both MUD (hazard ratio [HR], 1.05; 95% confidence interval [CI], .62 to 1.78; P = .85) and MisMUD (HR, 1.58; 95% CI, .88 to 2.83; P = .13) The relapse/progression was similar between UCB and MisMUD (HR, .62; 95% CI, .37 to 1.03; P = .07), but was significantly lower in MUD compared with UCB (HR, .60; 95% CI, .39 to .92; P = .02). The rate of extensive chronic graft-versus-host disease (GVHD) was similar between UCB and both MUD (HR, 2.15; 95% CI, .93 to 4.97; P = .08) and MisMUD (HR, 1.84; 95% CI, .68 to 4.95; P = .23). The rate of severe grade III and IV acute GVHD was significantly increased in MisMUD compared with UCB (HR, 2.61; 95% CI, 1.30 to 5.23; P = .007). There was no significant difference in overall survival between UCB and both MisMUD (HR, .98; 95% CI, .66 to 1.45; P = .92) and MUD (HR, .74; 95% CI, .52 to 1.03; P = .08). These data suggest that in the setting of RIC/NMA, allo-SCT UCB is a valid alternative graft source, with significantly less chronic GVHD, compared with MisMUD, when there is no MUD available or when urgent transplantation is needed. Copyright © 2015 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

An outbreak of mud-wrestling-induced pustular dermatitis in college students. Dermatitis palaestrae limosae.

PubMed

Adler, A I; Altman, J

1993-01-27

To investigate an outbreak of gram-negative folliculitis in relation to a common exposure, mud wrestling, and identify risk factors for dermatitis among those who mud wrestled. Case-control study. University of Washington, Seattle. Two college-residence groups of students. Cultures from affected students and from mud similar to that used for wrestling yielded Enterobacteriaceae. The odds ratio associated with mud wrestling was 79.5 (95% confidence interval, 13.9 to 895.4). Increased time spent wrestling was associated with increased risk. Skin trauma during wrestling or immersion in the mud increased the risk of infection (odds ratio, 23.1; 95% confidence interval, 1.7 to 1440.4). Mud wrestling is one cause of pustular follicular dermatitis. Trauma to the skin may be a necessary cofactor for the development of infection.

40 CFR 230.42 - Mud flats.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Mud flats. 230.42 Section 230.42 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING SECTION 404(b)(1... Aquatic Sites § 230.42 Mud flats. (a) Mud flats are broad flat areas along the sea coast and in coastal...

40 CFR 230.42 - Mud flats.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Mud flats. 230.42 Section 230.42 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING SECTION 404(b)(1... Aquatic Sites § 230.42 Mud flats. (a) Mud flats are broad flat areas along the sea coast and in coastal...

40 CFR 230.42 - Mud flats.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Mud flats. 230.42 Section 230.42 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING SECTION 404(b)(1... Aquatic Sites § 230.42 Mud flats. (a) Mud flats are broad flat areas along the sea coast and in coastal...

40 CFR 230.42 - Mud flats.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Mud flats. 230.42 Section 230.42 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING SECTION 404(b)(1... Aquatic Sites § 230.42 Mud flats. (a) Mud flats are broad flat areas along the sea coast and in coastal...

40 CFR 230.42 - Mud flats.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Mud flats. 230.42 Section 230.42 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) OCEAN DUMPING SECTION 404(b)(1... Aquatic Sites § 230.42 Mud flats. (a) Mud flats are broad flat areas along the sea coast and in coastal...

30 CFR 250.1614 - Mud program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Mud program. 250.1614 Section 250.1614 Mineral... OPERATIONS IN THE OUTER CONTINENTAL SHELF Sulphur Operations § 250.1614 Mud program. (a) The quantities, characteristics, use, and testing of drilling mud and the related drilling procedures shall be designed and...

MUD for Learning: Classification and Instruction

ERIC Educational Resources Information Center

Hsieh, Chung-Hsiang; Sun, Chuen-Tsai

2006-01-01

From a constructivist point of view, the importance of MUDs (Multiple User Dungeons) in education is justified based on their community-forming, learning, and role-playing functions. The authors propose a typology for educational MUDs and discuss their individual instructional approaches in order to measure MUD potential in ten-os of…

Toxicity of used drilling fluids to mysids (Mysidopsis bahia)

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

Gaetz, C.T.; Montgomery, R.; Duke, T.W.

1986-01-01

Static, acute toxicity tests were conducted with mysids (Mysidopsis bahia) and 11 used drilling fluids (also called drilling muds) obtained from active drilling platforms in the Gulf of Mexico, U.S.A. Each whole mud was tested, along with three phases of each mud: a liquid phase with all particulate materials removed; a suspended particulate phase composed of soluble and lighter particulate fractions; and a solid phase composed mainly of drill cuttings and rapidly settling particulates. These muds represented seven of the eight generic mud types described by the U.S. Environmental Protection Agency for use on the U.S. Outer Continental Shelf. Themore » toxicity of the 11 muds tested was apparently enhanced by the presence of aromatics. Furthermore, one mud tested repeatedly showed loss of toxicity with time, possibly from volatilization of aromatic fractions. The data demonstrated that aromatics in the drilling fluids affected their toxicity to M. bahia.« less

A study of iron mineral transformation to reduce red mud tailings.

PubMed

Li, L Y

2001-01-01

This study examines the effects of iron mineral transformation in an aluminum extraction process on the settling behavior, and the physical and chemical properties of the resulting red mud slurry that must be disposed of. By producing a red mud with a higher solid content, the total volume of mud slurry will also be reduced for a given alumina production rate and more caustic soda will be recovered. The settling behavior and the mineralogical, physical, and physico-chemical properties of one bauxite and three red muds processed under varying conditions were analyzed based on examination of the iron mineral transformations. The properties of red muds derived from the same bauxite can differ markedly due to variations in operating conditions of the Bayer process, such as temperature and the addition of a reducing agent. The settling of red mud can be improved by converting goethite into hematite and/or magnetite to produce a mud of larger particle size, smaller specific surface area, and larger specific gravity, characteristics which reduce the total volume of mud slurry to be disposed of and which allow for less potential contamination from caustic soda. This study also found that the by-product--Bayer sodalite--has the high exchange capacity for Na+ that might contribute to the long-term environmental problems.

Safety evaluation of traces of nickel and chrome in cosmetics: The case of Dead Sea mud.

PubMed

Ma'or, Ze'evi; Halicz, Ludwik; Portugal-Cohen, Meital; Russo, Matteo Zanotti; Robino, Federica; Vanhaecke, Tamara; Rogiers, Vera

2015-12-01

Metal impurities such as nickel and chrome are present in natural ingredients-containing cosmetic products. These traces are unavoidable due to the ubiquitous nature of these elements. Dead Sea mud is a popular natural ingredient of cosmetic products in which nickel and chrome residues are likely to occur. To analyze the potential systemic and local toxicity of Dead Sea mud taking into consideration Dead Sea muds' natural content of nickel and chrome. The following endpoints were evaluated: (Regulation No. 1223/20, 21/12/2009) systemic and (SCCS's Notes of Guidance) local toxicity of topical application of Dead Sea mud; health reports during the last five years of commercial marketing of Dead Sea mud. Following exposure to Dead Sea mud, MoS (margin of safety) calculations for nickel and chrome indicate no toxicological concern for systemic toxicity. Skin sensitization is also not to be expected by exposure of normal healthy skin to Dead Sea mud. Topical application, however, is not recommended for already nickel-or chrome-sensitized persons. As risk assessment of impurities present in cosmetics may be a difficult exercise, the case of Dead Sea mud is taken here as an example of a natural material that may contain traces of unavoidable metals. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Volume requirements for aerated mud drilling

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

Guo, B.; Rajtar, J.M.

1995-09-01

Aerated mud drilling has been recognized as having many advantages over conventional mud drilling, such ass higher penetration rate, less formation damage, minimized lost circulation, and lower drilling cost. In some areas, the use of aerated mud as a circulating medium for drilling oil and gas wells is becoming an attractive practice. Maintaining an optimum combination of liquid and air flow rates is important in aerated drilling operations. However, most drilling operators are unclear on what constitutes the ``optimum combination of the liquid and air flow rates.`` Guo et al. presented a mathematical approach to determining the flowing bottomhole pressuremore » (BHP) for aerated mud drilling. This paper addresses the use of Guo et al.`s mathematical model to determine liquid and air volume requirements considering wellbore stability, pipe sticking, and formation damage as well as the cuttings-carry capacity of the aerated mud. For a formation-damage-prevention point of view, the liquid fraction in the fluid stream should e as low as possible. However, a sufficient mud flow rate is always required to make the hole stable and to maintain the cuttings-carrying capacity of the aerated mud without injecting much air volume. This paper provides a simple approach to determining the liquid and air volume requirements for aerated mud drilling.« less

Mud extrusion and ring-fault gas seepage - upward branching fluid discharge at a deep-sea mud volcano.

PubMed

Loher, M; Pape, T; Marcon, Y; Römer, M; Wintersteller, P; Praeg, D; Torres, M; Sahling, H; Bohrmann, G

2018-04-19

Submarine mud volcanoes release sediments and gas-rich fluids at the seafloor via deeply-rooted plumbing systems that remain poorly understood. Here the functioning of Venere mud volcano, on the Calabrian accretionary prism in ~1,600 m water depth is investigated, based on multi-parameter hydroacoustic and visual seafloor data obtained using ship-borne methods, ROVs, and AUVs. Two seepage domains are recognized: mud breccia extrusion from a summit, and hydrocarbon venting from peripheral sites, hosting chemosynthetic ecosystems and authigenic carbonates indicative of long-term seepage. Pore fluids in freshly extruded mud breccia (up to 13 °C warmer than background sediments) contained methane concentrations exceeding saturation by 2.7 times and chloride concentrations up to five times lower than ambient seawater. Gas analyses indicate an underlying thermogenic hydrocarbon source with potential admixture of microbial methane during migration along ring faults to the peripheral sites. The gas and pore water analyses point to fluids sourced deep (>3 km) below Venere mud volcano. An upward-branching plumbing system is proposed to account for co-existing mud breccia extrusion and gas seepage via multiple surface vents that influence the distribution of seafloor ecosystems. This model of mud volcanism implies that methane-rich fluids may be released during prolonged phases of moderate activity.

Experiment study of mud to the moving process influent about viscous debris flow along slope

NASA Astrophysics Data System (ADS)

Jun, JiXian; Ying, Liang; Li, Pan Hua; Qiang, OuGuo

2018-01-01

Mud is the main component of viscous debris flow. The physical model experiments of viscous debris flow were carried out through the mixing mud with different density and fixed components of coarse particles. The width, longitudinal movement distance and motion velocity were recorded by video cameras during experiment. Through viscous debris flow physical model experiments, the influence of mud to transverse width, longitudinal movement distance and motion velocity was discussed. The physical model experiment results show that the motion forms change from inviscid particle flow to viscous debris flow and to the whole mass sliding with the increase of mud density; the width and the length along the slope decrease with mud density increasing; the movement process has classified phenomena about viscous debris flow composed by different mud densities: the velocity increases rapidly with time and the change gradient is steady when the density of mud is lower than 1.413g/cm3; the movement process can be divided into two stages when the density of mud is higher than 1.413g/cm3: the movement velocity is lower and the gradient change is small in the initial stage; but in the second stage, the movement velocity increases quickly, and the gradient is higher than the first stage, and with steady value.

Acoustic scattering from mud volcanoes and carbonate mounds.

PubMed

Holland, Charles W; Weber, Thomas C; Etiope, Giuseppe

2006-12-01

Submarine mud volcanoes occur in many parts of the world's oceans and form an aperture for gas and fluidized mud emission from within the earth's crust. Their characteristics are of considerable interest to the geology, geophysics, geochemistry, and underwater acoustics communities. For the latter, mud volcanoes are of interest in part because they pose a potential source of clutter for active sonar. Close-range (single-interaction) scattering measurements from a mud volcano in the Straits of Sicily show scattering 10-15 dB above the background. Three hypotheses were examined concerning the scattering mechanism: (1) gas entrained in sediment at/near mud volcano, (2) gas bubbles and/or particulates (emitted) in the water column, (3) the carbonate bio-construction covering the mud volcano edifice. The experimental evidence, including visual, acoustic, and nonacoustic sensors, rules out the second hypothesis (at least during the observation time) and suggests that, for this particular mud volcano the dominant mechanism is associated with carbonate chimneys on the mud volcano. In terms of scattering levels, target strengths of 4-14 dB were observed from 800 to 3600 Hz for a monostatic geometry with grazing angles of 3-5 degrees. Similar target strengths were measured for vertically bistatic paths with incident and scattered grazing angles of 3-5 degrees and 33-50 degrees, respectively.

Corrective Action Investigation Plan for Corrective Action Unit 560: Septic Systems, Nevada Test Site, Nevada with ROTC1, Revision 0

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

Grant Evenson

2008-05-01

Corrective Action Unit (CAU) 560 is located in Areas 3 and 6 of the Nevada Test Site, which is approximately 65 miles northwest of Las Vegas, Nevada. Corrective Action Unit 560 is comprised of the seven corrective action sites (CASs) listed below: • 03-51-01, Leach Pit • 06-04-02, Septic Tank • 06-05-03, Leach Pit • 06-05-04, Leach Bed • 06-59-03, Building CP-400 Septic System • 06-59-04, Office Trailer Complex Sewage Pond • 06-59-05, Control Point Septic System These sites are being investigated because existing information on the nature and extent of potential contamination is insufficient to evaluate and recommend correctivemore » action alternatives. Additional information will be obtained by conducting a corrective action investigation before evaluating corrective action alternatives and selecting the appropriate corrective action for each CAS. The results of the field investigation will support a defensible evaluation of viable corrective action alternatives that will be presented in the Corrective Action Decision Document. The sites will be investigated based on the data quality objectives (DQOs) developed on January 22, 2008, by representatives from the Nevada Division of Environmental Protection; U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office; Stoller-Navarro Joint Venture; and National Security Technologies, LLC. The DQO process was used to identify and define the type, amount, and quality of data needed to develop and evaluate appropriate corrective actions for CAU 560.« less

Utilization of red mud and Pb/Zn smelter waste for the synthesis of a red mud-based cementitious material.

PubMed

Li, Yuan-Cheng; Min, Xiao-Bo; Ke, Yong; Chai, Li-Yuan; Shi, Mei-Qing; Tang, Chong-Jian; Wang, Qing-Wei; Liang, Yan-Jie; Lei, Jie; Liu, De-Gang

2018-02-15

A new method in which Pb/Zn smelter waste containing arsenic and heavy metals (arsenic sludge), red mud and lime are utilized to prepare red mud-based cementitious material (RCM) is proposed in this study. XRD, SEM, FTIR and unconfined compressive strength (UCS) tests were employed to assess the physicochemical properties of RCM. In addition, ettringite and iron oxide-containing ettringite were used to study the hydration mechanism of RCM. The results show that the UCS of the RCM (red mud+arsenic sludge+lime) was higher than that of the binder (red mud+arsenic sludge). When the mass ratio of m (binder): m (lime) was 94:6 and then maintained 28days at ambient temperature, the UCS reached 12.05MPa. The red mud has potential cementitious characteristics, and the major source of those characteristics was the aluminium oxide. In the red mud-arsenic sludge-lime system, aluminium oxide was effectively activated by lime and gypsum to form complex hydration products. Some of the aluminium in ettringite was replaced by iron to form calcium sulfoferrite hydrate. The BCR and leaching toxicity results show that the leaching concentration was strongly dependent on the chemical speciation of arsenic and the hydration products. Therefore, the investigated red mud and arsenic sludge can be successfully utilized in cement composites to create a red mud-based cementitious material. Copyright © 2017 Elsevier B.V. All rights reserved.

Multi-Sensor Mud Detection

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.; Matthies, Larry H.

2010-01-01

Robust mud detection is a critical perception requirement for Unmanned Ground Vehicle (UGV) autonomous offroad navigation. A military UGV stuck in a mud body during a mission may have to be sacrificed or rescued, both of which are unattractive options. There are several characteristics of mud that may be detectable with appropriate UGV-mounted sensors. For example, mud only occurs on the ground surface, is cooler than surrounding dry soil during the daytime under nominal weather conditions, is generally darker than surrounding dry soil in visible imagery, and is highly polarized. However, none of these cues are definitive on their own. Dry soil also occurs on the ground surface, shadows, snow, ice, and water can also be cooler than surrounding dry soil, shadows are also darker than surrounding dry soil in visible imagery, and cars, water, and some vegetation are also highly polarized. Shadows, snow, ice, water, cars, and vegetation can all be disambiguated from mud by using a suite of sensors that span multiple bands in the electromagnetic spectrum. Because there are military operations when it is imperative for UGV's to operate without emitting strong, detectable electromagnetic signals, passive sensors are desirable. JPL has developed a daytime mud detection capability using multiple passive imaging sensors. Cues for mud from multiple passive imaging sensors are fused into a single mud detection image using a rule base, and the resultant mud detection is localized in a terrain map using range data generated from a stereo pair of color cameras.

Carbonate mud bodies in middle Mississippian strata of southern Indiana and northern Kentucky: End members of a middle Mississippian mud mound spectrum

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

Brown, M.A.; Dodd, J.R.

1990-06-01

Relatively small, lens-shaped carbonate mud bodies are common features in the Ramp Creek Formation and Harrodsburg Limestone (Mississippian) of southern Indiana and northern Kentucky. The outcrop dimensions of the lenses range from approximately 10 cm thick and 3 m wide to as much as 2 m thick and in excess of 100 m wide; their three-dimensional geometry is unknown. The lens cores consist of dolomitic mudstone that grades laterally and vertically into increasingly more fossiliferous wackestone to grainstone with fenestrate bryozoans and echinoderms being the dominant fossils. The great abundance of fenestrate bryozoan fragments surrounding the lenses suggests that lensmore » evolution was controlled by the trapping of carbonate mud by the baffling action of bryozoans. Wisps of organic material preserved in the lens cores may be remnants of some form of non-calcareous algae that also baffled and trapped carbonate mud. These mud lenses are end members of a spectrum of Mississippian carbonate mud bodies ranging in size from these small lenses to the classical Waulsortian mounds that may be hundreds of meters thick and a kilometer or more broad. All of these carbonate mud bodies may have in part formed by baffling and localizing of carbonate mud by organisms and in part by local production of carbonate mud. The major difference between large and small bodies is the water depth in which each formed. The Ramp Creek-Harrodsburg mud lenses may be miniature Waulsortian mounds that developed at or above fair-weather wave base on a relatively shallow carbonate platform rather than on shelf-to-basin slopes as proposed for the classical Waulsortian mounds.« less

Episodic Deep Fluid Expulsion at Mud Volcanoes in the Kumano Forearc Basin, SE Offshore Japan

NASA Astrophysics Data System (ADS)

Hammerschmidt, S.; Kopf, A.

2014-12-01

Compressional forces at convergent margins govern a variety of processes, most prominently earthquakes, landslides and mud volcanoes in the forearc. Although all seem related to fluid pressure changes, mud volcanoes are not only characterized by expulsion of fluids, but also fluidized mud and clasts that got ripped-up during mud ascension. They hence provide information regarding mobilization depth, diagenetic overprint, and geodynamic pathways. At the Nankai Trough subduction zone, SE offshore Japan, mud volcanism id common and supposed to be related to seismogenic processes. During MARUM Expedition SO-222 with R/V SONNE, mud volcanoes in the Kumano forearc basin were mapped, cored and sampled. By extending the Integrated Ocean Drilling Program (IODP) Kumano transect landwards, 5 new mud volcanoes were identified by multibeam mapping. Cores revealed mud breccia with semi-consolidated silt- to claystone clasts and gaseous fluid escape structures, while the hemipelagic background sediments are characterized by intercalations of turbidites, ash layers and calcareous fossils. Clasts were subject to thin-section analyses, and the cores were sampled for XRD analyses and radiocarbon dating. Clasts showed prominent deformation structures, neomorphism and pores and fractures filled with polycrystalline quartz and/or calcite cement, probably formed during deep burial and early metamorphosis. Illite crystallinity based on XRD measurements varies between 0.24 and 0.38, which implies that the material originates from the Anchizone at depths ≥ 4 km. Radiocarbon dating revealed ages between 4450 and 30300 yr cal. BP, with age reversals occurring not earlier than 17000 yr cal. BP. Radiocarbon dating beneath turbidites and ash layers found at mud volcano #9 points to an episodic occurrence of these earthquake-related features in intervals of ca. 620 yr, while the mud volcano itself remained inactive. In summary, the preliminary results suggest that the mud volcanoes are nurtured from a reservoir within the older part of the accretionary prism, but that mud volcanic activity is less frequent than major earthquakes. Future models will focus on source depth and temperature, and might elucidate the prerequisites for fluid migration and its role in seismogenesis at the Nankai Trough subduction zone.

Gypsum addition to soils contaminated by red mud: implications for aluminium, arsenic, molybdenum and vanadium solubility.

PubMed

Lehoux, Alizée P; Lockwood, Cindy L; Mayes, William M; Stewart, Douglas I; Mortimer, Robert J G; Gruiz, Katalin; Burke, Ian T

2013-10-01

Red mud is highly alkaline (pH 13), saline and can contain elevated concentrations of several potentially toxic elements (e.g. Al, As, Mo and V). Release of up to 1 million m(3) of bauxite residue (red mud) suspension from the Ajka repository, western Hungary, caused large-scale contamination of downstream rivers and floodplains. There is now concern about the potential leaching of toxic metal(loid)s from the red mud as some have enhanced solubility at high pH. This study investigated the impact of red mud addition to three different Hungarian soils with respect to trace element solubility and soil geochemistry. The effectiveness of gypsum amendment for the rehabilitation of red mud-contaminated soils was also examined. Red mud addition to soils caused a pH increase, proportional to red mud addition, of up to 4 pH units (e.g. pH 7 → 11). Increasing red mud addition also led to significant increases in salinity, dissolved organic carbon and aqueous trace element concentrations. However, the response was highly soil specific and one of the soils tested buffered pH to around pH 8.5 even with the highest red mud loading tested (33 % w/w); experiments using this soil also had much lower aqueous Al, As and V concentrations. Gypsum addition to soil/red mud mixtures, even at relatively low concentrations (1 % w/w), was sufficient to buffer experimental pH to 7.5-8.5. This effect was attributed to the reaction of Ca(2+) supplied by the gypsum with OH(-) and carbonate from the red mud to precipitate calcite. The lowered pH enhanced trace element sorption and largely inhibited the release of Al, As and V. Mo concentrations, however, were largely unaffected by gypsum induced pH buffering due to the greater solubility of Mo (as molybdate) at circumneutral pH. Gypsum addition also leads to significantly higher porewater salinities, and column experiments demonstrated that this increase in total dissolved solids persisted even after 25 pore volume replacements. Gypsum addition could therefore provide a cheaper alternative to recovery (dig and dump) for the treatment of red mud-affected soils. The observed inhibition of trace metal release within red mud-affected soils was relatively insensitive to either the percentage of red mud or gypsum present, making the treatment easy to apply. However, there is risk that over-application of gypsum could lead to detrimental long-term increases in soil salinity.

Diplomacy Through Earth Sciences: An Overview of US Geological Survey Technical Assistance Regarding the Ongoing LUSI Mud Eruption, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Casadevall, T. J.

2009-12-01

In June 2007, the US Department of State (DOS) requested assistance from the USGS to provide technical guidance and advice to the US Mission in Indonesia regarding the Lumpur Sidoarjo (LUSI) mud crisis. In May 2006, LUSI began as a mud eruption from a series of mud springs adjacent to an oil and gas exploration well being drilled near Surabaya, East Java, Indonesia. The production of mud and waters from the LUSI crater area has now continued for more than 3 years with no significant change in mud production rate (~110,000 cubic meters per day) nor in temperature of the mud (70-80 degrees C). Engineers suggest that mud production will continue at these rates for years to decades to come. Regardless of future activity at LUSI, the current mud accumulation of more than 100 million cubic meters poses a physical and environmental hazard which requires continuous monitoring and observation. The first response to the 2007 DOS request involved a site visit to Indonesia in September 2007. The result of that visit was to recommend to the Government of Indonesia (GOI) that they focus on long-term management of the mud rather than focus on the controversy as to the cause of the eruption or the debate about stopping the flow. Other recommendations from the initial 2007 technical visit included contracting for a US scientist to be co-located with engineers of the Sidoarjo Mud Management Board (BPLS) in Surabaya, East Java, to advise and consult on day-to-day developments at the site of the mud eruption. A second technical team visit by USGS scientists and an engineer from the US Army Corps of Engineers in October-November 2008 made additional recommendations on the long-term management of the mud and was followed in December by the start of a 6 month contract for the US mud adviser. From the start of activity in mid-2006 through late-2008, there was a clear sense of urgency at the US Mission in Indonesia to provide guidance and advice and included the personal intervention of the new US Ambassador. The USGS has completed the requests made in the June 2007 DOS cable, including an initial characterization of the mud and fluids; an analysis of land surface changes using the INSAR method; and an assessment of the seismic hazards in East Java. In the coming year, USGS will assist DOI agencies in the geophysical monitoring of the LUSI area and in the continued characterization of mud and fluids produced by the eruption.

Mud transportation on a steep shelf, Rio de La Plata shelf, Puerto Rico

USGS Publications Warehouse

Grove, K.A.; Pilkey, O.H.; Trumbull, J.V.A.

1982-01-01

Hurricanes David (August 29-30, 1979) and Frederick (September 2-5, 1979) caused major flooding of the Rio de La Plata in northern Puerto Rico. A thin mud layer was deposited across the narrow insular shelf adjacent to the river mouth. Within 5 months, fair-weather shelf-winnowing processes moved the mud layer entirely from the shelf, 0.5 to 2 km to the shelf break at the 50-m contour and beyond. The process of mud movement is termed 'mud hopping.' ?? 1982 A. M. Dowden, Inc.

Pore-scale Numerical Simulation Using Lattice Boltzmann Method for Mud Erosion in Methane Hydrate Bearing Layers

NASA Astrophysics Data System (ADS)

Yoshida, T.; Sato, T.; Oyama, H.

2014-12-01

Methane hydrates in subsea environments near Japan are believed to new natural gas resources. These methane hydrate crystals are very small and existed in the intergranular pores of sandy sediments in sand mud alternate layers. For gas production, several processes for recovering natural gas from the methane hydrate in a sedimentary reservoir have been proposed, but almost all technique are obtain dissociated gas from methane hydrates. When methane hydrates are dissociated, gas and water are existed. These gas and water are flown in pore space of sand mud alternate layers, and there is a possibility that the mud layer is eroded by these flows. It is considered that the mad erosion causes production trouble such as making skins or well instability. In this study, we carried out pore scale numerical simulation to represent mud erosion. This research aims to develop a fundamental simulation method based on LBM (Lattice Boltzmann Method). In the simulation, sand particles are generated numerically in simulation area which is approximately 200x200x200μm3. The periodic boundary condition is used except for mud layers. The water/gas flow in pore space is calculated by LBM, and shear stress distribution is obtained at the position flow interacting mud surface. From this shear stress, we consider that the driving force of mud erosion. As results, mud erosion can be reproduced numerically by adjusting the parameters such as critical shear stress. We confirmed that the simulation using LBM is appropriate for mud erosion.

Radiological characterization of clay mixed red mud in particular as regards its leaching features.

PubMed

Hegedűs, Miklós; Sas, Zoltán; Tóth-Bodrogi, Edit; Szántó, Tamás; Somlai, János; Kovács, Tibor

2016-10-01

The reuse of industrial by-products such as red mud is of great importance. In the case of the building material industry the reuse of red mud requires a cautious attitude, since the enhanced radionuclide content of red mud can have an effect on human health. The natural radionuclide content of red mud from the Ajka red mud reservoir and the clay sample from a Hungarian brick factory were determined by gamma spectrometry. It was found that maximum 27.8% red mud content can be added to fulfil the conditions of the EU-BSS. The effect of heat treatment was investigated on a red mud-clay mixture and it was found that in the case of radon and thoron exhalation the applied heat reduced remarkably the exhalation capacities. The leaching features of red mud and different mixtures were studied according to the MSZ-21470-50 Hungarian standard, the British CEN/TS 14429 standard and the Tessier sequential extraction method. The Tessier method and the MSZ-21470-50 standard are suitable for the characterization of materials; however, they do not provide enough information for waste deposition purposes. To this end, we propose using the CEN/TS 14429 method, because it is easy to use, and gives detailed information about the material's behaviour under different pH conditions, however, further measurements are necessary. Copyright © 2016 Elsevier Ltd. All rights reserved.

Boron-rich mud volcanoes of the Black Sea region: Modern analogues to ancient sea-floor tourmalinites associated with Sullivan-type Pb-Zn deposits?

NASA Astrophysics Data System (ADS)

Slack, John F.; Turner, Robert J. W.; Ware, Paul L. G.

1998-05-01

Large submarine mud volcanoes in the abyssal part of the Black Sea south of the Crimean Peninsula are similar in many respects to synsedimentary mud volcanoes in the Mesoproterozoic Belt-Purcell basin. One of the Belt-Purcell mud volcanoes directly underlies the giant Sullivan Pb-Zn-Ag deposit in southeastern British Columbia. Footwall rocks to the Sullivan deposit comprise variably tourmalinized siltstone, conglomerate, and related fragmental rock; local thin pyrrhotite-rich and spessartine-quartz beds are interpreted as Fe and Fe-Mn exhalites, respectively. Analogous Fe- and Mn-rich sediments occur near the abyssal Black Sea mud volcanoes. Massive pyrite crusts and associated carbonate chimneys discovered in relatively shallow waters (˜200 m depth) west of the Crimean Peninsula indicate an active sea-floor hydrothermal system. Subaerial mud volcanoes on the Kerch and Taman Peninsulas (˜100 km north of the abyssal mud volcanoes) contain saline thermal waters that locally have very high B contents (to 915 mg/L). These data suggest that tourmalinites might be forming in or near submarine Black Sea mud volcanoes, where potential may also exist for Sullivan-type Pb-Zn mineralization.

Observed salinity changes in the Alappuzha mud bank, southwest coast of India and its implication to hypothesis of mudbank formation

NASA Astrophysics Data System (ADS)

Muraleedharan, K. R.; Dinesh Kumar, P. K.; Prasanna Kumar, S.; Srijith, B.; John, Sebin; Naveen Kumar, K. R.

2017-04-01

Alappuzha mud bank draws special attention among the twenty-mud bank locations reported along the Kerala coast by its remoteness from riverine sources. Among several hypotheses proposed for the formation of mud bank, the subterranean hypothesis was most accepted because of the occurrence of low salinity in the bottom layers. The present study provides evidence to show that occurrence of low salinity waters near the bottom in the mud bank region is an artifact of measuring technique employed for the measurement of salinity. The usual technique of conductivity based salinity determination completely fails in the presence of water laden with high amount of suspended sediment. Laboratory experiments were conducted to determine the response of electrode and conductivity cell sensor types to determine the salinity using a range of suspended sediment in the water column. Actual sediment samples from the mud bank region were utilized for the above studies. Based on field observations and experiments, we conclude that the low salinity was the manifestation of the presence highly turbid fluid mud formation in the mud bank region rather than the influence of fresh water.

Mud Banks along the southwest coast of India are not too muddy for plankton.

PubMed

Jyothibabu, R; Balachandran, K K; Jagadeesan, L; Karnan, C; Arunpandi, N; Naqvi, S W A; Pandiyarajan, R S

2018-02-07

Considering Alappuzha Mud Bank in the southern Kerala coast as a typical case of biologically productive Mud Banks that form along the southwest coast of India during the Southwest Monsoon (June - September), the present study addresses several pertinent missing links between the physical environment in Mud Banks and their influence on plankton stock. This study showed that very strong coastal upwelling prevails in the entire study domain during the Southwest Monsoon, which manifests itself in the form of significantly cool, hypoxic and nitrate-rich waters surfacing near the coast. The upwelled water persisting throughout the Southwest Monsoon period was found to have fuelled the exceptionally high phytoplankton stock in the entire study area, including the Mud Bank region. Having accepted that Mud Banks are special because of the calm sea surface conditions and relatively high turbidity level in the water column around them, the present study showed that except at points close to the sea bottom, turbidity level in the Alappuzha Mud Bank was below the critical level to inhibit the plankton stock. The suspended sediments that form in the Mud Bank occasionally could be attributed to the disturbance of the bottom fluid muddy layer and their vertical spurts.

Removal of hexavalent chromium by using red mud activated with cetyltrimethylammonium bromide.

PubMed

Li, Deliang; Ding, Ying; Li, Lingling; Chang, Zhixian; Rao, Zhengyong; Lu, Ling

2015-01-01

The removal of hexavalent chromium [Cr(VI)] from aqueous solution by using red mud activated with cetyltrimethylammonium bromide (CTAB) was studied. The optimum operation parameters, such as CTAB concentration, pH values, contact time, and initial Cr(VI) concentration, were investigated. The best concentration of CTAB for modifying red mud was found to be 0.50% (mCTAB/VHCl,0.6 mol/L). The lower pH (<2) was found to be much more favourable for the removal of Cr(VI). Red mud activated with CTAB can greatly improve the removal ratio of Cr(VI) as high as four times than that of original red mud. Adsorption equilibrium was reached within 30 min under the initial Cr(VI) concentration of 100 mg L(-1). The isotherm data were analysed using Langmuir and Freundlich models. The adsorption of Cr(VI) on activated red mud fitted well to the Langmuir isotherm model, and the maximum adsorption capacity was estimated as 22.20 mg g(-1) (Cr/red mud). The adsorption process could be well described using the pseudo-second-order model. The result shows that activated red mud is a promising agent for low-cost water treatment.

Method and apparatus for optimizing determination of the originating depth of borehole cuttings

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

Mc Auley, J.A.; Eppler, S.G.

1987-11-24

This patent describes a method for determining the arrival at the surface of an identifiable material from a predetermined drilling depth independent of pump stroke rate and intermittent operations during the utilization of at least a drill bit, a positive displacement mud pump and drilling mud during the drilling of a well. The method comprises the steps of: adding identifiable material to the drilling mud as the drilling mud is being pumped downwardly into the well; initiate count of the pump strokes of the positive displacement mud pump as the previous step occurs; observe arrival of the identifiable material atmore » the surface of the earth as the drilling mud exits from the well; observe the accumulated count of the pump strokes of the positive displacement mud pump which occur between step one and step three; subtract, from the accumulated count of the previous step, the number of pump strokes of the positive displacement mud pump required to pump the identifiable material down to the drill bit to establish a number of lag strokes; and utilize the number obtained in the previous step to identify the arrival of drill cuttings from a predetermined depth.« less

Boron-rich mud volcanoes of the Black Sea region: modern analogues to ancient sea-floor tourmalinites associated with Sullivan-type Pb-Zn deposits?

USGS Publications Warehouse

Slack, J.F.; Turner, R.J.W.; Ware, P.L.G.

1998-01-01

Large submarine mud volcanoes in the abyssal part of the Black Sea south of the Crimean Peninsula are similar in many respects to synsedimentary mud volcanoes in the Mesoproterozoic Belt-Purcell basin. One of the Belt-Purcell mud volcanoes directly underlies the giant Sullivan Pb-Zn-Ag deposit in southeastern British Columbia. Footwall rocks to the Sullivan deposit comprise variably tourmalinized siltstone, conglomerate, and related fragmental rock; local thin pyrrhotite-rich and spessartine-quartz beds are interpreted as Fe and Fe-Mn exhalites, respectively. Analogous Fe- and Mn-rich sediments occur near the abyssal Black Sea mud volcanoes. Massive pyrite crusts and associated carbonate chimneys discovered in relatively shallow waters (~200 m depth) west of the Crimean Peninsula indicate an active sea-floor-hydrothermal system. Subaerial mud volcanoes on the Kerch and Taman Peninsulas (~100 km north of the abyssal mud volcanoes) contain saline thermal waters that locally have very high B contents (to 915 mg/L). These data suggest that tourmalinites might be forming in or near submarine Black Sea mud volcanoes, where potential may also exist for Sullivan-type Pb-Zn mineralization.

Geochemical recovery of the Torna-Marcal river system after the Ajka red mud spill, Hungary.

PubMed

Anton, Á D; Klebercz, O; Magyar, Á; Burke, I T; Jarvis, A P; Gruiz, K; Mayes, W M

2014-12-01

The failure of the Ajka red mud depository in October 2010 led to the largest single release of red mud into the surface water environment. This study provides a comparative assessment of stream sediment quality in the Torna-Marcal-Rába catchment between post-disaster surveys (2010) and follow up surveys at an identical suite of 21 locations in 2013. The signature of red mud apparent in initial surveys with high Al, As, Cr, Na, V was only apparent at a small number of sample stations in recent surveys. These constitute <1 km of stream, compared to the >20 km reach of affected sediments in the immediate aftermath of the spill. Concentrations of red mud-derived contaminants are predominately associated with fine fractions of the red mud (<8 μm). This enhances transport out of the system of red mud-derived contaminants and, along with extensive remedial efforts, has substantially limited the within-channel inventory of potentially ecotoxic metals and metalloids.

Calcification-carbonation method for red mud processing.

PubMed

Li, Ruibing; Zhang, Tingan; Liu, Yan; Lv, Guozhi; Xie, Liqun

2016-10-05

Red mud, the Bayer process residue, is generated from alumina industry and causes environmental problem. In this paper, a novel calcification-carbonation method that utilized a large amount of the Bayer process residue is proposed. Using this method, the red mud was calcified with lime to transform the silicon phase into hydrogarnet, and the alkali in red mud was recovered. Then, the resulting hydrogarnet was decomposed by CO2 carbonation, affording calcium silicate, calcium carbonate, and aluminum hydroxide. Alumina was recovered using an alkaline solution at a low temperature. The effects of the new process were analyzed by thermodynamics analysis and experiments. The extraction efficiency of the alumina and soda obtained from the red mud reached 49.4% and 96.8%, respectively. The new red mud with <0.3% alkali can be used in cement production. Using a combination of this method and cement production, the Bayer process red mud can be completely utilized. Copyright © 2016 Elsevier B.V. All rights reserved.

Resources Management Strategy For Mud Crabs (Scylla spp.) In Pemalang Regency

NASA Astrophysics Data System (ADS)

Purnama Fitri, Aristi Dian; Boesono, Herry; Sabdono, Agus; Adlina, Nadia

2017-02-01

The aim of this research is to develop resources management strategies of mud crab (Scylla spp.) in Pemalang Regency. The method used is descriptive survey in a case study. This research used primary data and secondary data. Primary data were collected through field observations and in-depth interviews with key stakeholders. Secondary data were collected from related publications and documents issued by the competent institutions. SWOT Analysis was used to inventory the strengths, weaknesses, opportunities and threats. TOWS matrix was used to develop an alternative of resources management strategies. SWOT analysis was obtained by 6 alternative strategies that can be applied for optimization of fisheries development in Pemalang Regency. The strategies is the control of mud crab fishing gear, restricted size allowable in mud crab, control of mud crab fishing season, catch monitoring of mud crab, needs a management institutions which ensure the implementation of the regulation, and implementation for mud crab aquaculture. Each alternative strategy can be synergized to optimize the resources development in Pemalang Regency.

Eruption of a deep-sea mud volcano triggers rapid sediment movement.

PubMed

Feseker, Tomas; Boetius, Antje; Wenzhöfer, Frank; Blandin, Jerome; Olu, Karine; Yoerger, Dana R; Camilli, Richard; German, Christopher R; de Beer, Dirk

2014-11-11

Submarine mud volcanoes are important sources of methane to the water column. However, the temporal variability of their mud and methane emissions is unknown. Methane emissions were previously proposed to result from a dynamic equilibrium between upward migration and consumption at the seabed by methane-consuming microbes. Here we show non-steady-state situations of vigorous mud movement that are revealed through variations in fluid flow, seabed temperature and seafloor bathymetry. Time series data for pressure, temperature, pH and seafloor photography were collected over 431 days using a benthic observatory at the active Håkon Mosby Mud Volcano. We documented 25 pulses of hot subsurface fluids, accompanied by eruptions that changed the landscape of the mud volcano. Four major events triggered rapid sediment uplift of more than a metre in height, substantial lateral flow of muds at average velocities of 0.4 m per day, and significant emissions of methane and CO₂ from the seafloor.

Eruption of a deep-sea mud volcano triggers rapid sediment movement

PubMed Central

Feseker, Tomas; Boetius, Antje; Wenzhöfer, Frank; Blandin, Jerome; Olu, Karine; Yoerger, Dana R.; Camilli, Richard; German, Christopher R.; de Beer, Dirk

2014-01-01

Submarine mud volcanoes are important sources of methane to the water column. However, the temporal variability of their mud and methane emissions is unknown. Methane emissions were previously proposed to result from a dynamic equilibrium between upward migration and consumption at the seabed by methane-consuming microbes. Here we show non-steady-state situations of vigorous mud movement that are revealed through variations in fluid flow, seabed temperature and seafloor bathymetry. Time series data for pressure, temperature, pH and seafloor photography were collected over 431 days using a benthic observatory at the active Håkon Mosby Mud Volcano. We documented 25 pulses of hot subsurface fluids, accompanied by eruptions that changed the landscape of the mud volcano. Four major events triggered rapid sediment uplift of more than a metre in height, substantial lateral flow of muds at average velocities of 0.4 m per day, and significant emissions of methane and CO2 from the seafloor. PMID:25384354

The role of fluvial sediment supply and river-mouth hydrology in the dynamics of the muddy, Amazon-dominated Amapá-Guianas coast, South America: A three-point research agenda

NASA Astrophysics Data System (ADS)

Anthony, Edward J.; Gardel, Antoine; Proisy, Christophe; Fromard, François; Gensac, Erwan; Peron, Christina; Walcker, Romain; Lesourd, Sandric

2013-07-01

The morphology and sediment dynamics of the 1500 km-long coast of South America between the mouths of the Amazon and the Orinoco Rivers are largely dependent on the massive suspended-sediment discharge of the Amazon, part of which is transported alongshore as mud banks. These mud banks have an overwhelming impact on the geology, the geomorphology, the ecology and the economy of this coast. Although numerous field investigations and remote sensing studies have considerably enhanced our understanding of the dynamics of this coast over the last three decades, much still remains to be understood of the unique functional mechanisms and processes driving its evolution. Among the themes that we deem as requiring further attention three come out as fundamental. The first concerns the mechanisms of formation of individual mud banks from mud streaming on the shelf off the mouth of the Amazon. An unknown quantity of the fluid mud generated by offshore estuarine front activity is transported shoreward and progressively forms mud banks on the Amapá coast, Brazil. The volume of each mud bank can contain from the equivalent of the annual mud supply of the Amazon to several times this annual sediment discharge. The mechanisms by which individual banks are generated from the Amazon turbidity maximum are still to be elucidated. Areas of research include regional mesoscale oceanographic conditions and mud supply from the Amazon. The second theme is that of variations in rates of migration of mud banks, which influence patterns of coastal accretion. Research emphasis needs to be placed on the analysis of both regional meteorological-hydrodynamic forcing and distant Atlantic forcing, as well as on the hydrology of the large rivers draining the Guyana Shield. The rivers appear to generate significant offshore deflection of mud banks in transit alongshore, through a hydraulic-groyne effect. This may favour both muddy accretion on the updrift coast and downdrift mud liquefaction with probably lessened muddy deposition. The third theme concerns sand supply by the Guiana Shield rivers. The rare sand deposits are important in providing sites for human settlements and routes and for nesting by marine turtles. The limited presence of sand bodies on this coast may reflect 'mud blanketing', a hypothesis that requires verification through high-resolution seismic analyses of shelf deposits and coring operations. The large Guiana Shield rivers, especially in Surinam and Guyana, have supplied sand for the construction of significant bands of cheniers, probably enhanced by the afore-mentioned downdrift hydraulic-groyne effect on hindered mud deposition. In all the three themes of this future research agenda, two central elements are the sediment input of the rivers of the Amazon basin, starting with the massive mud supply from the Amazon catchment itself, followed by sand inputs by the Guiana Shield rivers and their river-mouth effects on mud banks.

Feasibility study for an innovative industrial red mud utilisation method.

PubMed

Kounalakis, Petros; Aravossis, Konstantinos; Karayianni, ChS

2016-02-01

Red mud is a high volume industrial waste, and its management poses a unique challenge. For the utilisation of red mud, an economical, energy saving, environmental friendly and widely applicable method has been found. The proposed novel method is purely chemical, and achieves the recovery of all the oxides contained in red mud totally and transforms them into high value added products. The present work shows that an investment in an industrial plant, treating red mud and turning a toxic industrial waste in commercial products, is safe and viable. © The Author(s) 2015.

Micron-scale Analysis of Carbonate-Associated Sulfate by Secondary Ionization Mass Spectrometry: Insights into Spatial Variability in δ34SCAS

NASA Astrophysics Data System (ADS)

Fike, D. A.; Jones, D. S.

2012-12-01

The proliferation of carbonate-associated sulfate (CAS) isotope analyses in recent years has revolutionized our understanding of marine sulfur cycling over much of Earth history. In marine carbonate rocks, δ34SCAS is thought to be a faithful recorder of the isotopic composition of marine sulfate (δ34SSO4). However, as the chemostratigraphic record becomes better resolved in time and space, reports of coeval but discordant δ34SCAS values are becoming increasingly common. These differences could arise in part from a) water column stratification or physiographic separations between separate ocean basins (i.e., paleoceanographic variability in δ34SSO4); b) syndepositional processes that decouple the relationship between δ34SSO4 and δ34SCAS during deposition or prior to lithification; or c) diagenetic alteration of the δ34SCAS signal following deposition. To help disentangle these processes, we have developed a microanalytical approach to determine the abundance and isotopic composition of CAS using secondary ionization mass spectrometry (SIMS). While our current precision (~1‰) cannot compete with that obtained from traditional bulk analysis on gas source isotope ratio mass spectrometers, we believe that the unparalleled spatial resolution can provide substantial insights into many of the fundamental questions that remain regarding the mechanisms by which CAS concentration and isotopic composition can be altered during carbonate precipitation and/or recrystallization. With a spatial resolution as low as ~ 5 μm, it is possible to analyze suites of primary and diagenetic phases, including individual carbonate allochems, muds, and cements. Preliminary results indicate that δ34SCAS can vary by as much as 10‰ between phases in a single sample. This scale of analysis allows for a rigorous evaluation of the susceptibility of δ34SCAS to syndepositional and diagenetic alteration, especially when coupled with parallel analysis of δ13Ccarb/δ18Ocarb and diagnostic trace element abundances. Such detailed measurements illuminate the complex relationships between the isotopic composition of individual constituents of carbonate rocks and the bulk δ34SCAS values on which much of our understanding of sulfur cycling in deep time is based. The resulting insights can be used to re-examine existing δ34SCAS records and our understanding of the evolution of sulfur cycling over Earth history.

Parathyroidectomy in patients with chronic kidney disease: Impacts of different techniques on the biochemical and clinical evolution of secondary hyperparathyroidism.

PubMed

Albuquerque, Roxana de Fátima Camelo; Carbonara, Cinthia Esbrile Moraes; Martin, Rita de Cássia T; Dos Reis, Luciene Machado; do Nascimento, Climério Pereira; Arap, Sérgio Samir; Moysés, Rosa M A; Jorgetti, Vanda; Montenegro, Fábio L M; de Oliveira, Rodrigo Bueno

2018-02-01

Parathyroidectomy (PTx) decreases the mortality rate of refractory secondary hyperparathyroidism (rSHP) due to chronic kidney disease. A consensus regarding which techniques of PTx are associated with better outcomes is not available. The aims of this study are to evaluate the clinical and laboratory evolution of 49 hemodialysis patients with rSHP who underwent PTx using different techniques. Patients underwent subtotal PTx (sub-PTx) or total PTx with autotransplantation (AT) of 45 (PTx-AT 45 ) or 90 parathyroid fragments (PTx-AT 90 ) and were followed for 12 months. We analyzed the expression of proliferating cell nuclear antigen (PCNA), calcium-sensing receptor (CasR), vitamin D receptor (VDR), fibroblast growth factor receptor-1 (FGFR1), sodium-dependent phosphate cotransporter-1 (PIT1), and Klotho in parathyroid glands. Baseline median serum intact parathyroid hormone (iPTH) levels were 1,466 (1,087-2,125) pg/mL; vascular calcification scores correlated with serum iPTH (r = 0.529; P = .002) and serum phosphate levels (r = 0.389; P = .028); and Klotho expression was negatively correlated with serum phosphate levels (r = -0.4; P = .01). After 12 months, serum iPTH and alkaline phosphatase levels were significantly controlled in all groups, as was bone pain. The proportions of patients with serum iPTH levels within the ranges recommended by Kidney Disease: Improving Global Outcomes were similar among the treatment groups. During the hungry bone disease (HBS), patients received 3,786 g (1,412-7,580) of elemental calcium, and a trend toward a positive correlation between the cumulative calcium load at the end of follow up and VC score post-PTx was noted (r = 0.390; P = .06). Two cases evolved to clinically uncontrolled hyperparathyroidism in the sub-PTx group. The expression patterns of PCNA, VDR, CasR, PIT1, FGFR1, and Klotho in parathyroid glands did not correlate with serum systemic iPTH levels or the duration of HBS. All 3 operative techniques were effective at controlling rSHP, both in clinical and laboratory terms. Neither the quantity nor quality of parathyroid fragments influenced serum systemic iPTH and AT-iPTH levels. The cumulative calcium load appeared to correlate with the VC score and may have affected its progression. The effects of phosphate restriction on Klotho expression in human parathyroid glands and the subsequent decrease in FGF23 resistance must be addressed in further studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Characterization of MUDENG, a novel anti-apoptotic protein

PubMed Central

Choi, J-H; Lim, J-B; Wickramanayake, D D; Wagley, Y; Kim, J; Lee, H-C; Seo, H G; Kim, T-H; Oh, J-W

2016-01-01

MUDENG (Mu-2-related death-inducing gene, MuD) is revealed to be involved in cell death signaling. Astrocytes, the major glial cell type in the central nervous system, are a source of brain tumors. In this study, we examined MuD expression and function in human astroglioma cells. Stimulation of U251-MG cells with tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) resulted in a 40% decrease in cell viability and a 33% decrease in MuD protein levels, although not in MuD mRNA levels. To study the functional relevance of MuD expression, stable transfectants expressing high levels of MuD were generated. Stimulation of these transfectants with TRAIL resulted in enhanced cell survival (77% for stable and 46% for control transfectants). Depletion of MuD led to a marked reduction upon TRAIL stimulation in cell viability (22% in MuD-depleted cells and 54% in control cells). In addition, we observed that MuD depletion increased the susceptibility of the cells to TRAIL by enhancing the cleavage of caspase-3/-9 and BH3-interacting domain death agonist (Bid). A unique 25-kDa fragment of B-cell lymphoma 2 (Bcl-2) lacking BH4 was observed 60–180 min post TRAIL treatment in MuD-depleted cells, suggesting that Bcl-2 is converted from its anti-apoptotic form to the truncated pro-apoptotic form. Importantly, the TRAIL-mediated decrease in cell viability in MuD-depleted cells was abrogated upon Bid depletion, indicating that the role of MuD in apoptotic signaling takes place at the Bid and Bcl-2 junction. MuD localizes predominantly in the endoplasmic reticulum and partly in the mitochondria and its amounts are reduced 6 h post TRAIL stimulation, presumably via caspase-3-mediated MuD cleavage. Collectively, these results suggest that MuD, a novel signaling protein, not only possesses an anti-apoptotic function but may also constitute an important target for the design of ideal candidates for combinatorial treatment strategies for glioma cells. PMID:27136675

Comparing the efficacy of mature mud pack and hot pack treatments for knee osteoarthritis.

PubMed

Sarsan, Ayşe; Akkaya, Nuray; Ozgen, Merih; Yildiz, Necmettin; Atalay, Nilgun Simsir; Ardic, Fusun

2012-01-01

The objective of this study is to compare the efficacy of mature mud pack and hot pack therapies on patients with knee osteoarthritis. This study was designed as a prospective, randomized-controlled, and single-blinded clinical trial. Twenty-seven patients with clinical and radiologic evidence of knee osteoarthritis were randomly assigned into two groups and were treated with mature mud packs (n 15) or hot packs (n=12). Patients were evaluated for pain [based on the visual analog scale (VAS)], function (WOMAC, 6 min walking distance), quality of life [Short Form-36 (SF-36)], and serum levels of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and insulin-like growth factor-1 (IGF-1) at baseline, post-treatment, and 3 and 6~months after treatment. The mud pack group shows a significant improvement in VAS, pain, stifness, and physical function domains of WOMAC. The difference between groups of pain and physical activity domains is significant at post-treatment in favor of mud pack. For a 6 min walking distance, mud pack shows significant improvement, and the difference is significant between groups in favor of mud pack at post-treatment and 3 and 6 months after treatment. Mud pack shows significant improvement in the pain subscale of SF-36 at the third month continuing until the sixth month after the treatment. Significant improvements are found for the social function, vitality/energy, physical role disability, and general health subscales of SF-36 in favor of the mud pack compared with the hot pack group at post-treatment. A significant increase is detected for IGF-1 in the mud pack group 3 months after treatment compared with the baseline, and the difference is significant between groups 3 months after the treatment. Mud pack is a favorable option compared with hotpack for pain relief and for the improvement of functional conditions in treating patients with knee osteoarthritis.

Mud Flow Characteristics Occurred in Izuoshima Island, 2013

NASA Astrophysics Data System (ADS)

Takebayashi, H.; Egashira, S.; Fujita, M.

2015-12-01

Landslides and mud flows were occurred in the west part of the Izuoshima Island, Japan on 16 October 2013. The Izuoshima Island is a volcanic island and the land surface is covered by the volcanic ash sediment in 1m depth. Hence, the mud flow with high sediment concentration was formed. The laminar layer is formed in the debris flow from the bed to the fluid surface. On the other hand, the laminar flow is restricted near the bed in the mud flow and the turbulence flow is formed on the laminar flow layer. As a result, the equilibrium slope of the mud flow becomes smaller comparing to the debris flow. In this study, the numerical analysis mud flow model considering the effect of turbulence flow on the equilibrium slope of the mud flow is developed. Subsequently, the model is applied to the mud flow occurred in the Izuoshima Island and discussed the applicability of the model and the flow characteristics of the mud flow. The differences of the horizontal flow areas between the simulated results and the field data are compared and it was found that the outline of the horizontal shape of the flow areas is reproduced well. Furthermore, the horizontal distribution of the erosion and deposition area is reproduced by the numerical analysis well except for the residential area (Kandachi area). Kandachi area is judged as the erosion area by the field observation, but the sediment was deposited in the numerical analysis. It is considered that the 1.5hour heavy rain over 100mm/h after the mud flow makes the discrepancy. The difference of the horizontal distribution of the maximum flow surface elevation between the simulated results and the field data are compared and it was found that the simulated flow depth is overestimated slightly, because of the wider erosion area due to the coarse resolution elevation data. The averaged velocity and the depth of the mud flow was enough large to collapse the houses.

Comparison with Offshore and Onshore Mud Volcanoes in the Southwestern Taiwan

NASA Astrophysics Data System (ADS)

Chen, Y. H.; Su, C. C.; Chen, T. T.; Liu, C. S.; Paull, C. K.; Caress, D. W.; Gwiazda, R.; Lundsten, E. M.; Hsu, H. H.

2017-12-01

The offshore area southwest (SW) of Taiwan is on the convergent boundary between the Eurasian and Philippine Sea plates. The plate convergence manifests in this unique geological setting as a fold-and-thrust-belt. Multi-channel seismic profiles, and bathymetry and gravity anomaly data collected from Taiwan offshore to the SW show the presence of a large amount of mud volcanoes and diapirs with NE-SW orientations. In the absence of comprehensive sampling and detailed geochemistry data from submarine mud volcanoes, the relation between onshore and offshore mud volcanoes remains ambiguous. During two MBARI and IONTU joint cruises conducted in 2017 we collected high-resolution multibeam bathymetry data (1-m-resolution) and chirp sub-bottom profiles with an autonomous underwater vehicle (AUV) from submarine Mud Volcano III (MV3), and obtained precisely located samples and video observations with a remotely operated vehicle (ROV). MV3 is an active submarine mud volcano at 465 m water depth offshore SW Taiwan. This cone-shape mud volcano is almost 780 m wide, 150 m high, with 8° slopes, and a 30 m wide mound on the top. Several linear features are observed in the southwest of the mound, and these features are interpreted as a series of marks caused by rolling rocks that erupted from the top of MV3. We collected three rocks and push cores from MV3 and its top with the ROV, in order to compare their chemical and mineralogical composition to that of samples collected from mud volcanoes along the Chishan fault. The surface and X-radiography imaging, 210Pb chronology, grain size and X-ray diffractometer analyses were conducted to compare geochemical and sedimentary properties of offshore and onshore mud volcanoes. The results indicate that the offshore and onshore mud volcanoes have similar characteristics. We suggest that offshore and onshore mud volcanoes of SW Taiwan are no different in the source of their materials and their mechanism of creation and evolution.

Multiphase modelling of mud volcanoes

NASA Astrophysics Data System (ADS)

Colucci, Simone; de'Michieli Vitturi, Mattia; Clarke, Amanda B.

2015-04-01

Mud volcanism is a worldwide phenomenon, classically considered as the surface expression of piercement structures rooted in deep-seated over-pressured sediments in compressional tectonic settings. The release of fluids at mud volcanoes during repeated explosive episodes has been documented at numerous sites and the outflows resemble the eruption of basaltic magma. As magma, the material erupted from a mud volcano becomes more fluid and degasses while rising and decompressing. The release of those gases from mud volcanism is estimated to be a significant contributor both to fluid flux from the lithosphere to the hydrosphere, and to the atmospheric budget of some greenhouse gases, particularly methane. For these reasons, we simulated the fluid dynamics of mud volcanoes using a newly-developed compressible multiphase and multidimensional transient solver in the OpenFOAM framework, taking into account the multicomponent nature (CH4, CO2, H2O) of the fluid mixture, the gas exsolution during the ascent and the associated changes in the constitutive properties of the phases. The numerical model has been tested with conditions representative of the LUSI, a mud volcano that has been erupting since May 2006 in the densely populated Sidoarjo regency (East Java, Indonesia), forcing the evacuation of 40,000 people and destroying industry, farmland, and over 10,000 homes. The activity of LUSI mud volcano has been well documented (Vanderkluysen et al., 2014) and here we present a comparison of observed gas fluxes and mud extrusion rates with the outcomes of numerical simulations. Vanderkluysen, L.; Burton, M. R.; Clarke, A. B.; Hartnett, H. E. & Smekens, J.-F. Composition and flux of explosive gas release at LUSI mud volcano (East Java, Indonesia) Geochem. Geophys. Geosyst., Wiley-Blackwell, 2014, 15, 2932-2946

Evaluation of the Effect of Hévíz Mud in Patients with Hand Osteoarthritis: A Randomized, Controlled, Single-Blind Follow-Up Study.

PubMed

Gyarmati, Noémi; Kulisch, Ágota; Németh, András; Bergmann, Annamária; Horváth, József; Mándó, Zsuzsanna; Matán, Ágnes; Szakál, Erika; Sasné Péter, Tímea; Szántó, Dóra; Bender, Tamás

2017-03-01

Heat therapy is one of the most popular non-pharmacological treatments for osteoarthritis of the hand. To investigate the therapeutic and chemical effects of Hévíz mud on patients with hand osteoarthritis. We randomly assigned 47 patients with mild-to-moderate hand osteoarthritis to two groups. Patients in group 1 (n=23) received Hévíz mud applied directly to both hands, whereas patients in group 2 (n=24) also received mud to both hands, but nylon gloves separated the skin from the mud. Patients in both groups underwent five 20 minute treatment sessions per week for 3 weeks. The temperature of the mud was 42°C. Outcome measures were Visual Analogue Scale (VAS) scores, hand grip strength, the number of swollen and tender joints of the hand, the duration of morning joint stiffness, Health Assessment Questionnaire score, and EuroQoL Group 5-Dimension Self-Report Questionnaire score. The study parameters were evaluated at baseline, immediately after treatment, and after 16 weeks. Both groups showed improvement in nearly all assessed parameters at the end of treatment and at 16 weeks from the start of treatment. At the week 16 follow-up visit, the patient group directly treated with mud showed significantly better improvement in VAS for II and IV parameters and in swollen joint count in both hands compared to the nylon glove-mud group. Hévíz mud therapy significantly improved objective and subjective parameters in patients with hand osteoarthritis and had a beneficial effect on the patients' quality of life. Further studies are required to evaluate the chemical effects of the mud.

Mud Volcanism in a Canyon: Morphodynamic Evolution of the Active Venere Mud Volcano and Its Interplay With Squillace Canyon, Central Mediterranean

NASA Astrophysics Data System (ADS)

Loher, Markus; Ceramicola, Silvia; Wintersteller, Paul; Meinecke, Gerrit; Sahling, Heiko; Bohrmann, Gerhard

2018-02-01

Submarine mud volcanoes develop through the extrusion of methane-rich fluids and sediments onto the seafloor. The morphology of a mud volcano can record its extrusive history and processes of erosion and deformation affecting it. The study of offshore mud volcano dynamics is limited because only few have been mapped at resolutions that reveal their detailed surface structures. More importantly, rates and volumes of extruded sediment and methane are poorly constrained. The 100 m high twin cones of Venere mud volcano are situated at ˜1,600 m water depth within Squillace Canyon along the Ionian Calabrian margin, Mediterranean Sea. Seafloor bathymetry and backscatter data obtained by a ship-based system and an autonomous underwater vehicle (AUV) allow mapping of mudflow deposits of the mud volcano and bedforms in the surrounding canyon. Repeated surveying by AUV document active mud movement at the western summit in between 2014 and 2016. Through sediment coring and tephrochronology, ages of buried mudflow deposits are determined based on the sedimentation rate and the thickness of overlying hemipelagic sediments. An average extrusion rate of 27,000 m3/yr over the last ˜882 years is estimated. These results support a three-stage evolutionary model of Venere mud volcano since ˜4,000 years ago. It includes the onset of quiescence at the eastern cone (after ˜2,200 years ago), erosive events in Squillace Canyon (prior to ˜882 years ago), and mudflows from the eastern cone (since ˜882 years). This study reveals new interactions between a mud volcano and a canyon in the deep sea.

Effects of mud supply on large-scale estuary morphology and development over centuries to millennia

NASA Astrophysics Data System (ADS)

Braat, Lisanne; van Kessel, Thijs; Leuven, Jasper R. F. W.; Kleinhans, Maarten G.

2017-10-01

Alluvial river estuaries consist largely of sand but are typically flanked by mudflats and salt marshes. The analogy with meandering rivers that are kept narrower than braided rivers by cohesive floodplain formation raises the question of how large-scale estuarine morphology and the late Holocene development of estuaries are affected by cohesive sediment. In this study we combine sand and mud transport processes and study their interaction effects on morphologically modelled estuaries on centennial to millennial timescales. The numerical modelling package Delft3D was applied in 2-DH starting from an idealised convergent estuary. The mixed sediment was modelled with an active layer and storage module with fluxes predicted by the Partheniades-Krone relations for mud and Engelund-Hansen for sand. The model was subjected to a range of idealised boundary conditions of tidal range, river discharge, waves and mud input. The model results show that mud is predominantly stored in mudflats on the side of the estuary. Marine mud supply only influences the mouth of the estuary, whereas fluvial mud is distributed along the whole estuary. Coastal waves stir up mud and remove the tendency to form muddy coastlines and the formation of mudflats in the downstream part of the estuary. Widening continues in estuaries with only sand, while mud supply leads to a narrower constant width and reduced channel and bar dynamics. This self-confinement eventually leads to a dynamic equilibrium in which lateral channel migration and mudflat expansion are balanced on average. However, for higher mud concentrations, higher discharge and low tidal amplitude, the estuary narrows and fills to become a tidal delta.

Present Practice of Using Nautical Depth to Manage Navigation Channels in the Presence of Fluid Mud

DTIC Science & Technology

2017-05-01

material surfaces cannot be interpreted reliably unless other correlating information is developed. Surveying of fluid mud properties. At some locations...depth to manage navigation channels and ports requires a mud property that determines a navigability criteria, a practical method for surveying that...for managing navigation channels, (3) issues related to conducting hydrographic surveying in waterways with fluid mud bottoms, (4) the newest

Feasibility of co-reduction roasting of a saprolitic laterite ore and waste red mud

NASA Astrophysics Data System (ADS)

Wang, Xiao-ping; Sun, Ti-chang; Kou, Jue; Li, Zhao-chun; Tian, Yu

2018-06-01

Large scale utilization is still an urgent problem for waste red mud with a high content of alkaline metal component in the future. Laterite ores especially the saprolitic laterite ore are one refractory nickel resource, the nickel and iron of which can be effectively recovered by direct reduction and magnetic separation. Alkaline metal salts were usually added to enhance reduction of laterite ores. The feasibility of co-reduction roasting of a saprolitic laterite ore and red mud was investigated. Results show that the red mud addition promoted the reduction of the saprolitic laterite ore and the iron ores in the red mud were co-reduced and recovered. By adding 35wt% red mud, the nickel grade and recovery were 4.90wt% and 95.25wt%, and the corresponding iron grade and total recovery were 71.00wt% and 93.77wt%, respectively. The X-ray diffraction (XRD), scanning electron microscopy, and energy dispersive spectroscopy (SEM-EDS) analysis results revealed that red mud addition was helpful to increase the liquid phase and ferronickel grain growth. The chemical compositions "CaO and Na2O" in the red mud replaced FeO to react with SiO2 and MgSiO3 to form augite.

Identification of mud crab reovirus VP12 and its interaction with the voltage-dependent anion-selective channel protein of mud crab Scylla paramamosain.

PubMed

Xu, Hai-Dong; Su, Hong-Jun; Zou, Wei-Bin; Liu, Shan-Shan; Yan, Wen-Rui; Wang, Qian-Qian; Yuan, Li-Li; Chan, Siuming Francis; Yu, Xiao-Qiang; He, Jian-Guo; Weng, Shao-Ping

2015-05-01

Mud crab reovirus (MCRV) is the causative agent of a severe disease in cultured mud crab (Scylla paramamosain), which has caused huge economic losses in China. MCRV is a double-stranded RNA virus with 12 genomic segments. In this paper, SDS-PAGE, mass spectrometry and Western blot analyses revealed that the VP12 protein encoded by S12 gene is a structural protein of MCRV. Immune electron microscopy assay indicated that MCRV VP12 is a component of MCRV outer shell capsid. Yeast two hybrid cDNA library of mud crab was constructed and mud crab voltage-dependent anion-selective channel (mcVDAC) was obtained by MCRV VP12 screening. The full length of mcVDAC was 1180 bp with an open reading frame (ORF) of 849 bp encoding a 282 amino acid protein. The mcVDAC had a constitutive expression pattern in different tissues of mud crab. The interaction between MCRV VP12 and mcVDAC was determined by co-immunoprecipitation assay. The results of this study have provided an insight on the mechanisms of MCRV infection and the interactions between the virus and mud crab. Copyright © 2015 Elsevier Ltd. All rights reserved.

Radiochemical analysis of waters and mud of Euganean spas (Padua)

NASA Astrophysics Data System (ADS)

Cantaluppi, C.; Fasson, A.; Ceccotto, F.; Cianchi, A.; Degetto, S.

2012-04-01

The area around the Euganean Hills (North-East Italy) is concerned with thermal phenomena known and used for therapeutic purposes since ancient times. The thermal waters collected in this area have taken up a natural radionuclides content due to the leaching of hot and permeable deep rocks, with which they come into contact, before their rising to the surface. During the "maturation" process of the mud used for treatment purposes, the thermal waters make happen a complex series of biochemical changes and release a series of chemical species to the mud, resulting, in particular, in an enrichment phenomenon for some radionuclides. In this work, the first radiochemical analysis extended to all the Euganean Thermal District is reported. In particular, chemical analyses of mud, as well as radiochemical analyses of both mud and waters were performed; the enrichment of the radioisotopes in mud used for treatments was also documented. The results show that the 226Ra content in mud, during the "maturation" process, presents an enrichment even of one order of magnitude with respect to the value found in the unprocessed mud. Furthermore, in the same thermal waters, high concentrations of "unsupported" 222Rn have been found, which have shown to be not completely negligible both for people under treatment and particularly for spa workers.

Hollow Nodules Gas Escape Sedimentary Structures in Lacustrine Deposits on Earth and Gale Crater

NASA Astrophysics Data System (ADS)

Bonaccorsi, R.; Willson, D.; Fairen, A. G.; Baker, L.; McKay, C.; Zent, A.; Mahaffy, P. R.

2015-12-01

Curiosity's Mastcam and MAHLI instruments in Gale Crater (GC) imaged mm-sized circular rimmed hollow nodules (HNs) (Figure 1A), pitting the Sheepbed mudstone of Yellowknife Bay Formation [1,2]. HNs are significantly smaller than the solid nodules within the outcrop, with an external mean diameter of 1.2 mm and an interior one of 0.7 mm [2] Several formation mechanisms of HNs have been discussed, such as: (1) Diagenetic dissolution of soluble mineral phases; or, (2) Gas bubbles released shortly after sediment deposition [1-3]. In an ephemeral pond in Ubehebe Crater (Death Valley, CA) we observed the formation of hollow nodule sedimentary structures produced by gas bubbles (Figure 1C) preserved in smectite-rich mud that are strikingly similar to those imaged in GC (Figure 1A). This finding supports the gas bubble hypothesis [2]. Ubehebe Crater (UC) surface sediment hollow nodules were sampled, imaged, and their internal diameter measured (200 hollow structures) showing similar shape, distribution, and composition to those imaged by Curiosity in GC. UC in-situ observations suggest the gas bubbles were generated within the slightly reducing ephemerally submerged mud. These intra-crater deposits remain otherwise extremely dry year round, i.e., Air_rH ~2-5%; ground H2O wt%: 1-2%; Summer air/ground T: 45-48ºC/67-70ºC [4-5]. Data from the Sample Analysis at Mars (SAM), CheMin, and ChemCam instruments onboard the rover revealed that HNs-bearing mudstone are rich in smectite clay e.g., ~18-20% [6,7] deposited in a neutral to mildly alkaline environment, capturing a period when the surface was potentially habitable [1]. The UC HNs-hosting deposits are also rich in smectite clays (~30%) and occur in an ephemeral shallow freshwater setting [4-5]. If present, surface hollow nodules are easy to find in dry clay-rich mud in lacustrine sediments, so they could represent a new indicator of ephemeral but habitable/inhabited environments on both Earth and early Mars. References: [1] Grotzinger J.P. et al. (2014), Science 343, 124277. [2] Stack et al. (2014) JGR,Planets 119343. [4] Bonaccorsi R. et al. (2012) AGU Fall Meeting, Abstract #P11B-1839. [5] Bonaccorsi, R. et al. (2014) AGU Fall Meeting, Paper #EP53A-3632. [6] McLennan, S.M. et al. (2014) Science 343, 1244734. [7] Ming D.W. et al. (2014) Science, 343, 1245267.

A comprehensive sediment dynamics study of a major mud belt system on the inner shelf along an energetic coast.

PubMed

Liu, James T; Hsu, Ray T; Yang, Rick J; Wang, Ya Ping; Wu, Hui; Du, Xiaoqin; Li, Anchun; Chien, Steven C; Lee, Jay; Yang, Shouye; Zhu, Jianrong; Su, Chih-Chieh; Chang, Yi; Huh, Chih-An

2018-03-09

Globally mud areas on continental shelves are conduits for the dispersal of fluvial-sourced sediment. We address fundamental issues in sediment dynamics focusing on how mud is retained on the seabed on shallow inner shelves and what are the sources of mud. Through a process-based comprehensive study that integrates dynamics, provenance, and sedimentology, here we show that the key mechanism to keep mud on the seabed is the water-column stratification that forms a dynamic barrier in the vertical that restricts the upward mixing of suspended sediment. We studied the 1000 km-long mud belt that extends from the mouth of the Changjiang (Yangtze) River along the coast of Zhejiang and Fujian Provinces of China and ends on the west coast of Taiwan. This mud belt system is dynamically attached to the fluvial sources, of which the Changjiang River is the primary source. Winter is the constructive phase when active deposition takes place of fine-grained sediment carried mainly by the Changjiang plume driven by Zhe-Min Coastal Currents southwestward along the coast.

The Dead Sea Mud and Salt: A Review of Its Characterization, Contaminants, and Beneficial Effects

NASA Astrophysics Data System (ADS)

Bawab, Abeer Al; Bozeya, Ayat; Abu-Mallouh, Saida; Abu Irmaileh, Basha'er; Daqour, Ismail; Abu-Zurayk, Rund A.

2018-02-01

The Dead Sea has been known for its therapeutic and cosmetic properties. The unique climatic conditions in the Dead Sea area make it a renowned site worldwide for the field of climatotherapy, which is a natural approach for the provision of medications for many human diseases including unusual exclusive salt composition of the water, a special natural mud, thermal mineral springs, solar irradiation, oxygen-rich and bromine-rich haze. This review focuses on the physical, chemical, and biological characteristics of the Dead Sea mud and salts, in addition to their contaminants, allowing this review to serve as a guide to interested researchers to their risks and the importance of treatment. Beneficial effects of Dead Sea mud and salts are discussed in terms of therapy and cosmetics. Additional benefits of both Dead Sea mud and salts are also discussed, such as antimicrobial action of the mud in relation to its therapeutic properties, and the potency of mud and salts to be a good medium for the growth of a halophilic unicellular algae, used for the commercial production of β-carotene Dunaliella.

Removal of Organophosphorus Pesticides from Aqueous Solution by Magnetic Fe3O4/Red Mud-Nanoparticles.

PubMed

Aydin, Senar

2016-12-01

  The aim of this study was to investigate the usability of magnetic Fe3O4/red mud nanoparticles (NPs) for the removal of organophosphorus pesticides from water samples. The effect of various experimental parameters such as red mud amount in Fe3O4/red mud-NPs, pH, contact time, initial pesticide concentrations and adsorbent dose was studied in order to find the optimum conditions for their removal in a batch process. The Fe3O4/red mud-NPs were characterized by using TGA, SEM, XRD, VSM, and determination of the BET surface area. After the regenerated Fe3O4/red mud-NPs were used three times, the sorption capacity and the magnetic separability were observed to be unaffected. Freundlich model described the sorption process better than Langmuir isotherm and the pseudo second-order kinetic model was determined as the best-fit model. The film diffusion mechanism was found to be a main rate control mechanism. The Fe3O4/red mud-NPs satisfactorily removed the OPPS from real water samples.

Radiological restrictions of using red mud as building material additive.

PubMed

Gu, Hannian; Wang, Ning; Liu, Shirong

2012-09-01

Red mud remains as residue from the processing of bauxite using different methods. The chemical composition of red mud varies widely with respect to the types of bauxite ore and processing parameters. Red mud samples from Guizhou, China, were investigated using a X-ray fluorescence spectroscope, a quadrupole inductively coupled plasma mass spectrometer and a electron probe micro-analyzer. The results showed that red mud consisted of eight main chemical components--CaO, Al(2)O(3), SiO(2), Fe(2)O(3), TiO(2), Na(2)O, K(2)O and MgO--and dozens of trace elements, including natural radioactive elements, such as uranium and thorium. Gamma spectrometric analysis showed that the values of internal exposure index I (Ra) and external exposure index I (γ) of Guizhou red mud were 1.1-2.4 and 2.3-3.5 respectively. Thus, it should not be used as a main building material indiscriminately. The amount of red mud from Guizhou when it is used for main building materials in China should be less than 28-44%.

Utilization of drilling cuttings with extraction of ground for recultivation of disturbed soils

NASA Astrophysics Data System (ADS)

Gaevaya, E. V.; Bogaychuk, Y. E.; Tarasova, S. S.; Skipin, L. N.; Zakharova, E. V.

2017-10-01

Drilling of wells is connected with formation of the bore mud represented by the drill cutting with waste drilling mud. Bore mud has negative physical-chemical, physical and chemical properties: high content of salts, increased alkalinity, ash structure, soil overcrust, low airing, weak filterability and so on. In case of phosphogypsum adding to the bore mud, pH level decreases from the alkaline (10.5 U) to weakly alkaline 7.6 U, decrease of pH is connected with the influence of phosphogypsum acidity and neutralization of the more mud. Concentration of chloride ions and sulphate ions in reclaimed bore mud was 70±7 and 456±46 correspondingly. Presence of oil products in received soil was 198.0-219.0 mg/kg. When adding phosphogypsum, sand, sorbent and humic formulation «Rostok» to the bore mud, it has shown good germinating ability of cultures- phytomeliorants (93,3%). 100% germinating ability was observed in meadow grass with a height of overground sprouts 10.7 cm, germinating ability of red fescue was 80% with height of overground sprouts 9.6 cm.

Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex.

PubMed

Fagerlund, Robert D; Wilkinson, Max E; Klykov, Oleg; Barendregt, Arjan; Pearce, F Grant; Kieper, Sebastian N; Maxwell, Howard W R; Capolupo, Angela; Heck, Albert J R; Krause, Kurt L; Bostina, Mihnea; Scheltema, Richard A; Staals, Raymond H J; Fineran, Peter C

2017-06-27

CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas1 4 -Cas2-3 2 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.

Broadband Scattering from Sand and Sand/Mud Sediments with Extensive Environmental Characterization

DTIC Science & Technology

2015-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Broadband Scattering from Sand and Sand/ Mud Sediments...TERM GOALS To model the effects of volume heterogeneities, both discrete and continuous, in scattering from sand and mud sediments. A better...IMP2 has been used extensively during TREX13 and BayEx14 to measure the porosity in both sand and mud sediments. Analysis of this recent data inspired a

New technology of extracting the amount of rare earth metals from the red mud

NASA Astrophysics Data System (ADS)

Martoyan, G. A.; Karamyan, G. G.; Vardan, G. A.

2016-01-01

The paper outlined the environmental and economic problems associated with red mud - the waste generated in processing of bauxite ore for aluminum production. The chemical analysis of red mud has identified a number of useful elements including rare earth metals. The electromembrane technology of red mud processing with extraction of valuable elements is described. A possible scheme of separation of these metals through electrolysis is also given.

Characterization of a Mud Deposit Offshore of the Patos Lagoon, Southern Brazil

DTIC Science & Technology

2009-02-01

Journal Article 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Characterization of mud deposit offshore of the Patos lagoon, southern Brazil 5a...deposition of mud on the beach along the shoreface of Rio Grande do Sul, Brazil dramatically influences the normal operations in the littoral zone...Continental Shelf Research journal homepage: www.elsevier.com/locate/csr Characterization of a mud deposit offshore of the Patos Lagoon, southern Brazil

Bioleaching of rare earth and radioactive elements from red mud using Penicillium tricolor RM-10.

PubMed

Qu, Yang; Lian, Bin

2013-05-01

The aim of this work is to investigate biological leaching of rare earth elements (REEs) and radioactive elements from red mud, and to evaluate the radioactivity of the bioleached red mud used for construction materials. A filamentous, acid-producing fungi named RM-10, identified as Penicillium tricolor, is isolated from red mud. In our bioleaching experiments by using RM-10, a total concentration of 2% (w/v) red mud under one-step bioleaching process was generally found to give the maximum leaching ratios of the REEs and radioactive elements. However, the highest extraction yields are achieved under two-step bioleaching process at 10% (w/v) pulp density. At pulp densities of 2% and 5% (w/v), red mud processed under both one- and two-step bioleaching can meet the radioactivity regulations in China. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mud volcanoes of trinidad as astrobiological analogs for martian environments.

PubMed

Hosein, Riad; Haque, Shirin; Beckles, Denise M

2014-10-13

Eleven onshore mud volcanoes in the southern region of Trinidad have been studied as analog habitats for possible microbial life on Mars. The profiles of the 11 mud volcanoes are presented in terms of their physical, chemical, mineralogical, and soil properties. The mud volcanoes sampled all emitted methane gas consistently at 3% volume. The average pH for the mud volcanic soil was 7.98. The average Cation Exchange Capacity (CEC) was found to be 2.16 kg/mol, and the average Percentage Water Content was 34.5%. Samples from three of the volcanoes, (i) Digity; (ii) Piparo and (iii) Devil's Woodyard were used to culture bacterial colonies under anaerobic conditions indicating possible presence of methanogenic microorganisms. The Trinidad mud volcanoes can serve as analogs for the Martian environment due to similar geological features found extensively on Mars in Acidalia Planitia and the Arabia Terra region.

Mud Volcanoes of Trinidad as Astrobiological Analogs for Martian Environments

PubMed Central

Hosein, Riad; Haque, Shirin; Beckles, Denise M.

2014-01-01

Eleven onshore mud volcanoes in the southern region of Trinidad have been studied as analog habitats for possible microbial life on Mars. The profiles of the 11 mud volcanoes are presented in terms of their physical, chemical, mineralogical, and soil properties. The mud volcanoes sampled all emitted methane gas consistently at 3% volume. The average pH for the mud volcanic soil was 7.98. The average Cation Exchange Capacity (CEC) was found to be 2.16 kg/mol, and the average Percentage Water Content was 34.5%. Samples from three of the volcanoes, (i) Digity; (ii) Piparo and (iii) Devil’s Woodyard were used to culture bacterial colonies under anaerobic conditions indicating possible presence of methanogenic microorganisms. The Trinidad mud volcanoes can serve as analogs for the Martian environment due to similar geological features found extensively on Mars in Acidalia Planitia and the Arabia Terra region. PMID:25370529

Structural characteristics of cohesive flow deposits, and a sedimentological approach on their flow mechanisms.

NASA Astrophysics Data System (ADS)

Tripsanas, E. K.; Bryant, W. R.; Prior, D. B.

2003-04-01

A large number of Jumbo Piston cores (up to 20 m long), acquired from the continental slope and rise of the Northwest Gulf of Mexico (Bryant Canyon area and eastern Sigsbee Escarpment), have recovered various mass-transport deposits. The main cause of slope instabilities over these areas is oversteepening of the slopes due to the seaward mobilization of the underlying allochthonous salt masses. Cohesive flow deposits were the most common recoveries in the sediment cores. Four types of cohesive flow deposits have been recognized: a) fluid debris flow, b) mud flow, c) mud-matrix dominated debris flow, and d) clast-dominated debris flow deposits. The first type is characterized by its relatively small thickness (less than 1 m), a mud matrix with small (less than 0.5 cm) and soft mud-clasts, and a faint layering. The mud-clasts reveal a normal grading and become more abundant towards the base of each layer. That reveals that their deposition resulted by several successive surges/pulses, developed in the main flow, than the sudden “freezing” of the whole flow. The main difference between mud flow and mud-matrix dominated debris flow deposits is the presence of small to large mud-clasts in the later. Both deposits consist of a chaotic mud-matrix, and a basal shear laminated zone, where the strongest shearing of the flow was exhibited. Convolute laminations, fault-like surfaces, thrust faults, and microfaults are interpreted as occurring during the “freezing” of the flows and/or by adjustments of the rested deposits. Clast-dominated debris flow deposits consist of three zones: a) an upper plug-zone, characterized by large interlocked clasts, b) a mid-zone, of higher reworked, inversely graded clasts, floating in a mud-matrix, and c) a lower shear laminated zone. The structure of the last three cohesive flow deposits indicate that they represent deposition of typical Bingham flows, consisting of an upper plug-zone in which the yield stress is not exceeded and an underlain shearing zone, where the shear stress exceeded the yield strength of the sediments. Mud-matrix, and clast-dominated debris flow deposits are the pervasive ones. Intensely sheared thin layers (5- to 20 cm) with sharp bases, displayed as successive layers at the base of mud/debris flow deposits, or as isolated depositional units interbedded in hemipelagic sediments, are as interesting, as enigmatic. They are interpreted as basal self-lubricating layers, of having high shear stress and pore pressures, over which the mud/debris flows were able to travel for very long distances.

Transcriptome analysis of mud crab (Scylla paramamosain) gills in response to Mud crab reovirus (MCRV).

PubMed

Liu, Shanshan; Chen, Guanxing; Xu, Haidong; Zou, Weibin; Yan, Wenrui; Wang, Qianqian; Deng, Hengwei; Zhang, Heqian; Yu, Guojiao; He, Jianguo; Weng, Shaoping

2017-01-01

Mud crab (Scylla paramamosain) is an economically important marine cultured species in China's coastal area. Mud crab reovirus (MCRV) is the most important pathogen of mud crab, resulting in large economic losses in crab farming. In this paper, next-generation sequencing technology and bioinformatics analysis are used to study transcriptome differences between MCRV-infected mud crab and normal control. A total of 104.3 million clean reads were obtained, including 52.7 million and 51.6 million clean reads from MCRV-infected (CA) and controlled (HA) mud crabs respectively. 81,901, 70,059 and 67,279 unigenes were gained respectively from HA reads, CA reads and HA&CA reads. A total of 32,547 unigenes from HA&CA reads called All-Unigenes were matched to at least one database among Nr, Nt, Swiss-prot, COG, GO and KEGG databases. Among these, 13,039, 20,260 and 11,866 unigenes belonged to the 3, 258 and 25 categories of GO, KEGG pathway, and COG databases, respectively. Solexa/Illumina's DGE platform was also used, and about 13,856 differentially expressed genes (DEGs), including 4444 significantly upregulated and 9412 downregulated DEGs were detected in diseased crabs compared with the control. KEGG pathway analysis revealed that DEGs were obviously enriched in the pathways related to different diseases or infections. This transcriptome analysis provided valuable information on gene functions associated with the response to MCRV in mud crab, as well as detail information for identifying novel genes in the absence of the mud crab genome database. Copyright © 2016. Published by Elsevier Ltd.

Neutralization of red mud with pickling waste liquor using Taguchi's design of experimental methodology.

PubMed

Rai, Suchita; Wasewar, Kailas L; Lataye, Dilip H; Mishra, Rajshekhar S; Puttewar, Suresh P; Chaddha, Mukesh J; Mahindiran, P; Mukhopadhyay, Jyoti

2012-09-01

'Red mud' or 'bauxite residue', a waste generated from alumina refinery is highly alkaline in nature with a pH of 10.5-12.5. Red mud poses serious environmental problems such as alkali seepage in ground water and alkaline dust generation. One of the options to make red mud less hazardous and environmentally benign is its neutralization with acid or an acidic waste. Hence, in the present study, neutralization of alkaline red mud was carried out using a highly acidic waste (pickling waste liquor). Pickling waste liquor is a mixture of strong acids used for descaling or cleaning the surfaces in steel making industry. The aim of the study was to look into the feasibility of neutralization process of the two wastes using Taguchi's design of experimental methodology. This would make both the wastes less hazardous and safe for disposal. The effect of slurry solids, volume of pickling liquor, stirring time and temperature on the neutralization process were investigated. The analysis of variance (ANOVA) shows that the volume of the pickling liquor is the most significant parameter followed by quantity of red mud with 69.18% and 18.48% contribution each respectively. Under the optimized parameters, pH value of 7 can be achieved by mixing the two wastes. About 25-30% of the total soda from the red mud is being neutralized and alkalinity is getting reduced by 80-85%. Mineralogy and morphology of the neutralized red mud have also been studied. The data presented will be useful in view of environmental concern of red mud disposal.

Management of fluid mud in estuaries, bays, and lakes. II: Measurement, modeling, and management

USGS Publications Warehouse

McAnally, W.H.; Teeter, A.; Schoellhamer, David H.; Friedrichs, C.; Hamilton, D.; Hayter, E.; Shrestha, P.; Rodriguez, H.; Sheremet, A.; Kirby, R.

2007-01-01

Techniques for measurement, modeling, and management of fluid mud are available, but research is needed to improve them. Fluid mud can be difficult to detect, measure, or sample, which has led to new instruments and new ways of using existing instruments. Multifrequency acoustic fathometers sense neither density nor viscosity and are, therefore, unreliable in measuring fluid mud. Nuclear density probes, towed sleds, seismic, and drop probes equipped with density meters offer the potential for accurate measurements. Numerical modeling of fluid mud requires solving governing equations for flow velocity, density, pressure, salinity, water surface, plus sediment submodels. A number of such models exist in one-, two-, and three-dimensional form, but they rely on empirical relationships that require substantial site-specific validation to observations. Management of fluid mud techniques can be classified as those that accomplish: Source control, formation control, and removal. Nautical depth, a fourth category, defines the channel bottom as a specific fluid mud density or alternative parameter as safe for navigation. Source control includes watershed management measures to keep fine sediment out of waterways and in-water measures such as structures and traps. Formation control methods include streamlined channels and structures plus other measures to reduce flocculation and structures that train currents. Removal methods include the traditional dredging and transport of dredged material plus agitation that contributes to formation control and/or nautical depth. Conditioning of fluid mud by dredging and aerating offers the possibility of improved navigability. Two examples—the Atchafalaya Bar Channel and Savannah Harbor—illustrate the use of measurements and management of fluid mud.

The protein network surrounding the human telomere repeat binding factors TRF1, TRF2, and POT1

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

Giannone, Richard J; McDonald, W Hayes; Hurst, Gregory

Telomere integrity (including telomere length and capping) is critical in overall genomic stability. Telomere repeat binding factors and their associated proteins play vital roles in telomere length regulation and end protection. In this study, we explore the protein network surrounding telomere repeat binding factors, TRF1, TRF2, and POT1 using dual-tag affinity purification in combination with multidimensional protein identification technology liquid chromatography - tandem mass spectrometry (MudPIT LC-MS/MS). After control subtraction and data filtering, we found that TRF2 and POT1 co-purified all six members of the telomere protein complex, while TRF1 identified five of six components at frequencies that lend evidencemore » towards the currently accepted telomere architecture. Many of the known TRF1 or TRF2 interacting proteins were also identified. Moreover, putative associating partners identified for each of the three core components fell into functional categories such as DNA damage repair, ubiquitination, chromosome cohesion, chromatin modification/remodeling, DNA replication, cell cycle and transcription regulation, nucleotide metabolism, RNA processing, and nuclear transport. These putative protein-protein associations may participate in different biological processes at telomeres or, intriguingly, outside telomeres.« less

DEAF-1 regulates immunity gene expression in Drosophila.

PubMed

Reed, Darien E; Huang, Xinhua M; Wohlschlegel, James A; Levine, Michael S; Senger, Kate

2008-06-17

Immunity genes are activated in the Drosophila fat body by Rel and GATA transcription factors. Here, we present evidence that an additional regulatory factor, deformed epidermal autoregulatory factor-1 (DEAF-1), also contributes to the immune response and is specifically important for the induction of two genes encoding antimicrobial peptides, Metchnikowin (Mtk) and Drosomycin (Drs). The systematic mutagenesis of a minimal Mtk 5' enhancer identified a sequence motif essential for both a response to LPS preparations in S2 cells and activation in the larval fat body in response to bacterial infection. Using affinity chromatography coupled to multidimensional protein identification technology (MudPIT), we identified DEAF-1 as a candidate regulator. DEAF-1 activates the expression of Mtk and Drs promoter-luciferase fusion genes in S2 cells. SELEX assays and footprinting data indicate that DEAF-1 binds to and activates Mtk and Drs regulatory DNAs via a TTCGGBT motif. The insertion of this motif into the Diptericin (Dpt) regulatory region confers DEAF-1 responsiveness to this normally DEAF-1-independent enhancer. The coexpression of DEAF-1 with Dorsal, Dif, and Relish results in the synergistic activation of transcription. We propose that DEAF-1 is a regulator of Drosophila immunity.

Sedimentary Facies and Stratigraphy of the Changjiang (Yangtze River) Delta

NASA Astrophysics Data System (ADS)

Dalrymple, R. W.; Zhang, X.; Lin, C. M.

2017-12-01

A disproportionate number of the world's largest deltas are tide-dominated or strongly tide-influenced, in part because the low gradient of these rivers allows the tide to penetrate far inland, generating strong tidal currents at the river mouth. These deltas also tend to be mud-dominated because a significant fraction of the bedload is trapped farther inland. Despite their great importance as sediment depo-centers, as analogues for ancient sedimentary successions, and as areas of intense human occupation, they are the most poorly understood coastal system. The Changjiang (Yangtze River), the 4th largest river in the world in terms of sediment discharge, is one such tide-dominated system, with a mean tidal range of 2.7 m and tidal-current speeds of 1 m/s at its mouth. It shows a fairly typical series of low-relief channels and bars in the mouth-bar area and passes seaward and down-drift into a coastal mud belt that extends 800 km to the south of the river mouth. The deposits from both the transgressive-phase and modern delta are all dominated by mud, except for the fluvial-channel deposits that are clean sand. Channel-floor deposits in areas with appreciable tidal influence contain abundant fluid-mud layers (1-3 cm thick), intercalated with relatively coarse sand; such mud layers show evidence of tidal cyclicity. The overlying tidal-bar deposits commonly become sandier upward because of the upward loss of fluid-mud layers. The tidal channels and bars that characterize the mouth-bar and delta-front area are dominated by randomly organized structureless mud layers, 5-30 cm thick, that are interpreted to be storm-generated fluid-mud deposits. These mud layers become less abundant upward, generating upward-sanding successions. These facies are very similar to those seen in the Amazon and Fly River deltas, suggesting that this is a common motif, and indicating the importance of fluid mud in the dynamics of such systems. Facies proximality can be determined by careful comparison of sand-size trends, tidal mud-layer thicknesses (relative to the turbidity maximum) and the abundance of wave-generated fluid-mud layers. Application of these concepts shows that the transgressive phase of the delta consists of three retrogradationally stacked parasequences, each 7-15 m thick, overlain by the 40 m-thick highstand delta.

Effect of formulation variables on the physical properties and stability of Dead Sea mud masks.

PubMed

Shahin, Sawsan; Hamed, Saja; Alkhatib, Hatim S

2015-01-01

The physical stability of Dead Sea mud mask formulations under different conditions and their rheological properties were evaluated as a function of the type and level of thickeners, level of the humectant, incorporation of ethanol, and mode of mud treatment. Formulations were evaluated in terms of visual appearance, pH, moisture content, spreadability, extrudability, separation, rate of drying at 32 degrees C, and rheological properties. Prepared mud formulations and over-the-shelf products showed viscoplastic shear thinning behavior; satisfactory rheological behavior was observed with formulations containing a total concentration of thickeners less than 10% (w/w). Casson and Herschel-Bulkley models were found the most suitable to describe the rheological data of the prepared formulations. Thickener incorporation decreased phase separation and improved formulation stability. Bentonite incorporation in the mud prevented color changes during stability studies while glycerin improved spreadability. Addition of 5% (w/w) ethanol improved mud extrudability, slightly increased percent separation, accelerated drying at 32 degrees C, and decreased viscosity and yield stress values. Different mud treatment techniques did not cause a clear behavioral change in the final mud preparation. B10G and K5B5G were labeled as "best formulas" based on having satisfactory physical and aesthetic criteria investigated in this study, while other formulations failed in one or more of the tests we have performed.

Anatomy Of The ‘LuSi’ Mud Eruption, East Java

NASA Astrophysics Data System (ADS)

Tingay, M. R.

2009-12-01

Early in the morning of the 29th of May 2006, hot mud started erupting from the ground in the densely populated Porong District of Sidoarjo, East Java. With initial flow rates of ~5000 cubic meters per day, the mud quickly inundated neighbouring villages. Over two years later and the ‘Lusi’ eruption has increased in strength, expelling over 90 million cubic meters of mud at an average rate of approximately 100000 cubic meters per day. The mud flow has now covered over 700 hectares of land to depths of over 25 meters, engulfing a dozen villages and displacing approximately 40000 people. In addition to the inundated areas, other areas are also at risk from subsidence and distant eruptions of gas. However, efforts to stem the mud flow or monitor its evolution are hampered by our overall lack of knowledge and consensus on the subsurface anatomy of the Lusi mud volcanic system. In particular, the largest and most significant uncertainties are the source of the erupted water (shales versus deep carbonates), the fluid flow pathways (purely fractures versus mixed fracture and wellbore) and disputes over the subsurface geology (nature of deep carbonates, lithology of rocks between shale and carbonates). This study will present and overview of the anatomy of the Lusi mud volcanic system with particular emphasis on these critical uncertainties and their influence on the likely evolution of disaster.

Post-Transplantation Cyclophosphamide-Based Haploidentical Transplantation as Alternative to Matched Sibling or Unrelated Donor Transplantation for Hodgkin Lymphoma: A Registry Study of the Lymphoma Working Party of the European Society for Blood and Marrow Transplantation.

PubMed

Martínez, Carmen; Gayoso, Jorge; Canals, Carmen; Finel, Hervé; Peggs, Karl; Dominietto, Alida; Castagna, Luca; Afanasyev, Boris; Robinson, Stephen; Blaise, Didier; Corradini, Paolo; Itälä-Remes, Maija; Bermúdez, Arancha; Forcade, Edouard; Russo, Domenico; Potter, Michael; McQuaker, Grant; Yakoub-Agha, Ibrahim; Scheid, Christof; Bloor, Adrian; Montoto, Silvia; Dreger, Peter; Sureda, Anna

2017-10-20

Purpose To compare the outcome of patients with Hodgkin lymphoma who received post-transplantation cyclophosphamide-based haploidentical (HAPLO) allogeneic hematopoietic cell transplantation with the outcome of patients who received conventional HLA-matched sibling donor (SIB) and HLA-matched unrelated donor (MUD). Patients and Methods We retrospectively evaluated 709 adult patients with Hodgkin lymphoma who were registered in the European Society for Blood and Marrow Transplantation database who received HAPLO (n = 98), SIB (n = 338), or MUD (n = 273) transplantation. Results Median follow-up of survivors was 29 months. No differences were observed between groups in the incidence of acute graft-versus-host disease (GVHD). HAPLO was associated with a lower risk of chronic GVHD (26%) compared with MUD (41%; P = .04). Cumulative incidence of nonrelapse mortality at 1 year was 17%, 13%, and 21% in HAPLO, SIB, and MUD, respectively, and corresponding 2-year cumulative incidence of relapse or progression was 39%, 49%, and 32%, respectively. On multivariable analysis, relative to SIB, nonrelapse mortality was similar in HAPLO ( P = .26) and higher in MUD ( P = .003), and risk of relapse was lower in both HAPLO ( P = .047) and MUD ( P < .001). Two-year overall survival and progression-free survival were 67% and 43% for HAPLO, 71% and 38% for SIB, and 62% and 45% for MUD, respectively. There were no significant differences in overall survival or progression-free survival between HAPLO and SIB or MUD. The rate of the composite end point of extensive chronic GVHD and relapse-free survival was significantly better for HAPLO (40%) compared with SIB (28%; P = .049) and similar to MUD (38%; P = .59). Conclusion Post-transplantation cyclophosphamide-based HAPLO transplantation results in similar survival outcomes compared with SIB and MUD, which confirms its suitability when no conventional donor is available. Our results also suggest that HAPLO results in a lower risk of chronic GVHD than MUD transplantation.

Sodium-dependent phosphate cotransporters and phosphate-induced calcification of vascular smooth muscle cells: Redundant roles for PiT-1 and PiT-2

PubMed Central

Crouthamel, Matthew H.; Lau, Wei Ling; Leaf, Elizabeth M.; Chavkin, Nick; Wallingford, Mary C.; Peterson, Danielle F.; Li, Xianwu; Liu, Yonggang; Chin, Michael T.; Levi, Moshe; Giachelli, Cecilia M.

2014-01-01

Objective Elevated serum phosphate has emerged as a major risk factor for vascular calcification. The sodium-dependent phosphate cotransporter, PiT-1, was previously shown to be required for phosphate-induced osteogenic differentiation and calcification of cultured human VSMCs, but its importance in vascular calcification in vivo, as well as the potential role of its homologue, PiT-2, have not been determined. We investigated the in vivo requirement for PiT-1 in vascular calcification using a mouse model of chronic kidney disease, and the potential compensatory role of PiT-2 using in vitro knockdown and over-expression strategies. Approach and Results Mice with targeted deletion of PiT-1 in VSMCs were generated (PiT-1Δsm). PiT-1 mRNA levels were undetectable whereas PiT-2 mRNA levels were increased 2 fold in the vascular aortic media of PiT-1Δsm compared to PiT-1flox/flox control. When arterial medial calcification was induced in PiT-1Δsm and PiT-1flox/flox by chronic kidney disease followed by dietary phosphate loading, the degree of aortic calcification was not different between genotypes, suggesting compensation by PiT-2. Consistent with this possibility, VSMCs isolated from PiT-1Δsm mice had no PiT-1 mRNA expression, increased PiT-2 mRNA levels, and no difference in sodium-dependent phosphate uptake or phosphate-induced matrix calcification compared to PiT-1flox/flox VSMCs. Knockdown of PiT-2 decreased phosphate uptake and phosphate-induced calcification of PiT-1Δsm VSMCs. Furthermore, over-expression of PiT-2 restored these parameters in human PiT-1-deficient VSMCs. Conclusions PiT-2 can mediate phosphate uptake and calcification of VSMCs in the absence of PiT-1. Mechanistically, PiT-1 and PiT-2 appear to serve redundant roles in phosphate-induced calcification of vascular smooth muscle cells. PMID:23968976

Post-Closure Inspection Report for the Tonopah Test Range, Nevada: For Calendar Year 2017, Revision 0

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

Alvarado, Juan; Matthews, Patrick

This report provides the results of the annual post-closure inspections conducted at the closed corrective action units (CAUs) located on the Tonopah Test Range (TTR) and the Nevada Test and Training Range (NTTR). This report covers calendar year 2017 and includes visual inspection and repair activities completed at the following CAUs: CAU 400: Bomblet Pit and Five Points Landfill (TTR) CAU 407: Roller Coaster RadSafe Area (TTR) CAU 424: Area 3 Landfill Complexes (TTR) CAU 453: Area 9 UXO Landfill (TTR) CAU 487: Thunderwell Site (TTR) Visual inspections were conducted according to the post-closure plans in the approved closure reportsmore » and subsequent correspondence with the Nevada Division of Environmental Protection. The annual post-closure inspections were conducted on May 23, 2017. No maintenance or repair issues were noted at CAU 400 and CAU 487. Maintenance items and subsequent repairs include the following: CAU 407: A large animal burrow was observed in the southeast corner of the cover during the inspection. Two additional animal burrows were discovered during repair actions. All cover defects were repaired on January 9, 2018. CAU 424: CAS 03-08-002-A304 (Landfill Cell A3-4): A new monument was installed and the subsidence area was repaired on January 9, 2018. CAU 424: CAS 03-08-002-A308 (Landfill Cell A3-8): Lava rock, used to mark the two eastern monument locations, was noted as missing during the inspection. The lava rock was replaced on January 9, 2018. CAU 453: Five large animal burrows, located near the east–central portion of cover, was noted during the inspection. Eight additional animal burrows were discovered during repair actions. All cover defects were repaired on January 9, 2018.« less

The thermal structure of the mud diapir/volcano and its influence on gas hydrate stability in northern South China Sea

NASA Astrophysics Data System (ADS)

Wan, Z.; Xu, X.; Wang, X.

2016-12-01

The mud diapir/volcano is an important indicator for gas hydrate exploration, which develops widely in continental slopes. There are many mud diapirs/volcanoes developed in northern South China Sea continental slope. Guangzhou Marine Geological Survey (GMGS) of the Chinese Ministry of Land and Resources targeted mud diapirs/volcanoes and deployed gas hydrate drilling in the Shenhu area. An obvious mud diapir developed below borehole number SH5, and bottom-simulating reflection (BSR) was also detected, but no gas hydrates were found at this borehole. We analyzed the thermal structure of mud diapirs and their relationship to the occurrence of gas hydrates. The in situ temperature at the seafloor is approximately 2.2 2.5oC in the study area. Seafloor heat flow values of SH5 is 71.4mW/m2. Temperature increases rapidly to 17oC from 40 m to 100 m and stays in the range of 17 to 19oC below 100 m. And the thermal conductivity value of SH5 is approximately 1.0 W/m·k from top to bottom. The evolution of the mud diapir/volcanoes can be divided into three stages within a continuous geological process controlling the gas hydrate reservoir. During the late stage, liquid from the mud diapir/volcanoes begins to invade the gas hydrate stability zone . Because of the high unit heat capacity of liquid, the whole temperature field of the surrounding layers increases significantly when the mud diapir/volcanoes pierces upwards. This high heat flow leads to decomposition of the gas hydrates. Therefore, the reason of SH5 did not find gas hydrates may be that the mud diapir had pierced through during the late stage, leading to gas hydrate decomposition, even though there is an obvious BSR. This work was supported by Science and Technology Program of Guangzhou (No. 201607010214) and National Nature Science Foundation of China (No. 91128203,41102077).

Thermal mud maturation: organic matter and biological activity.

PubMed

Centini, M; Tredici, M R; Biondi, N; Buonocore, A; Maffei Facino, R; Anselmi, C

2015-06-01

Many of the therapeutic and cosmetic treatments offered in spas are centred on mud therapy, to moisturize the skin and prevent skin ageing and rheumatic diseases. Thermal mud is a complex matrix composed of organic and inorganic elements which contribute to its functions. It is a natural product derived from the long mixing of clay and thermal water. During its maturation, organic substances are provided by the microalgae, which develop characteristic of the composition of thermal water. The aim of this study was to identify methods for introducing objective parameters as a basis for characterizing thermal mud and assessing its efficacy. Samples of thermal mud were collected at the Saturnia spa, where there are several sulphureous pools. The maturation of the mud was evaluated by organic component determination using extractive methods and chromatographic analysis (HPLC, GC-MS, SPME). We also studied the radical scavenging activity of mud samples at different stages of maturation, in a homogeneous phase, using several tests (DPPH, ORAC, ABTS). We identified several classes of compounds: saturated and unsaturated fatty acids, hydroxyl acids, dicarboxylic acids, ketoacids, alcohols and others. SPME analysis showed the presence of various hydrocarbons compounds (C(11) -C(17)) and long-chain alcohols (C(12) -C(16)). Six or seven months seemed appropriate to complete the process of maturation, and the main effect of maturation time was the increase of lipids. Six-month mud showed the highest activity. The hydrophilic extract was more active than the lipophilic extract. The results indicate that maturation of thermal mud can be followed on the basis of the changes in its organic composition and antioxidant properties along the time. They also highlight the need to develop reference standards for thermal muds in relation to assess their use for therapeutic and cosmetic purposes. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Invasion of drilling mud into gas-hydrate-bearing sediments. Part I: effect of drilling mud properties

NASA Astrophysics Data System (ADS)

Ning, Fulong; Zhang, Keni; Wu, Nengyou; Zhang, Ling; Li, Gang; Jiang, Guosheng; Yu, Yibing; Liu, Li; Qin, Yinghong

2013-06-01

To our knowledge, this study is the first to perform a numerical simulation and analysis of the dynamic behaviour of drilling mud invasion into oceanic gas-hydrate-bearing sediment (GHBS) and to consider the effects of such an invasion on borehole stability and the reliability of well logging. As a case study, the simulation background sets up the conditions of mud temperature over hydrate equilibrium temperature and overbalanced drilling, considering the first Chinese expedition to drill gas hydrate (GMGS-1). The results show that dissociating gas may form secondary hydrates in the sediment around borehole by the combined effects of increased pore pressure (caused by mud invasion and flow resistance), endothermic cooling that accompanies hydrate dissociation compounded by the Joule-Thompson effect and the lagged effect of heat transfer in sediments. The secondary hydrate ring around the borehole may be more highly saturated than the in situ sediment. Mud invasion in GHBS is a dynamic process of thermal, fluid (mud invasion), chemical (hydrate dissociation and reformation) and mechanical couplings. All of these factors interact and influence the pore pressure, flow ability, saturation of fluid and hydrates, mechanical parameters and electrical properties of sediments around the borehole, thereby having a strong effect on borehole stability and the results of well logging. The effect is particularly clear in the borehole SH7 of GMGS-1 project. The borehole collapse and resistivity distortion were observed during practical drilling and wireline logging operations in borehole SH7 of the GMGS-1.mud density (i.e. the corresponding borehole pressure), temperature and salinity have a marked influence on the dynamics of mud invasion and on hydrate stability. Therefore, perhaps well-logging distortion caused by mud invasion, hydrate dissociation and reformation should be considered for identifying and evaluating gas hydrate reservoirs. And some suitable drilling measurements need to be adopted to reduce the risk of well-logging distortion and borehole instability.

Discovery of siderite in marine sediment: Source and effect of violent gas venting at the Tsanyao Mud Volcano, offshore SW Taiwan

NASA Astrophysics Data System (ADS)

Tseng, Y.; Lin, S.; Hsieh, I. C.; Lien, K. L.

2016-12-01

Tsanyao mud volcano is a 400 meters high, 5 kilometers in diameter, a center crater of 50 meters width activing venting mud diapir. The gigantic size of mud volcano indicate massive transportation of material, i.e., gas, fluid, and breccia from deep to the sea floor in building up the mud volcano. The mud volcano is located at the upper slope of the accretionary wedge with a surrounding water depth of about xx m, offshore Southwestern Taiwan. On shore, a series of active mud volcanos also exist in a trend similar to those found offshore. In order to understand sources of gas, fluid, solid materials and the effect of gas migration and associate authigenic mineral formation, we have obtained multibeam bathymetry, water column echo sounding, together with sediment XRD and SEM and pore water composition of methane, sulfide, sulfate, chloride, potassium, lithium, boron, and water O-18 at the study mud volcano. We have observed more than 30 flares around the main cone within a perimeter of 10 square miles. δ13C values of methane in the pore water ranged from -30 to -50 ‰. The lower C13 ratios, together with high C2+/C1 ratios demonstrated that vent gas is mostly thermogenic in origin. Higher thermal gradient and water temperature indicated that cone top is unfavorable for gas-hydrate formation, however, gas hydrate may exist at a deeper part of the mud volcano system. High concentration of sulfide presence right near the sulfate-methane interface, a result of anoxic methane oxidation. However, low concentrations of pyrite in sediments indicated that AOM did not favor pyrite formation at depth. In addition, abundant siderite were found in the sediments collected in the mud volcano cone. Rapid consumption of sulfate through AOM reaction generated a condition favor the siderite fomation, instead of the typical pyrite formation commonly observed.

Nobody’s perfect: can irregularities in pit structure influence vulnerability to cavitation?

PubMed Central

Plavcová, Lenka; Jansen, Steven; Klepsch, Matthias; Hacke, Uwe G.

2013-01-01

Recent studies have suggested that species-specific pit properties such as pit membrane thickness, pit membrane porosity, torus-to-aperture diameter ratio and pit chamber depth influence xylem vulnerability to cavitation. Despite the indisputable importance of using mean pit characteristics, considerable variability in pit structure within a single species or even within a single pit field should be acknowledged. According to the rare pit hypothesis, a single pit that is more air-permeable than many neighboring pits is sufficient to allow air-seeding. Therefore, any irregularities or morphological abnormalities in pit structure allowing air-seeding should be associated with increased vulnerability to cavitation. Considering the currently proposed models of air-seeding, pit features such as rare, large pores in the pit membrane, torus extensions, and plasmodesmatal pores in a torus can represent potential glitches. These aberrations in pit structure could either result from inherent developmental flaws, or from damage caused to the pit membrane by chemical and physical agents. This suggests the existence of interesting feedbacks between abiotic and biotic stresses in xylem physiology. PMID:24273549

Influence of dust and mud on the optical, chemical, and mechanical properties of a pv protective glass

NASA Astrophysics Data System (ADS)

Yilbas, Bekir Sami.; Ali, Haider; Khaled, Mazen M.; Al-Aqeeli, Nasser; Abu-Dheir, Numan; Varanasi, Kripa K.

2015-10-01

Recent developments in climate change have increased the frequency of dust storms in the Middle East. Dust storms significantly influence the performances of solar energy harvesting systems, particularly (photovoltaic) PV systems. The characteristics of the dust and the mud formed from this dust are examined using various analytical tools, including optical, scanning electron, and atomic force microscopies, X-ray diffraction, energy spectroscopy, and Fourier transform infrared spectroscopy. The adhesion, cohesion and frictional forces present during the removal of dry mud from the glass surface are determined using a microtribometer. Alkali and alkaline earth metal compounds in the dust dissolve in water to form a chemically active solution at the glass surface. This solution modifies the texture of the glass surface, thereby increasing the microhardness and decreasing the transmittance of the incident optical radiation. The force required to remove the dry mud from the glass surface is high due to the cohesive forces that result from the dried mud solution at the interface between the mud and the glass. The ability altering the characteristics of the glass surface could address the dust/mud-related limitations of protective surfaces and has implications for efficiency enhancements in solar energy systems.

Influence of dust and mud on the optical, chemical, and mechanical properties of a pv protective glass.

PubMed

Yilbas, Bekir Sami; Ali, Haider; Khaled, Mazen M; Al-Aqeeli, Nasser; Abu-Dheir, Numan; Varanasi, Kripa K

2015-10-30

Recent developments in climate change have increased the frequency of dust storms in the Middle East. Dust storms significantly influence the performances of solar energy harvesting systems, particularly (photovoltaic) PV systems. The characteristics of the dust and the mud formed from this dust are examined using various analytical tools, including optical, scanning electron, and atomic force microscopies, X-ray diffraction, energy spectroscopy, and Fourier transform infrared spectroscopy. The adhesion, cohesion and frictional forces present during the removal of dry mud from the glass surface are determined using a microtribometer. Alkali and alkaline earth metal compounds in the dust dissolve in water to form a chemically active solution at the glass surface. This solution modifies the texture of the glass surface, thereby increasing the microhardness and decreasing the transmittance of the incident optical radiation. The force required to remove the dry mud from the glass surface is high due to the cohesive forces that result from the dried mud solution at the interface between the mud and the glass. The ability altering the characteristics of the glass surface could address the dust/mud-related limitations of protective surfaces and has implications for efficiency enhancements in solar energy systems.

Comparative study of the thermal properties of mud and peat solutions applied in clinical practice.

PubMed

Beer, A M; Grozeva, A; Sagorchev, P; Lukanov, J

2003-11-01

Different peloids as e.g. mud and peat have been traditionally used for therapeutic purposes successfully, especially of there thermal actions. It was the aim of the experimental study to compare the thermal properties of two peloids, mud and peat, with a view to assessing their thermal effects when they are applied in clinical practice. The studies were carried out using peat of the marsh type of peats (Hochmoor), and curative Pomorie (Bulgaria) mud. As important parameters were determined the specific thermal capacity at constant pressure (Cp), the density of solutions (rho), the cooling rate (m), the coefficient of temperature transfer (a) of solutions and the coefficient of thermal conductivity (lambda) of solutions of peat and curative mud, compared to water bath. The comparative studies of the thermal properties of water and water solutions of peat and curative mud show that the thermal effect of the water bath is substantially smaller than that of the peat and mud applications. This difference is due to a greater extent to the high values of the dynamic viscosity, not allowing cooling by convection and protecting the surface of the skin upon applications of peloid solutions with a higher temperature.

Mud Volcanoes - Analogs to Martian Cones and Domes (by the Thousands!)

NASA Technical Reports Server (NTRS)

Allen, Carlton C.; Oehler, Dorothy

2010-01-01

Mud volcanoes are mounds formed by low temperature slurries of gas, liquid, sediments and rock that erupt to the surface from depths of meters to kilometers. They are common on Earth, with estimates of thousands onshore and tens of thousands offshore. Mud volcanoes occur in basins with rapidly-deposited accumulations of fine-grained sediments. Such settings are ideal for concentration and preservation of organic materials, and mud volcanoes typically occur in sedimentary basins that are rich in organic biosignatures. Domes and cones, cited as possible mud volcanoes by previous authors, are common on the northern plains of Mars. Our analysis of selected regions in southern Acidalia Planitia has revealed over 18,000 such features, and we estimate that more than 40,000 occur across the area. These domes and cones strongly resemble terrestrial mud volcanoes in size, shape, morphology, associated flow structures and geologic setting. Geologic and mineralogic arguments rule out alternative formation mechanisms involving lava, ice and impacts. We are studying terrestrial mud volcanoes from onshore and submarine locations. The largest concentration of onshore features is in Azerbaijan, near the western edge of the Caspian Sea. These features are typically hundreds of meters to several kilometers in diameter, and tens to hundreds of meters in height. Satellite images show spatial densities of 20 to 40 eruptive centers per 1000 square km. Many of the features remain active, and fresh mud flows as long as several kilometers are common. A large field of submarine mud volcanoes is located in the Gulf of Cadiz, off the Atlantic coasts of Morocco and Spain. High-resolution sonar bathymetry reveals numerous km-scale mud volcanoes, hundreds of meters in height. Seismic profiles demonstrate that the mud erupts from depths of several hundred meters. These submarine mud volcanoes are the closest morphologic analogs yet found to the features in Acidalia Planitia. We are also conducting laboratory analyses of surface samples collected from mud volcanoes in Azerbaijan, Taiwan and Japan. X-ray diffraction, visible / near infrared reflectance spectroscopy and Raman spectroscopy show that the samples are dominated by mixed-layer smectite clays, along with quartz, calcite and pyrite. Thin section analysis by optical and scanning electron microscopy confirms the mineral identifications. These samples also contain chemical and morphological biosignatures, including common microfossils, with evidence of partial replacement by pyrite. The bulk samples contain approximately 1 wt% total organic carbon and 0.4 mg / gm volatile hydrocarbons. The thousands of features in Acidalia Planitia cited as analogous to terrestrial mud volcanoes clearly represent an important element in the sedimentary record of Mars. Their location, in the distal depocenter for massive Hesperian-age floods, suggests that they contain fine-grained sediments from a large catchment area in the martian highlands. We have proposed these features as a new class of exploration target that can provide access to minimally-altered material from significant depth. By analogy to terrestrial mud volcanoes, these features may also be excellent sites for the sampling martian organics and subsurface microbial life, if such exist or ever existed.

[Effect of naphthalan and therapeutic mud applications on clinical and roentgenological characteristics in patients with protracted pneumonia].

PubMed

Rassulova, M A; Siziakova, L A; Aĭrapetova, N S

2009-01-01

The influence of application of naftalan and therapeutic muds on clinical and roentgenological parameters, external respiration function, biochemical and immunological characteristics of the inflammatory process was studied in 82 patients presenting with protracted pneumonia and compared with the outcome of therapy using no physical factors. The application of naftalan and therapeutic muds was shown to reduce activity of inflammatory processes, improve airway patency and the state ofbronchial mucosa. Naftalan produced better therapeutic effect than muds.

Triggering and dynamic evolution of the LUSI mud volcano, Indonesia

NASA Astrophysics Data System (ADS)

Mazzini, A.; Svensen, H.; Akhmanov, G. G.; Aloisi, G.; Planke, S.; Malthe-Sørenssen, A.; Istadi, B.

2007-09-01

Mud volcanoes are geologically important manifestations of vertical fluid flow and mud eruption in sedimentary basins worldwide. Their formation is predominantly ascribed to release of overpressure from clay- and organic-rich sediments, leading to impressive build-up of mud mountains in submarine and subaerial settings. Here we report on a newly born mud volcano appearing close to an active magmatic complex in a backarc sedimentary basin in Indonesia. The location of the mud volcano close to magmatic volcanoes results in a high background temperature gradient that triggers mineralogical transformations and geochemical reactions at shallow depth. The eruption of 100 °C mud and gas that started the 29th of May 2006 flooded a large area within the Sidoarjo village in Northeast Java. Thousands of people have so far been evacuated due to the mud flood hazards from the eruption. Since the initial eruption, the flow rate escalated from 5000 to 120,000 m 3/d during the first eleven weeks. Then the erupted volume started to pulsate between almost zero and 120,000 m 3/d in the period August 14 to September 10, whereas it increased dramatically following swarms of earthquakes in September, before reaching almost 180,000 m 3/d in December 2006. Sampling and observations were completed during two fieldwork campaigns on the site. The eruption of boiling water is accompanied by mud, aqueous vapour, CO 2 and CH 4. Based on geochemical and field results, we propose a mechanism where the eruptions started following the 27th of May earthquake due to fracturing and accompanied depressurization of > 100 °C pore fluids from > 1700 m depth. This resulted in the formation of a quasi-hydrothermal system with a geyser-like surface expression and with an activity influenced by the regional seismicity.

Do mud deposition events on sandy beaches affect surf zone ichthyofauna? A southern Brazilian case study

NASA Astrophysics Data System (ADS)

Mont'Alverne, Renata; Moraes, Leonardo E.; Rodrigues, Fábio L.; Vieira, João P.

2012-05-01

Using fluid mud deposition events which occur regularly at Cassino Beach in south Brazil, we evaluated the influence of such events on the structure of the ichthyofauna inhabiting its shallow surf zone. Wave action was the dominant factor in differentiating between sampling sites, being lower or even absent at the mud-influenced sectors compared to beach area without mud. Samples were collected using a beach seine net at two control locations (A1 and A2), and at three locations influenced by mud deposition (B1, B2, and B3). During the study period (21 April-04 August 2009), 15,245 fishes were captured and separated into 26 taxonomic groups, from species to family. Individuals of a total length (TL) up to 50 mm accounted for 65% of the catch, while individuals of TL < 30 mm were the most numerous and more responsible for the total abundance spatial pattern. The area with higher wave action (A2) had the lowest relative species abundance and greatest diversity, whereas the areas with mud-forced lowest wave action (B2 and B3) had the highest species abundance values. Three hypotheses were proposed to explain the higher concentration and capture of juvenile fishes at mud locations. First, longshore currents may be responsible for the displacement of juvenile aggregations toward areas of lower energy. Second, individuals may select habitats with turbid waters, which may provide greater protection from predators and increased food availability. Third, areas under the influence of fluid mud deposition show higher values of viscosity, which may reduce swimming activity and hinder the escape of juvenile fishes from nets, resulting in an increased capture of individuals compared to areas without mud.

Use of inorganic and organic wastes for in situ immobilisation of Pb and Zn in a contaminated alkaline soil.

PubMed

Zhou, Y-F; Haynes, R J; Naidu, R

2012-05-01

This study aims to examine whether addition of immobilising agents to a sandy, alkaline (pH = 8.1) soil, which had been contaminated with Pb and Zn by airborne particles from a Pb/Zn smelter, would substantially reduce metal bioavailability. The effectiveness of five waste materials (blast furnace (BF) slag, alum water treatment (WT) sludge, red mud, sugar mill mud and green waste compost) as metal immobilising agents was evaluated by incubating them with a contaminated soil for a period of 12 months at rates of 5% and 10% (w/w), after which, Rhodes grass was grown in the soils in a greenhouse study. Additions of WT sludge, BF slag and red mud reduced CaCl(2), CH(3)COOH, HCl and EDTA-extractable Zn but compost and mill mud had no appreciable immobilising effects. Additions of all amendments reduced levels of CaCl(2), CH(3)COOH and HCl-extractable Pb although concentrations of EDTA-extractable Pb remained unchanged. A sequential extraction procedure showed that additions of mill mud and compost increased the percentage of total Pb and Zn present in the oxidisable fraction whilst additions of the other materials increased the percentage present in the residual fraction. Rhodes grass yields were promoted greatly by additions of red mud, compost and particularly mill mud, and yields were negatively correlated with tissue Pb concentrations and extractable Pb. Red mud was the most effective material for lowering extractable Pb and Zn levels simultaneously while mill mud and compost were notably effective for Pb. A field evaluation in the study area is justified.

Viral infections stimulate the metabolism and shape prokaryotic assemblages in submarine mud volcanoes.

PubMed

Corinaldesi, Cinzia; Dell'Anno, Antonio; Danovaro, Roberto

2012-06-01

Mud volcanoes are geological structures in the oceans that have key roles in the functioning of the global ecosystem. Information on the dynamics of benthic viruses and their interactions with prokaryotes in mud volcano ecosystems is still completely lacking. We investigated the impact of viral infection on the mortality and assemblage structure of benthic prokaryotes of five mud volcanoes in the Mediterranean Sea. Mud volcano sediments promote high rates of viral production (1.65-7.89 × 10(9) viruses g(-1) d(-1)), viral-induced prokaryotic mortality (VIPM) (33% cells killed per day) and heterotrophic prokaryotic production (3.0-8.3 μgC g(-1) d(-1)) when compared with sediments outside the mud volcano area. The viral shunt (that is, the microbial biomass converted into dissolved organic matter as a result of viral infection, and thus diverted away from higher trophic levels) provides 49 mgC m(-2) d(-1), thus fuelling the metabolism of uninfected prokaryotes and contributing to the total C budget. Bacteria are the dominant components of prokaryotic assemblages in surface sediments of mud volcanoes, whereas archaea dominate the subsurface sediment layers. Multivariate multiple regression analyses show that prokaryotic assemblage composition is not only dependant on the geochemical features and processes of mud volcano ecosystems but also on synergistic interactions between bottom-up (that is, trophic resources) and top-down (that is, VIPM) controlling factors. Overall, these findings highlight the significant role of the viral shunt in sustaining the metabolism of prokaryotes and shaping their assemblage structure in mud volcano sediments, and they provide new clues for our understanding of the functioning of cold-seep ecosystems.

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

Guliyev, I.A.; Aliyev, A.A.; Rahmanov, R.R.

Azerbaijan is a classic region for the study of mud volcanism. Of the 700 mud volcanoes known in the world, 220 are in Azerbaijan. These are of great interest, not least in relation to oil and gas exploration since they give information on subsurface sediments beyond the reach of drilling. Mud volcanoes are clearly visible on satellite images. They are confined to structural lineaments and associated fractures. Changes in the morphology of some mud volcanoes post-eruption can be detected from a series of images pre-dating and post-dating eruptions. Mud volcanoes are notable for gradients of temperature that are by anmore » order of magnitude or a factor of 102 greater than the temperature gradients established elsewhere. The gases of mud volcanoes consist mainly of methane (95-100%). There are small amounts of C{sub 2-6}, CO{sub 2}, N{sub 2}, He and Ar. The isotopic composition of carbon (ICC) within the methane varies from -61.29. to -35.W{close_quotes} which is isotopically heavier than the methane from producing fields. The ICC of the CO{sub 2} has a very wide range (from -49.6% to +23.1%), indicating several sources of its formation. The isotopically superheavy CO{sub 2} (+5%) is especially interesting. Oils from mud volcanoes are typically severely biodegraded. Their ICC ranges from -24.76% to -28.2%. A relationship between {partial_derivative}{sup l3}C of oils and ages of accumulations has been established. Waters of mud volcanoes are lightly mineralised, containing chiefly bicarbonates and sodium. The hydrogen composition of the water is abnormally heavy. Ejected rocks from mud volcanoes range in age from Cretaceous - Pliocene. Their study suggests that deeply buried reservoirs maintain good poroperm characteristics because of relatively little catagenesis.« less

Viral infections stimulate the metabolism and shape prokaryotic assemblages in submarine mud volcanoes

PubMed Central

Corinaldesi, Cinzia; Dell'Anno, Antonio; Danovaro, Roberto

2012-01-01

Mud volcanoes are geological structures in the oceans that have key roles in the functioning of the global ecosystem. Information on the dynamics of benthic viruses and their interactions with prokaryotes in mud volcano ecosystems is still completely lacking. We investigated the impact of viral infection on the mortality and assemblage structure of benthic prokaryotes of five mud volcanoes in the Mediterranean Sea. Mud volcano sediments promote high rates of viral production (1.65–7.89 × 109 viruses g−1 d−1), viral-induced prokaryotic mortality (VIPM) (33% cells killed per day) and heterotrophic prokaryotic production (3.0–8.3 μgC g−1 d−1) when compared with sediments outside the mud volcano area. The viral shunt (that is, the microbial biomass converted into dissolved organic matter as a result of viral infection, and thus diverted away from higher trophic levels) provides 49 mgC m−2 d−1, thus fuelling the metabolism of uninfected prokaryotes and contributing to the total C budget. Bacteria are the dominant components of prokaryotic assemblages in surface sediments of mud volcanoes, whereas archaea dominate the subsurface sediment layers. Multivariate multiple regression analyses show that prokaryotic assemblage composition is not only dependant on the geochemical features and processes of mud volcano ecosystems but also on synergistic interactions between bottom-up (that is, trophic resources) and top-down (that is, VIPM) controlling factors. Overall, these findings highlight the significant role of the viral shunt in sustaining the metabolism of prokaryotes and shaping their assemblage structure in mud volcano sediments, and they provide new clues for our understanding of the functioning of cold-seep ecosystems. PMID:22170423

Mineralogic-chemical and physical characteristics of the mud in Ä°zmir (western Turkey): suitability for use in pelotherapy

NASA Astrophysics Data System (ADS)

Çelik Karakaya, Muazzez; Karakaya, Necati

2013-04-01

The study conducted on peloid used spas in İzmir city region (western part of Turkey) included the investigation of the mineralogical, physico-chemical and geochemical properties of the three types of peloid samples in order to assess the suitability of the material for healing- aesthetic-related purposes. In situ formed muds in lagoons near the Aegean Sea (named as first group) and inner swamp muds (second group) unprocessed and raw have been using therapy and thermal baths. Mud and hot springs at around the Aegean Sea have been popular since ancient times for the treatment of rheumatic diseases, musculoskeletal disorders in the region. The mineralogical characteristics of the thermal muds are in accordance with the geological origin of the material and water sources. Mineralogic composition, mineral content and morphologic properties of the samples were determined by X-ray diffraction (XRD) and scanning electron microscopy (SEM-EDS). Chemical composition of the muds and thermal waters were determined by ICP-EAS and ICP-MS. Both of the sediment is fine- to medium size-grained and composed mostly of clay minerals, partially quartz, feldspar, carbonates, and halite, and rarely gypsum. The mineralogic composition of the muds controls the physico-chemical properties of the muds. Anion e.g., Cl, Br, and SO4, contents the thermal waters of the first group is extremely different and so the springs contain a high level of sodium chloride, magnesium sulphate, and calcium bicarbonate. The water temperature is 45 oC with a pH of 6.95 and electrical conductivity (EC) is 4.5 mS/lt in the first group while 71 oC with a pH 6.58 and EC is 2.52 mS/lt in the second ones. However, major and some of the trace element concentration of the mud samples are nearly similar, As, Cd, Cu, Hg, Ni, Sb, Se, T and Zn content of the first group is exceptionally lower than the second ones. And the hazardous element concentrations are extremely higher than the pharmaceutical clay in the second group peloids and also in thermal water, the element concentrations is not acceptable limits for peloids and waters. The element concentration is sourced from active fault system and low temperature precious metal deposits in the area which is widespread the thermal water circulated in. The anion contents of the water are related to sea water interaction. BET surface areas, plasticity, adsorbing, abrasiveness, hygroscopic water and cooling kinetics the characteristics both of the muds are nearly similar. However, cation exchange capacity and viscosity properties of the second group muds are better than the second, the physico-chemical properties both of the mud material are in acceptable level to some extent. Nevertheless, the appropriate characteristics of the second group muds when compared to some commercial used mud for medicinal and aesthetic purposes, if the hazardous element concentrations regulated.

Aluminium leaching from red mud by filamentous fungi.

PubMed

Urík, Martin; Bujdoš, Marek; Milová-Žiaková, Barbora; Mikušová, Petra; Slovák, Marek; Matúš, Peter

2015-11-01

This contribution investigates the efficient and environmentally friendly aluminium leaching from red mud (bauxite residue) by 17 species of filamentous fungi. Bioleaching experiments were examined in batch cultures with the red mud in static, 7-day cultivation. The most efficient fungal strains in aluminium bioleaching were Penicillium crustosum G-140 and Aspergillus niger G-10. The A. niger G-10 strain was capable to extract up to approximately 141 mg·L(-1) of aluminium from 0.2 g dry weight red mud. Chemical leaching with organic acids mixture, prepared according to A. niger G-10 strain's respective fungal excretion during cultivation, proved that organic acids significantly contribute to aluminium solubilization from red mud. Copyright © 2015 Elsevier Inc. All rights reserved.

Red mud enhances methanogenesis with the simultaneous improvement of hydrolysis-acidification and electrical conductivity.

PubMed

Ye, Jie; Hu, Andong; Ren, Guoping; Zhou, Ting; Zhang, Guangming; Zhou, Shungui

2018-01-01

The role of red mud in the improvement of methanogenesis during sludge anaerobic digestion was innovatively investigated in this study. The results demonstrated that the addition of 20g/L red mud resulted in a 35.5% increase in methane accumulation. Red mud effectively promoted the hydrolysis-acidification of organic compounds in the sludge, which resulted in the increase of protein, polysaccharide, and VFAs by 5.1-94.5%. The activities of key enzymes were improved by 41.4-257.3%. Electrochemical measurements presented direct evidence that the electrical conductivity was significantly improved with red mud. More conductive magnetite was formed during the secondary mineralization after Fe(III) reduction by Fe (III)-reducing genes such as Clostridiaceae and Ruminococcaceae. The higher conductivity enhanced the electron transfer between the syntrophic bacteria (Geobacteraceae) and methanogens (Methanosaeta and Methanosarcina), and then improved the methanogenesis. This research provides a novel perspective on the synergism between sludge and red mud for methane production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of Environmental Dust in the Dammam Area and Mud After-Effects on Bisphenol-A Polycarbonate Sheets.

PubMed

Yilbas, Bekir Sami; Ali, Haider; Al-Aqeeli, Naseer; Khaled, Mazen M; Said, Syed; Abu-Dheir, Numan; Merah, Necar; Youcef-Toumi, Kamal; Varanasi, Kripa K

2016-04-14

Owing to recent climate changes, dust storms are increasingly common, particularly in the Middle East region. Dust accumulation and subsequent mud formation on solid surfaces in humid environments typically have adverse effects on surface properties such as optical transmittance, surface texture, and microhardness. This is usually because the mud, which contains alkaline and ionic species, adheres strongly to the surface, often through chemical bonds, and is therefore difficult to remove. In this study, environmental dust and the after-effects of mud formed on a polycarbonate sheet, which is commonly used as a protective glass in photovoltaic cells. Ionic compounds (OH(-)) are shown to significantly affect the optical, mechanical, and textural characteristics of the polycarbonate surface, and to increase the adhesion work required to remove the dry mud from the polycarbonate surface upon drying. Such ability to modify characteristics of the polycarbonate surface could address the dust/mud-related limitations of superhydrophobic surfaces.

Characterization of Environmental Dust in the Dammam Area and Mud After-Effects on Bisphenol-A Polycarbonate Sheets

PubMed Central

Yilbas, Bekir Sami.; Ali, Haider; Al-Aqeeli, Naseer; Khaled, Mazen M.; Said, Syed; Abu-Dheir, Numan; Merah, Necar; Youcef-Toumi, Kamal; Varanasi, Kripa K.

2016-01-01

Owing to recent climate changes, dust storms are increasingly common, particularly in the Middle East region. Dust accumulation and subsequent mud formation on solid surfaces in humid environments typically have adverse effects on surface properties such as optical transmittance, surface texture, and microhardness. This is usually because the mud, which contains alkaline and ionic species, adheres strongly to the surface, often through chemical bonds, and is therefore difficult to remove. In this study, environmental dust and the after-effects of mud formed on a polycarbonate sheet, which is commonly used as a protective glass in photovoltaic cells. Ionic compounds (OH−) are shown to significantly affect the optical, mechanical, and textural characteristics of the polycarbonate surface, and to increase the adhesion work required to remove the dry mud from the polycarbonate surface upon drying. Such ability to modify characteristics of the polycarbonate surface could address the dust/mud-related limitations of superhydrophobic surfaces. PMID:27076199

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

Lagunova, I.A.

A characteristic feature of the products of mud-volcano activity in the Kerch-Taman region is their high boron content. Distribution of boron in waters of mud volcanoes is characterized by restriction of anomalously high concentrations of boron to mud volcanoes actively operating at the present time in general, and to the most active period of operation of the individual volcano; there is a direct correlation between boron and the hydrocarbonate ion (r/sub B//HCO/sub 3// = 0.5), and between boron and carbon dioxide from the mud-volcano gases (r/sub B//CO/sub 2// = 0.4). The correlation is lacking between boron and mineralization, and betweenmore » boron and chlorine, the correlation is close to inverse. A spatial connection between areas of development of mud volcanism and belts of boron mineralization has been established. Anomalously high boron concentrations in the products of mud volcanism in the Kerch-Taman region are part of the overall increased boron capacity of the Crimea and the Caucasus, which has been controlled by recent magmatic activity.« less

Durability of Bricks Coated with Red mud Based Geopolymer Paste

NASA Astrophysics Data System (ADS)

Singh, Smita; Basavanagowda, S. N.; Aswath, M. U.; Ranganath, R. V.

2016-09-01

The present study is undertaken to assess the durability of concrete blocks coated with red mud - fly ash based geopolymer paste. Concrete blocks of size 200 x 200 x 100mm were coated with geopolymer paste synthesized by varying the percentages of red mud and fly ash. Uncoated concrete blocks were also tested for the durability for comparison. In thermal resistance test, the blocks were subjected to 600°C for an hour whereas in acid resistance test, they were kept in 5% sulphuric acid solution for 4 weeks. The specimens were thereafter studied for surface degradation, strength loss and weight loss. Pastes with red mud percentage greater than 50% developed lot of shrinkage cracks. The blocks coated with 30% and 50% red mud paste showed better durability than the other blocks. The use of blocks coated with red mud - fly ash geopolymer paste improves the aesthetics, eliminates the use of plaster and improves the durability of the structure.

Elastomers in mud motors for oil field applications

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

Hendrik, J.

1997-08-01

Mud motors, the most frequently used downhole drilling motors in modern drilling systems, are described in their application and function. The elastomeric liner in a mud motor acts as a huge continuous seal. Important properties of elastomers such as chemical resistance, fatigue resistance, mechanical strength, abrasion resistance, bonding to steel and processability are discussed. Advantages and disadvantages of NBR, HNBR, FKM, TFEP, and EPDM elastomers for mud motor applications are briefly described. The importance of drilling fluids and their physical and chemical impact on motor elastomers are described. Drilling fluids are categorized in: oil based-, synthetic-, and water based. Resultsmore » of compatibility tests in the different drilling muds of the presented categories demonstrate the complexity of elastomer development. Elastomers with an equally good performance in all drilling muds are not available. Future developments and improvements are directed towards higher chemical resistance at higher service temperatures. This will be possible only with improved elastomer-to-metal bonding, increased mechanical and better dynamic properties.« less

Corrective Action Plan for Corrective Action Unit 271: Areas 25, 26, and 27 Septic Systems, Nevada Test Site, Nevada

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

R. B. Jackson

2003-05-01

The Areas 25, 26 and 27 Septic Systems are in the Federal Facility Agreement and Consent Order (FFACO) of 1996 as Corrective Action Unit (CAU) 271. This Corrective Action Plan (CAP) provides selected corrective action alternatives and proposes the closure methodology for CAU 271. CAU 271 is located on the Nevada Test Site (NTS) approximately 105 kilometers (65 miles) northwest of Las Vegas, Nevada, and consists of the following 15 Corrective Action Sites (CAS): CAS 25-04-1, Septic System; CAS 25-04-03, Septic System; CAS25-04-04, Septic System; CAS 25-04-08, Septic System; CAS 25-04-09, Septic System; CAS 25-04-10, Septic System; CAS 25-04-11, Septicmore » System; CAS 26-03-01, Contaminated Water Reservoir; CAS 26-04-1, Septic System; CAS 26-04-02, Septic System; CAS 26-05-01, Radioactive Leachfield; CAS-26-05-03, Septic System; CAS 26-05-04, Septic System; CAS 26-05-05, Septic System; and CAS 27-05-02, Leachfield.« less

Cas4-Dependent Prespacer Processing Ensures High-Fidelity Programming of CRISPR Arrays.

PubMed

Lee, Hayun; Zhou, Yi; Taylor, David W; Sashital, Dipali G

2018-04-05

CRISPR-Cas immune systems integrate short segments of foreign DNA as spacers into the host CRISPR locus to provide molecular memory of infection. Cas4 proteins are widespread in CRISPR-Cas systems and are thought to participate in spacer acquisition, although their exact function remains unknown. Here we show that Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4 interacts tightly with the Cas1 integrase, forming a heterohexameric complex containing two Cas1 dimers and two Cas4 subunits. In the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Our results reveal the critical role of Cas4 in maintaining fidelity during CRISPR adaptation, providing a structural and mechanistic model for prespacer processing and integration. Copyright © 2018 Elsevier Inc. All rights reserved.

Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System.

PubMed

Ka, Donghyun; Lee, Hasup; Jung, Yi-Deun; Kim, Kyunggon; Seok, Chaok; Suh, Nayoung; Bae, Euiyoung

2016-01-05

CRISPRs and Cas proteins constitute an RNA-guided microbial immune system against invading nucleic acids. Cas1 is a universal Cas protein found in all three types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition during CRISPR-mediated adaptive immunity. Here, we report the crystal structure of Streptococcus pyogenes Cas1 (SpCas1) in a type II CRISPR-Cas system and characterize its interaction with S. pyogenes Csn2 (SpCsn2). The SpCas1 structure reveals a unique conformational state distinct from type I Cas1 structures, resulting in a more extensive dimerization interface, a more globular overall structure, and a disruption of potential metal-binding sites for catalysis. We demonstrate that SpCas1 directly interacts with SpCsn2, and identify the binding interface and key residues for Cas complex formation. These results provide structural information for a type II Cas1 protein, and lay a foundation for studying multiprotein Cas complexes functioning in type II CRISPR-Cas systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantifying Sediment Characteristics and Infilling Rate within a Ship Shoal Dredge Borrow Area, Offshore Louisiana

NASA Astrophysics Data System (ADS)

Xue, Z.; Wilson, C.; Bentley, S. J.; Xu, K.; Liu, H.; Li, C.; Miner, M. D.

2017-12-01

Barrier islands provide protection to interior wetlands and maintain estuarine gradients. Mississippi River delta plain barrier islands are undergoing rapid disintegration due to high rates of subsidence and a deficit in the coastal sand supply. To mitigate for barrier island land loss, Louisiana has implemented a restoration program that intends to supplement coastal sand deficits by introducing sand from outside of the active coastal system. Inner-shelf shoals offshore Louisiana are one of the only sand resource options containing large volumes of restoration quality sand. Ship Shoal is one of these inner-shelf shoals that was produced by marine reworking of former Mississippi River Delta barrier island sediments during late Holocene time. Though indirect effects to protected areas or infrastructure adjacent to excavations have been considered, there is a paucity of observational data on their evolution. Caminada borrow area, dredged in 2013-2016 for the Caminada Headland Restoration Project, provides a valuable opportunity to validate and improve predictive models for how borrow areas evolve. In July 2017, a subbottom and bathymetric geophysical survey was conducted and sediment cores were collected to test the hypothesis that sedimentation within the excavation is affected by lateral bedload transport after initial rapid infill as slopes equilibrate. Preliminary results show the sediment within the excavation is predominantly very fine sand with isolated mud drapes. These sediments overlay older delta complex muddy strata. This contrasts strongly with other dredge pits outside of shoal areas and closer to shore, which have been infilled largely by advection of fine suspended sediments of fluvial origin. Laboratory work on cores will include laser grain size, x-ray analyses of sedimentary structures, and radiochemistry analyses for rates and age of deposition. With the knowledge of stratigraphy and sediment dynamics surrounding the dredge pit, we can quantify and better understand the timeline of these depositional processes to provide vital knowledge to coastal managers for future borrow area design and management.

Leaching of copper and nickel in soil-water systems contaminated by bauxite residue (red mud) from Ajka, Hungary: the importance of soil organic matter.

PubMed

Lockwood, Cindy L; Stewart, Douglas I; Mortimer, Robert J G; Mayes, William M; Jarvis, Adam P; Gruiz, Katalin; Burke, Ian T

2015-07-01

Red mud is a highly alkaline (pH >12) waste product from bauxite ore processing. The red mud spill at Ajka, Hungary, in 2010 released 1 million m(3) of caustic red mud into the surrounding area with devastating results. Aerobic and anaerobic batch experiments and solid phase extraction techniques were used to assess the impact of red mud addition on the mobility of Cu and Ni in soils from near the Ajka spill site. Red mud addition increases aqueous dissolved organic carbon (DOC) concentrations due to soil alkalisation, and this led to increased mobility of Cu and Ni complexed to organic matter. With Ajka soils, more Cu was mobilised by contact with red mud than Ni, despite a higher overall Ni concentration in the solid phase. This is most probably because Cu has a higher affinity to form complexes with organic matter than Ni. In aerobic experiments, contact with the atmosphere reduced soil pH via carbonation reactions, and this reduced organic matter dissolution and thereby lowered Cu/Ni mobility. These data show that the mixing of red mud into organic rich soils is an area of concern, as there is a potential to mobilise Cu and Ni as organically bound complexes, via soil alkalisation. This could be especially problematic in locations where anaerobic conditions can prevail, such as wetland areas contaminated by the spill.

Partitioning of Metals Throughout a Winter Storm-Generated Fluid Mud Event, Atchafalaya Shelf, Louisiana

NASA Astrophysics Data System (ADS)

Clark, F. R.; McKee, B. A.; Duncan, D. D.

2002-12-01

Particulate and dissolved phases of a suite of metals and radionuclides were analyzed in fluid mud samples collected during a time series. This time series was taken during the passage of a winter storm on the Atchafalaya Shelf off the coast of Louisiana. The shelf receives an estimated 30% of the flow of the Mississippi River from its distributary, the Atchafalaya River. This input contributes a high sediment load to the shelf. Frequent winter storms provide shear stress to resuspend sediments and form fluid mud. Samples of fluid mud and overlying water were collected every two hours for 56 hours. Meteorological data as well as turbidity measurements by OBS were collected throughout the study. Bottom sediments were also collected before and after the time series. Partitioning effects were investigated on Be7, Th234, and Pb210 by gamma spectroscopy. These effects were also studied on several redox-sensitive metals, including Fe, Mn, Mo, Te, Re, U, Al, Ti, and V by ICP-MS analysis. Preliminary results indicate a rapid establishment of reducing conditions in fluid mud immediately overlying the seabed. These conditions persist until the suspended sediments in the fluid mud settle, and the fluid mud dissipates. The recurrence of storm front passages and their subsequent fluid mud formation cause repeated cycling from oxic to suboxic conditions in these coastal bottom waters. This redox cycling could potentially alter the fates of redox-sensitive metals, especially those associated with metal oxide carrier phases.

Lime-mud layers in high-energy tidal channels: A record of hurricane deposition

NASA Astrophysics Data System (ADS)

Shinn, Eugene A.; Steinen, Randolph P.; Dill, Robert F.; Major, Richard

1993-07-01

During or immediately following the transit of Hurricane Andrew (August 23-24, 1992) across the northern part of the Great Bahama Bank, thin laminated beds of carbonate mud were deposited in high-energy subtidal channels (4 m depth) through the ooid shoals of south Cat Cay and Joulters Cays. During our reconnaissance seven weeks later, we observed lime-mud beds exposed in the troughs of submarine oolite dunes and ripples. The mud layers were underlain and locally covered by ooid sand. The mud beds were lenticular and up to 5 cm thick. Their bases cast the underlying rippled surface. The layers were composed of soft silt- and sand-sized pellets and peloids and in some areas contained freshly preserved Thalassia blades and other organic debris along planes of lamination. The beds had a gelatinous consistency and locally had been penetrated by burrowers and plants. Layers of lime mud had also settled on bioturbated, plant-stabilized flats and in lagoonal settings but were quickly reworked and made unrecognizable by the burrowing of organisms. Thicker, more cohesive (and therefore older) mud beds and angular mud fragments associated with ooids from Joulters Cays have similar characteristics but lack fresh plant fragments. We infer that these older beds were similarly deposited and thus record the passage of previous hurricanes or tropical storms. Storm layers are preserved within channel sediments because migrating ooids prevent attack by the burrowing activity off organisms.

Limitations of microbial hydrocarbon degradation at the Amon Mud Volcano (Nile Deep Sea Fan)

NASA Astrophysics Data System (ADS)

Felden, J.; Lichtschlag, A.; Wenzhöfer, F.; de Beer, D.; Feseker, T.; Pop Ristova, P.; de Lange, G.; Boetius, A.

2013-01-01

The Amon mud volcano (MV), located at 1250 m water depth on the Nile Deep Sea Fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulphate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition and microbial activities over three years, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulphide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. Furthermore, within three years, cell numbers and hydrocarbon degrading activity increased at the gas-seeping sites. The low microbial activity in the hydrocarbon-vented areas of Amon mud volcano is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer mud volcano area is limited by hydrocarbon transport.

33 CFR 117.177 - Mud Slough.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Mud Slough. 117.177 Section 117.177 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements California § 117.177 Mud Slough. The draw of the Union Pacific...

The Mud Center: Recapturing Childhood.

ERIC Educational Resources Information Center

Jensen, Becky J.; Bullard, Julie A.

2002-01-01

Describes a Montana child development center's creation of an area in which children could enjoy messy, creative, sensory experiences playing with mud and a wide variety of outdoor props. Discusses how mud play contributed to young children's emerging interests and provided opportunities for expressing creativity, enhancing fine motor skills, and…

Teaching Ecological Interactions with Mud Dauber Nests.

ERIC Educational Resources Information Center

Matthews, Robert W.

1997-01-01

Describes the use of mud dauber wasp nests in laboratory activities in ecology and behavior and life science classes. Provides students with an opportunity to develop and practice basic skills including dissection, identification, observation, measurement, and communication. Discusses the life of mud daubers, obtaining and storing nests,…

β-Carbonic Anhydrases Play a Role in Fruiting Body Development and Ascospore Germination in the Filamentous Fungus Sordaria macrospora

PubMed Central

Elleuche, Skander; Pöggeler, Stefanie

2009-01-01

Carbon dioxide (CO2) is among the most important gases for all organisms. Its reversible interconversion to bicarbonate (HCO3 −) reaches equilibrium spontaneously, but slowly, and can be accelerated by a ubiquitous group of enzymes called carbonic anhydrases (CAs). These enzymes are grouped by their distinct structural features into α-, β-, γ-, δ- and ζ-classes. While physiological functions of mammalian, prokaryotic, plant and algal CAs have been extensively studied over the past years, the role of β-CAs in yeasts and the human pathogen Cryptococcus neoformans has been elucidated only recently, and the function of CAs in multicellular filamentous ascomycetes is mostly unknown. To assess the role of CAs in the development of filamentous ascomycetes, the function of three genes, cas1, cas2 and cas3 (carbonic anhydrase of Sordaria) encoding β-class carbonic anhydrases was characterized in the filamentous ascomycetous fungus Sordaria macrospora. Fluorescence microscopy was used to determine the localization of GFP- and DsRED-tagged CAs. While CAS1 and CAS3 are cytoplasmic enzymes, CAS2 is localized to the mitochondria. To assess the function of the three isoenzymes, we generated knock-out strains for all three cas genes (Δcas1, Δcas2, and Δcas3) as well as all combinations of double mutants. No effect on vegetative growth, fruiting-body and ascospore development was seen in the single mutant strains lacking cas1 or cas3, while single mutant Δcas2 was affected in vegetative growth, fruiting-body development and ascospore germination, and the double mutant strain Δcas1/2 was completely sterile. Defects caused by the lack of cas2 could be partially complemented by elevated CO2 levels or overexpression of cas1, cas3, or a non-mitochondrial cas2 variant. The results suggest that CAs are required for sexual reproduction in filamentous ascomycetes and that the multiplicity of isoforms results in redundancy of specific and non-specific functions. PMID:19365544

Interference activity of a minimal Type I CRISPR–Cas system from Shewanella putrefaciens

PubMed Central

Dwarakanath, Srivatsa; Brenzinger, Susanne; Gleditzsch, Daniel; Plagens, André; Klingl, Andreas; Thormann, Kai; Randau, Lennart

2015-01-01

Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)–Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minimal variant of the Type I-F system was identified in proteobacterial species including Shewanella putrefaciens CN-32. This variant lacks a large subunit (Csy1), Csy2 and Csy3 and contains two unclassified cas genes. The genome of S. putrefaciens CN-32 contains only five Cas proteins (Cas1, Cas3, Cas6f, Cas1821 and Cas1822) and a single CRISPR array with 81 spacers. RNA-Seq analyses revealed the transcription of this array and the maturation of crRNAs (CRISPR RNAs). Interference assays based on plasmid conjugation demonstrated that this CRISPR-Cas system is active in vivo and that activity is dependent on the recognition of the dinucleotide GG PAM (Protospacer Adjacent Motif) sequence and crRNA abundance. The deletion of cas1821 and cas1822 reduced the cellular crRNA pool. Recombinant Cas1821 was shown to form helical filaments bound to RNA molecules, which suggests its role as the Cascade backbone protein. A Cascade complex was isolated which contained multiple Cas1821 copies, Cas1822, Cas6f and mature crRNAs. PMID:26350210

The CRISPR-Associated Gene cas2 of Legionella pneumophila Is Required for Intracellular Infection of Amoebae

PubMed Central

Gunderson, Felizza F.; Cianciotto, Nicholas P.

2013-01-01

ABSTRACT Recent studies have shown that the clustered regularly interspaced palindromic repeats (CRISPR) array and its associated (cas) genes can play a key role in bacterial immunity against phage and plasmids. Upon analysis of the Legionella pneumophila strain 130b chromosome, we detected a subtype II-B CRISPR-Cas locus that contains cas9, cas1, cas2, cas4, and an array with 60 repeats and 58 unique spacers. Reverse transcription (RT)-PCR analysis demonstrated that the entire CRISPR-Cas locus is expressed during 130b extracellular growth in both rich and minimal media as well as during intracellular infection of macrophages and aquatic amoebae. Quantitative reverse transcription-PCR (RT-PCR) further showed that the levels of cas transcripts, especially those of cas1 and cas2, are elevated during intracellular growth relative to exponential-phase growth in broth. Mutants lacking components of the CRISPR-Cas locus were made and found to grow normally in broth and on agar media. cas9, cas1, cas4, and CRISPR array mutants also grew normally in macrophages and amoebae. However, cas2 mutants, although they grew typically in macrophages, were significantly impaired for infection of both Hartmannella and Acanthamoeba species. A complemented cas2 mutant infected the amoebae at wild-type levels, confirming that cas2 is required for intracellular infection of these host cells. PMID:23481601

Titanium leaching from red mud by diluted sulfuric acid at atmospheric pressure.

PubMed

Agatzini-Leonardou, S; Oustadakis, P; Tsakiridis, P E; Markopoulos, Ch

2008-09-15

Laboratory-scale research has focused on the recovery of titanium from red mud, which is obtained from bauxite during the Bayer process for alumina production. The leaching process is based on the extraction of this element with diluted sulfuric acid from red mud under atmospheric conditions and without using any preliminary treatment. Statistical design and analysis of experiments were used, in order to determine the main effects and interactions of the leaching process factors, which were: acid normality, temperature and solid to liquid ratio. The titanium recovery efficiency on the basis of red mud weight reached 64.5%. The characterization of the initial red mud, as well as this of the leached residues was carried out by X-ray diffraction, TG-DTA and scanning electron microscopy.

Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink.

PubMed

Niemann, Helge; Lösekann, Tina; de Beer, Dirk; Elvert, Marcus; Nadalig, Thierry; Knittel, Katrin; Amann, Rudolf; Sauter, Eberhard J; Schlüter, Michael; Klages, Michael; Foucher, Jean Paul; Boetius, Antje

2006-10-19

Mud volcanism is an important natural source of the greenhouse gas methane to the hydrosphere and atmosphere. Recent investigations show that the number of active submarine mud volcanoes might be much higher than anticipated (for example, see refs 3-5), and that gas emitted from deep-sea seeps might reach the upper mixed ocean. Unfortunately, global methane emission from active submarine mud volcanoes cannot be quantified because their number and gas release are unknown. It is also unclear how efficiently methane-oxidizing microorganisms remove methane. Here we investigate the methane-emitting Haakon Mosby Mud Volcano (HMMV, Barents Sea, 72 degrees N, 14 degrees 44' E; 1,250 m water depth) to provide quantitative estimates of the in situ composition, distribution and activity of methanotrophs in relation to gas emission. The HMMV hosts three key communities: aerobic methanotrophic bacteria (Methylococcales), anaerobic methanotrophic archaea (ANME-2) thriving below siboglinid tubeworms, and a previously undescribed clade of archaea (ANME-3) associated with bacterial mats. We found that the upward flow of sulphate- and oxygen-free mud volcano fluids restricts the availability of these electron acceptors for methane oxidation, and hence the habitat range of methanotrophs. This mechanism limits the capacity of the microbial methane filter at active marine mud volcanoes to <40% of the total flux.

Determination of effects of turbulence flow in a cathode environment on electricity generation using a tidal mud-based cylindrical-type sediment microbial fuel cell.

PubMed

An, Junyeong; Lee, Soo-Jin; Ng, How Yong; Chang, In Seop

2010-12-01

We examined the possibility of harvesting electricity from the surface of a tidal mud flat using a cylindrical-type sediment microbial fuel cell (SMFC), a marine mud battery (MMB), which can be applied in a sea environment where the ebb and flow occur due to tidal difference. In addition, we indirectly investigated the influence of ebb and flow in a lab, using aeration, argon gassing, and by agitating the cathodic solution. The MMBs consisted of cylindrical acrylic compartments containing a nylon membrane, an anode, and a cathode in a single body. The MMBs were stuck vertically into an artificial tidal mud flat such that the anode electrode was in direct contact with the tidal mud surface. As a result, the maximum current and power density generated were 35 mA/m(2) and 9 mW/m(2), respectively, thus verifying that it is possible to harvest electricity from the surface of a tidal mud flat using an MMB without burying the anode electrode in the tidal mud. Furthermore, the results of tests using an artificial turbulence flow showed the flow induced by the tidal ebb and flow could allow the performance of MMBs to be enhanced. Copyright © 2010 Elsevier Ltd. All rights reserved.

Effect of strong acids on red mud structural and fluoride adsorption properties.

PubMed

Liang, Wentao; Couperthwaite, Sara J; Kaur, Gurkiran; Yan, Cheng; Johnstone, Dean W; Millar, Graeme J

2014-06-01

The removal of fluoride using red mud has been improved by acidifying red mud with hydrochloric, nitric and sulphuric acid. The acidification of red mud causes sodalite and cancrinite phases to dissociate, confirmed by the release of sodium and aluminium into solution as well as the disappearance of sodalite bands and peaks in infrared and X-ray diffraction data. The dissolution of these mineral phases increases the amount of available iron and aluminium oxide/hydroxide sites that are accessible for the adsorption of fluoride. However, concentrated acids have a negative effect on adsorption due to the dissolution of these iron and aluminium oxide/hydroxide sites. The removal of fluoride is dependent on the charge of iron and aluminium oxide/hydroxides on the surface of red mud. Acidifying red mud with hydrochloric, nitric and sulphuric acid resulted in surface sites of the form ≡SOH2(+) and ≡SOH. Optimum removal is obtained when the majority of surface sites are in the form ≡SOH2(+) as the substitution of a fluoride ion does not cause a significant increase in pH. This investigation shows the importance of having a low and consistent pH for the removal of fluoride from aqueous solutions using red mud. Copyright © 2014 Elsevier Inc. All rights reserved.

Capping hazardous red mud using acidic soil with an embedded layer of zeolite for plant growth.

PubMed

Ma, Yingqun; Si, Chunhua; Lin, Chuxia

2014-01-01

A nearly three-year microcosm experiment was conducted to test the effectiveness of capping red mud using acidic soil with an embedded layer of zeolite in sustaining the growth of a grass species. This 'sandwich-structured' design allowed self-sustaining growth of the plants under rain-fed conditions no matter whether the underlying red mud was neutralized or not. During the initial stage, the plants grew better when the red mud was not neutralized with MgCl2 probably due to pH rise in the root zone. Neutralization of red mud led to salinization and pH decrease in the root zone. However, the difference in plant growth performance between these scenarios became less remarkable over time due to gradual improvement of soil conditions in the neutralized scenarios. Continuous leaching of soluble salts and alkali by rainwater extended the root zone to the red mud layer. As a result of vegetative production, soil organic matter rapidly accumulated. This, combined with increase in pH and decrease in salinity, markedly facilitated microbial activities and consequently improved the supply of nutrients. This study provides abasis for field-scale experimental design that will have implications for effectively establishing vegetative cover in red mud disposal sites to control dust hazards.

Automatic mouse ultrasound detector (A-MUD): A new tool for processing rodent vocalizations.

PubMed

Zala, Sarah M; Reitschmidt, Doris; Noll, Anton; Balazs, Peter; Penn, Dustin J

2017-01-01

House mice (Mus musculus) emit complex ultrasonic vocalizations (USVs) during social and sexual interactions, which have features similar to bird song (i.e., they are composed of several different types of syllables, uttered in succession over time to form a pattern of sequences). Manually processing complex vocalization data is time-consuming and potentially subjective, and therefore, we developed an algorithm that automatically detects mouse ultrasonic vocalizations (Automatic Mouse Ultrasound Detector or A-MUD). A-MUD is a script that runs on STx acoustic software (S_TOOLS-STx version 4.2.2), which is free for scientific use. This algorithm improved the efficiency of processing USV files, as it was 4-12 times faster than manual segmentation, depending upon the size of the file. We evaluated A-MUD error rates using manually segmented sound files as a 'gold standard' reference, and compared them to a commercially available program. A-MUD had lower error rates than the commercial software, as it detected significantly more correct positives, and fewer false positives and false negatives. The errors generated by A-MUD were mainly false negatives, rather than false positives. This study is the first to systematically compare error rates for automatic ultrasonic vocalization detection methods, and A-MUD and subsequent versions will be made available for the scientific community.

Biological properties of mud extracts derived from various spa resorts.

PubMed

Spilioti, Eliana; Vargiami, Margarita; Letsiou, Sophia; Gardikis, Konstantinos; Sygouni, Varvara; Koutsoukos, Petros; Chinou, Ioanna; Kassi, Eva; Moutsatsou, Paraskevi

2017-08-01

Spa resorts are known for thousands of years for their healing properties and have been empirically used for the treatment of many inflammatory conditions. Mud is one of the most often used natural materials for preventive, healing and cosmetic reasons and although it has been used since the antiquity, little light has been shed on its physical, chemical and biological properties. In this study we examined the effect of mud extracts on the expression of adhesion molecules (CAMs) by endothelial cells as well as their effects on monocyte adhesion to activated endothelial cells. Most of mud extracts inhibited the expression of VCAM-1 by endothelial cells and reduced monocyte adhesion to activated endothelial cells, indicating a potent anti-inflammatory activity. Furthermore, the mud extracts were tested for their antimicrobial activity; however, most of them appeared inactive against S. aureus and S. epidermidis. One of the mud extracts (showing the best stabilization features) increased significantly the expression of genes involved in cell protection, longevity and hydration of human keratinocytes, such as, collagen 6A1, forkhead box O3, sirtuin-1, superoxide dismutase 1 and aquaporin-3. The present study reveals that mud exerts important beneficial effects including anti-inflammatory and anti-aging activity as well as moisturizing effects, implicating important cosmeceutical applications.

Characterization of red mud-epoxy intumescent char using surface imaging and micro analysis

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

Arogundade, A. I., E-mail: ajiunolorioba@gmail.com; Megat-Yusoff, P. S. M., E-mail: puteris@petronas.com.my; Faiz, A.

In this study, red mud (RM), an oxide waste was proposed as reinforcing, synergistic filler for the traditional epoxy intumescent coating (IC). 5.5 wt% of acid-modified and unmodified red mud were introduced into the basic intumescent formulation of ammonium polyphosphate (APP), pentaerythritol (PER) and melamine (MEL). In order to predict effect of modification on its suitability, Field emission electron scanning microscopy and Fourier transform infra red were used to obtain detailed characteristics such as the cell size, pore distribution, homogeneity and chemical composition of the red mud-epoxy carbonaceous char. Both acid-modified and unmodified RM-filled ICs produced chars with smaller andmore » more closely packed cells compared to chars from the unfilled coating. Both coating types had hard carbonaceous metal phosphate coverings that could act as heat barriers. The unmodified red mud was found to be antagonistic to the intumescent action with an expansion of only 2 times the initial thickness. The leached, low iron-red mud produced an expansion of 15 times the initial thickness, but possessed a hollow interior. From these findings, it may be deduced that while acid leaching of red mud may improve intumescent expansion, it would be necessary to optimize the percent filler loading to improve residual mass.« less

Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea.

PubMed

Lazar, Cassandre Sara; Parkes, R John; Cragg, Barry A; L'Haridon, Stéphane; Toffin, Laurent

2011-08-01

Submarine mud volcanoes are a significant source of methane to the atmosphere. The Napoli mud volcano, situated in the brine-impacted Olimpi Area of the Eastern Mediterranean Sea, emits mainly biogenic methane particularly at the centre of the mud volcano. Temperature gradients support the suggestion that Napoli is a cold mud volcano with moderate fluid flow rates. Biogeochemical and molecular genetic analyses were carried out to assess the methanogenic activity rates, pathways and diversity in the hypersaline sediments of the centre of the Napoli mud volcano. Methylotrophic methanogenesis was the only significant methanogenic pathway in the shallow sediments (0-40 cm) but was also measured throughout the sediment core, confirming that methylotrophic methanogens could be well adapted to hypersaline environments. Hydrogenotrophic methanogenesis was the dominant pathway below 50 cm; however, low rates of acetoclastic methanogenesis were also present, even in sediment layers with the highest salinity, showing that these methanogens can thrive in this extreme environment. PCR-DGGE and methyl coenzyme M reductase gene libraries detected sequences affiliated with anaerobic methanotrophs (mainly ANME-1) as well as Methanococcoides methanogens. Results show that the hypersaline conditions in the centre of the Napoli mud volcano influence active biogenic methane fluxes and methanogenic/methylotrophic diversity. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Influence of dust and mud on the optical, chemical, and mechanical properties of a pv protective glass

PubMed Central

Yilbas, Bekir Sami.; Ali, Haider; Khaled, Mazen M.; Al-Aqeeli, Nasser; Abu-Dheir, Numan; Varanasi, Kripa K.

2015-01-01

Recent developments in climate change have increased the frequency of dust storms in the Middle East. Dust storms significantly influence the performances of solar energy harvesting systems, particularly (photovoltaic) PV systems. The characteristics of the dust and the mud formed from this dust are examined using various analytical tools, including optical, scanning electron, and atomic force microscopies, X-ray diffraction, energy spectroscopy, and Fourier transform infrared spectroscopy. The adhesion, cohesion and frictional forces present during the removal of dry mud from the glass surface are determined using a microtribometer. Alkali and alkaline earth metal compounds in the dust dissolve in water to form a chemically active solution at the glass surface. This solution modifies the texture of the glass surface, thereby increasing the microhardness and decreasing the transmittance of the incident optical radiation. The force required to remove the dry mud from the glass surface is high due to the cohesive forces that result from the dried mud solution at the interface between the mud and the glass. The ability altering the characteristics of the glass surface could address the dust/mud-related limitations of protective surfaces and has implications for efficiency enhancements in solar energy systems. PMID:26514102

Source Signature of Sr Isotopes in Fluids Emitting From Mud volcanoes in Taiwan

NASA Astrophysics Data System (ADS)

Chung, C.; You, C.; Chao, H.

2003-12-01

Located at the boundary between the Philippine Sea Plate and the Asia Continental Plate, abundance of mud volcanoes were erupted on land in Taiwan. According to their occurrences and associated tectonic settings, these mud volcanoes were classified into four groupies. The group (I) mud volcanoes are located in the western coastal plane, whereas group (II) and (III) are situated near the Kutinkung anticline axis and the Chishan fault respectively. The group (IV) mud volcanoes are discovered at the Coastal Range. Although there are numerous studies focused on morphology, possible fluid migration paths and sources are poorly understood. We have collected and analyzed major ions and Sr isotopic ratios in fluids separated from various mud volcanoes in Taiwan. Chemical contents of these fluids were measured by IC and the emitted gasses were analyzed by GC. The Sr concentrations in these fluids were determined using AA and the isotopic compositions were analyzed by TIMS. The dominated ions in fluids are Na and Cl which account for 98% of dissolved materials. All fluids show similar Na/Cl ratios(0.7-0.8), slightly higher than seawater but each group has unique Sr isotopic signature. Waters expelled from group I mud volcanoes featured with low salinity and high Sr isotopic ratios ranged from 0.71150 to 0.71175. Groups II and III were outcroped in the Kutinkung formation but show distinctive chemical compositions. Group II fluids have four times Cl concentrations(358-522mM) compared with those of group III(85-162mM). The latter fluids appear to be more radiogenic(0.71012- 0.71075) indicating possible influence due to water-rock interactions. Low 87Sr/86Sr(0.70692-0.70939) is typical characteristic of mud volcano fluids in group IV where large Mg and K depletion were discovered, suggesting effects due to sediment diagenetic processes. The chemical compositions of mud volcano associated gasses show similar distribution pattern. The major gas constituents in mud volcano zones II and III are methane(>80%), air(1-10%) and carbon dioxide(1-5%). Gases collected from zone IV display significantly higher air content(5-20%) with low carbon dioxide(<0.2%). These results are useful for gaining a better understanding of mud volcano fluid sources.

Addition of an organic amendment and/or residue mud to bauxite residue sand in order to improve its properties as a growth medium.

PubMed

Jones, B E H; Haynes, R J; Phillips, I R

2012-03-01

The effects of addition of carbonated residue mud (RMC) or seawater neutralized residue mud (RMS), at two rates, in the presence or absence of added green waste compost, on the chemical, physical and microbial properties of gypsum-treated bauxite residue sand were studied in a laboratory incubation study. The growth of two species commonly used in revegetation of residue sand (Lolium rigidum and Acacia saligna) in the treatments was then studied in a 18-week greenhouse study. Addition of green waste-based compost increased ammonium acetate-extractable (exchangeable) Mg, K and Na. Addition of residue mud at 5 and 10% w/w reduced exchangeable Ca but increased that of Mg and Na (and K for RMS). Concentrations of K, Na, Mg and level of EC in saturation paste extracts were increased by residue mud additions. Concentrations of cations in water extracts were considerably higher than those in saturation paste extracts but trends with treatment were broadly similar. Addition of both compost and residue mud caused a significant decrease in macroporosity with a concomitant increase in mesoporosity and microporosity, available water holding capacity and the quantity of water held at field capacity. Increasing rates of added residue mud reduced the percentage of sample present as discrete sand particles and increased that in aggregated form (particularly in the 1-2 and >10mm diameter ranges). Organic C content, C/N ratio, soluble organic C, microbial biomass C and basal respiration were increased by compost additions. Where compost was added, residue mud additions caused a substantial increase in microbial biomass and basal respiration. L. rigidum grew satisfactorily in all treatments although yields tended to be reduced by additions of mud (especially RMC) particularly in the absence of added compost. Growth of A. saligna was poor in sand alone and mud-amended sand and was greatly promoted by additions of compost. However, in the presence of compost, addition of carbonated mud had a marked depressive effect on both top and root growth. The significant positive effect of compost was attributed to substantial inputs of K and marked reductions in the Na/K ratio in soil solution while the depressive effect of RMC was attributed to its greater alkalinity and consequently higher concentrations of HCO(3)(-) in solution. Copyright © 2011 Elsevier Ltd. All rights reserved.

Experimental Evidence that Abrasion of Carbonate Sand is a Significant Source of Carbonate Mud

NASA Astrophysics Data System (ADS)

Trower, L.; Kivrak, L.; Lamb, M. P.; Fischer, W. W.

2017-12-01

Carbonate mud is a major sedimentary component of modern and ancient tropical carbonate environments, yet its enigmatic origin remains debated. Early views on the origin of carbonate mud considered the abrasion of carbonate sand during sediment transport as a possible mechanism. In recent decades, however, prevailing thought has generally settled on a binary explanation: 1) precipitation of aragonite needles within the water column, and 2) post-mortem dispersal of biological aragonite, in particular from algae, and perhaps aided by fish. To test these different hypotheses, we designed a model and a set of laboratory experiments to quantify the rates of mud production associated with sediment transport. We adapted a recent model of ooid abrasion rate to predict the rate of mud production by abrasion of carbonate sand as a function of grain size and sediment transport mode. This model predicts large mud production rates, ranging from 103 to 104 g CaCO3/m2/yr for typical grain sizes and transport conditions. These rate estimates are at least one order of magnitude more rapid than the 102 g CaCO3/m2/yr estimates for other mechanisms like algal biomineralization, indicating that abrasion could produce much larger mud fluxes per area as other mechanisms. We tested these estimates using wet abrasion mill experiments; these experiments generated mud through mechanical abrasion of both ooid and skeletal carbonate sand for grain sizes ranging from 250 µm to >1000 µm over a range of sediment transport modes. Experiments were run in artificial seawater, including a series of controls demonstrating that no mud was produced via homogenous nucleation and precipitation in the absence of sand. Our experimental rates match the model predictions well, although we observed small systematic differences in rates between abrasion ooid sand and skeletal carbonate sand that likely stems from innate differences in grain angularity. Electron microscopy of the experimental products revealed aragonite needles 1-3 µm in length identical to those described in carbonate mud from a range of modern environments. Our results suggest that abrasion during bed load and suspended load transport of carbonate sand, even over small areas, is likely a significant potential source of carbonate mud in both modern and ancient carbonate environments.

Can mud (silt and clay) concentration be used to predict soil organic carbon content within seagrass ecosystems?

NASA Astrophysics Data System (ADS)

Serrano, Oscar; Lavery, Paul S.; Duarte, Carlos M.; Kendrick, Gary A.; Calafat, Antoni; York, Paul H.; Steven, Andy; Macreadie, Peter I.

2016-09-01

The emerging field of blue carbon science is seeking cost-effective ways to estimate the organic carbon content of soils that are bound by coastal vegetated ecosystems. Organic carbon (Corg) content in terrestrial soils and marine sediments has been correlated with mud content (i.e., silt and clay, particle sizes < 63 µm), however, empirical tests of this theory are lacking for coastal vegetated ecosystems. Here, we compiled data (n = 1345) on the relationship between Corg and mud contents in seagrass ecosystems (79 cores) and adjacent bare sediments (21 cores) to address whether mud can be used to predict soil Corg content. We also combined these data with the δ13C signatures of the soil Corg to understand the sources of Corg stores. The results showed that mud is positively correlated with soil Corg content only when the contribution of seagrass-derived Corg to the sedimentary Corg pool is relatively low, such as in small and fast-growing meadows of the genera Zostera, Halodule and Halophila, and in bare sediments adjacent to seagrass ecosystems. In large and long-living seagrass meadows of the genera Posidonia and Amphibolis there was a lack of, or poor relationship between mud and soil Corg content, related to a higher contribution of seagrass-derived Corg to the sedimentary Corg pool in these meadows. The relatively high soil Corg contents with relatively low mud contents (e.g., mud-Corg saturation) in bare sediments and Zostera, Halodule and Halophila meadows was related to significant allochthonous inputs of terrestrial organic matter, while higher contribution of seagrass detritus in Amphibolis and Posidonia meadows disrupted the correlation expected between soil Corg and mud contents. This study shows that mud is not a universal proxy for blue carbon content in seagrass ecosystems, and therefore should not be applied generally across all seagrass habitats. Mud content can only be used as a proxy to estimate soil Corg content for scaling up purposes when opportunistic and/or low biomass seagrass species (i.e., Zostera, Halodule and Halophila) are present (explaining 34 to 91 % of variability), and in bare sediments (explaining 78 % of the variability). The results obtained could enable robust scaling up exercises at a low cost as part of blue carbon stock assessments.

[Detection of CRSPR-Cas system in Streptococcus thermophiles].

PubMed

Li, Wan; Liang, Hongzhang; Zhang, Danqing; Wang, Nana; Tang, Yaru; Li, Bailiang; Huo, Guicheng

2016-04-14

We aimed to detect the CRSPR-Cas system of six Streptococcus thermophilus. Bioinformatics method was used to predict CRSPR-Cas system of nine S. thermophilus that published in National Center for Biotechnology Information. Four primers were designed according to the flanking sequences of standard strains and the CRISPR-Cas system of six S. thermophilus have been detected by PCR method. S. thermophilus S4 had a Cas9 gene, others all had Cas9 gene, Cas10 gene and Cas9* gene. In addition, 79 and KLDS3.0207 still had Cas3 gene. Signature genes amplification of CRSPR-Cas system could predict the type of CRSPR-Cas system in unsequenced strains, these findings will help establish the foundation for the study of CRSPR-Cas system in lactic acid bacteria.

Multidisciplinary research for the safe fruition of an active geosite: the Salse di Nirano mud volcanoes (Northern Apennines, Italy)

NASA Astrophysics Data System (ADS)

Coratza, Paola; Albarello, Dario; Cipriani, Anna; Cantucci, Barbara; Castaldini, Doriano; Conventi, Marzia; Dadomo, Andrea; De Nardo, Maria Teresa; Macini, Paolo; Martinelli, Giovanni; Mesini, Ezio; Papazzoni, Cesare Andrea; Quartieri, Simona; Ricci, Tullio; Santagata, Tommaso; Sciarra, Alessandra; Vezzalini, Giovanna

2017-04-01

Mud volcanoes are emissions of cold mud due to the ascent to the surface of salty and muddy waters mixed with gaseous (methane) and, in minor part, fluid hydrocarbons (petroleum veils) along faults and fractures. In the Northern Apennines mud volcanoes are closely linked to the active tectonic compression associated with thrusts of regional importance. They are mostly cone-shaped and show variable geometry and size, ranging from one to few metres, and are located in 19 sites in the northwestern part of the Apennines. Particularly noteworthy is the Nirano mud volcano field, located in the Fiorano Modenese district, which, with a surface area of approximately 75,000 m2, is one of the best developed and largest mud volcano field of the entire Italian territory and among the largest in Europe; it is thus protected as natural reserve (Salse di Nirano) since 1982. The Nirano mud volcanoes are found at the bottom of an elliptical depression, interpreted as a collapse-like structure (caldera) that may have developed in response to the deflation of a shallow mud chamber triggered by several ejections and evacuation of fluid sediments. There are several individual or multiple cones within the field of the mud volcanoes of Nirano, with a rather discontinuous activity; apparatuses become dormant or even extinct whereas new vents can appear in other spots. In the research here presented about 50 vents have been mapped and few of them appeared in May 2016. The mud volcanoes of the region have been known since a long time and have always aroused great interest due to their outstanding scenic value, and, in the past the mud volcano emissions have been used in many ways. Beside their cultural value, the mud volcanoes of the study area represent a tourist attractiveness as testified by the increasing number of visitors (e.g. about 70,000 visitors in 2015 in the Salse di Nirano Natural Reserve). Numerous initiatives, targeted at various potential users, have been developed in the last decades. In particular, tourist environmental maps, geotourism maps, books in hard copy and digital format, videos, virtual flights, multimedia and audio CDs have been implemented. Although the hazard from mud volcanoes is generally low, sometimes they may lead to sudden and violent eruptions and isolated casualties have been reported. Very notable case in this regard is the event that occurred in September 2014 in the Natural Reserve of Macalube di Aragona in Sicily where a mud volcano erupted, with an ejection of mud up to about 20 m above the ground and causing the burial of two children killing them. When a given geological site acquires a tourism value, it is necessary to assess the possible natural hazard processes which might threaten the safety of visitors. In particular, fast-occurring processes might directly involve tourists in proximity of the site of interest or along access roads and footpaths. In this context, multidisciplinary research, aiming at analysing the causes and understanding triggering mechanisms of paroxysmal and dangerous phenomena in the Natural Reserve of Nirano, are in progress, funded by the Fiorano municipality. The research team is composed by experts of different disciplines (geology, geomorphology, geophysics, geochemistry, palaeontology, mineralogy, topography) from different institutions. The first results of the multidisciplinary research here presented seem to confirm that no significant and dangerous phenomena can affect visitors along the pathways of the Reserve.

Nucleation sites of Ge nanoislands grown on pit-patterned Si substrate prepared by electron-beam lithography

NASA Astrophysics Data System (ADS)

Smagina, Zh. V.; Zinovyev, V. A.; Rudin, S. A.; Novikov, P. L.; Rodyakina, E. E.; Dvurechenskii, A. V.

2018-04-01

Regular pit-patterned Si(001) substrates were prepared by electron-beam lithography followed by plasma chemical etching. The geometry of the pits was controlled by varying the etching conditions and the electron-beam exposure duration. It was shown that the location of three-dimensional (3D) Ge nanoislands subsequently grown on the pit-patterned Si substrates depends on the shape of the pit bottom. In the case of pits having a sharp bottom, 3D Ge islands nucleate inside the pits. For pits with a wide flat bottom, the 3D Ge island nucleation takes place at the pit periphery. This effect is attributed to the strain relaxation depending not only on the initial pit shape, but also on its evolution during the Ge wetting layer deposition. It was shown by Monte Carlo simulations that in the case of a pit with a pointed bottom, the relaxation is most effective inside the pit, while for a pit with a wide bottom, the most relaxed area migrates during Ge deposition from the pit bottom to its edges, where 3D Ge islands nucleate.

Apport de l'imagerie dans le diagnostic des sacroiliites infectieuses : à propos de 19 cas

PubMed Central

Abid, Hanen; Chaabouni, Salim; Frikha, Faten; Toumi, Nozha; Souissi, Basma; Lahiani, Dorra; Bahloul, Zouhir; Ben Mahfoudh, Khaireddine

2014-01-01

Les sacro-iliites infectieuses méritent d’être mieux connues. Leur diagnostic est souvent retardé en raison d'une symptomatologie trompeuse et des diffcultés d'exploration de l'articulation sacro-iliaque. Notre travail est basé sur une étude rétrospective portant sur les cas de SII, recueillis sur une période comprise entre 1997 et 2008 dans notre centre universitaire Sfax-Tunisie. Le diagnostic de sacro-iliite était retenu en présence d'arguments cliniques et radiologiques d'atteinte sacroiliaque. Nous rapportons dix neuf cas de sacroiliites infectieuses (10 hommes et 9 femmes), avec un âge moyen de 32 ans. L'atteinte était unilatérale dans tous les cas. Les radiographies standard faites dans tous les cas ont été suggestives dans 14 cas et normales dans les autres cas. La TDM faite dans 13 cas a montré, un abcès des parties molles dans 8 cas et un séquestre osseux dans 2 cas. L'IRM réalisée dans 8 cas, a objectivé une infiltration des parties molles dans tous les cas et un abcès dans 3 cas. Le germe a été identifié dans 9 cas (3 cas de tuberculose, 3 cas de brucellose, 2 sacro-iliites à pyogène et un cas de candidose). Cette identification était faite par biopsie dans 3 cas, hémocultures dans 2 cas, prélèvement au niveau de la porte d'entrée dans 1 cas et sérodiagnostic dans 3 cas. Pour les autres cas, l'origine pyogène a été retenue sur des arguments cliniques et biologiques. L'imagerie joue un rôle primordial dans le diagnostic précoce et l'orientation étiologique d'une sacroiliite infectieuse. PMID:25120884

Study on analysis of waste edible oil with deterioration and removal of acid value, carbonyl value, and free fatty acid by a food additive (calcium silicate).

PubMed

Ogata, Fumihiko; Tanaka, Yuko; Tominaga, Hisato; Kangawa, Moe; Inoue, Kenji; Ueda, Ayaka; Iwata, Yuka; Kawasaki, Naohito

2013-01-01

This study investigated the regeneration of waste edible oil using a food additive (calcium silicate, CAS). Waste edible oil was prepared by combined heat and aeration treatment. Moreover, the deterioration of edible oil by combined heat and aeration treatment was greater than that by heat treatment alone. The acid value (AV) and carbonyl value (CV) increased with increasing deterioration; conversely, the tocopherol concentration decreased with increasing deterioration. The specific surface area, pore volume, and mean pore diameter of the 3 CAS formulations used (CAS30, CAS60, and CAS90) were evaluated, and scanning electron microscopic images were taken. The specific surface area increased in the order of CAS30 (115.54 m(2)/g) < CAS60 (163.93 m(2)/g) < CAS90 (187.47 m(2)/g). The mean pore diameter increased in the order of CAS90 (170.59 Å) < CAS60 (211.60 Å) < CAS30 (249.70 Å). The regeneration of waste edible oil was possible with CAS treatment. The AV reduced by 15.2%, 10.8%, and 23.1% by CAS30, CAS60, and CAS90 treatment, respectively, and the CV was reduced by 35.6%, 29.8%, and 31.3% by these 3 treatments, respectively. Moreover, the concentrations of tocopherol and free fatty acids did not change with CAS treatment. The characteristics of CAS were not related to the degree of change of AV and CV. However, the adsorption mechanism of polar and non-polar compounds generated in waste edible oil by CAS was related with the presence of silica gel molecules in CAS. The findings indicated that CAS was useful for the regeneration of waste edible oil.

Martian Central Pit Craters

NASA Technical Reports Server (NTRS)

Hillman, E.; Barlow, N. G.

2005-01-01

Impact craters containing central pits are rare on the terrestrial planets but common on icy bodies. Mars is the exception among the terrestrial planets, where central pits are seen on crater floors ( floor pits ) as well as on top of central peaks ( summit pits ). Wood et al. [1] proposed that degassing of subsurface volatiles during crater formation produced central pits. Croft [2] argued instead that central pits might form during the impact of volatile-rich comets. Although central pits are seen in impact craters on icy moons such as Ganymede, they do show some significant differences from their martian counterparts: (a) only floor pits are seen on Ganymede, and (b) central pits begin to occur at crater diameters where the peak ring interior morphology begins to appear in terrestrial planet craters [3]. A study of craters containing central pits was conducted by Barlow and Bradley [4] using Viking imagery. They found that 28% of craters displaying an interior morphology on Mars contain central pits. Diameters of craters containing central pits ranged from 16 to 64 km. Barlow and Bradley noted that summit pit craters tended to be smaller than craters containing floor pits. They also noted a correlation of central pit craters with the proposed rings of large impact basins. They argued that basin ring formation fractured the martian crust and allowed subsurface volatiles to concentrate in these locations. They favored the model that degassing of the substrate during crater formation was responsible for central pit formation due to the preferential location of central pit craters along these basin rings.

Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens.

PubMed

Dwarakanath, Srivatsa; Brenzinger, Susanne; Gleditzsch, Daniel; Plagens, André; Klingl, Andreas; Thormann, Kai; Randau, Lennart

2015-10-15

Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minimal variant of the Type I-F system was identified in proteobacterial species including Shewanella putrefaciens CN-32. This variant lacks a large subunit (Csy1), Csy2 and Csy3 and contains two unclassified cas genes. The genome of S. putrefaciens CN-32 contains only five Cas proteins (Cas1, Cas3, Cas6f, Cas1821 and Cas1822) and a single CRISPR array with 81 spacers. RNA-Seq analyses revealed the transcription of this array and the maturation of crRNAs (CRISPR RNAs). Interference assays based on plasmid conjugation demonstrated that this CRISPR-Cas system is active in vivo and that activity is dependent on the recognition of the dinucleotide GG PAM (Protospacer Adjacent Motif) sequence and crRNA abundance. The deletion of cas1821 and cas1822 reduced the cellular crRNA pool. Recombinant Cas1821 was shown to form helical filaments bound to RNA molecules, which suggests its role as the Cascade backbone protein. A Cascade complex was isolated which contained multiple Cas1821 copies, Cas1822, Cas6f and mature crRNAs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

PubMed Central

Fonfara, Ines; Le Rhun, Anaïs; Chylinski, Krzysztof; Makarova, Kira S.; Lécrivain, Anne-Laure; Bzdrenga, Janek; Koonin, Eugene V.; Charpentier, Emmanuelle

2014-01-01

The CRISPR-Cas-derived RNA-guided Cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. The DNA-targeting mechanism of the type II CRISPR-Cas system involves maturation of tracrRNA:crRNA duplex (dual-RNA), which directs Cas9 to cleave invading DNA in a sequence-specific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target. We show that evolution of dual-RNA and Cas9 in bacteria produced remarkable sequence diversity. We selected eight representatives of phylogenetically defined type II CRISPR-Cas groups to analyze possible coevolution of Cas9 and dual-RNA. We demonstrate that these two components are interchangeable only between closely related type II systems when the PAM sequence is adjusted to the investigated Cas9 protein. Comparison of the taxonomy of bacterial species that harbor type II CRISPR-Cas systems with the Cas9 phylogeny corroborates horizontal transfer of the CRISPR-Cas loci. The reported collection of dual-RNA:Cas9 with associated PAMs expands the possibilities for multiplex genome editing and could provide means to improve the specificity of the RNA-programmable Cas9 tool. PMID:24270795

Adding worms during composting of organic waste with red mud and fly ash reduces CO2 emissions and increases plant available nutrient contents.

PubMed

Barthod, J; Rumpel, C; Calabi-Floody, M; Mora, M-L; Bolan, N S; Dignac, M-F

2018-09-15

Alkaline industrial wastes such as red mud and fly ash are produced in large quantities. They may be recycled as bulking agent during composting and vermicomposting, converting organic waste into soil amendments or plant growth media. The aim of this study was to assess the microbial parameters, greenhouse gas emissions and nutrient availability during composting and vermicomposting of household waste with red mud and fly ash 15% (dry weight). CO 2 , CH 4 and N 2 O emissions were monitored during 6 months in controlled laboratory conditions and microbial biomass and phospholipid acids, N and P availability were analysed in the end-products. Higher CO 2 emissions were observed during vermicomposting compared to composting. These emissions were decreased by red mud addition, while fly ash had no effect. Nitrate (NO 3 -N) content of the end-products were more affected by worms than by alkaline materials, while higher ammonium (NH 4 -N) contents were recorded for composts than vermicomposts. Red mud vermicompost showed higher soluble P proportion than red mud compost, suggesting that worm presence can counterbalance P adsorption to the inorganic matrix. Final composts produced with red mud showed no harmful heavy metal concentrations. Adding worms during composting thus improved the product nutrient availability and did not increase metal toxicity. From a practical point of view, this study suggests that for carbon stabilisation and end-product quality, the addition of red mud during composting should be accompanied by worm addition to counterbalance negative effects on nutrient availability. Copyright © 2018. Published by Elsevier Ltd.

Effects of red mud based passivator on the transformation of Cd fraction in acidic Cd-polluted paddy soil and Cd absorption in rice.

PubMed

Li, Hui; Liu, Yan; Zhou, Yaoyu; Zhang, Jiachao; Mao, Qiming; Yang, Yuan; Huang, Hongli; Liu, Zhaohui; Peng, Qinghui; Luo, Lin

2018-06-04

Highly effective, economical, and replicable ways of Cd-polluted paddy field remediation (in situ) are urgently needed. In this work, a yearlong field experiment (both early and late rice) was conducted to investigate the effects of red mud based passivator [red mud, diatomite, and lime (5:3:2)] on remediation of an acidic Cd-polluted paddy field in Hunan Province. Compared with the control, the addition of red mud based passivator in the early and late rice reduced Cd concentration in each part of the rice plant (with the most significant decrease rate of 59.18% and 72.11% for brown rice in the early rice and late rice seasons respectively). The effect of Cd reduction in the rice plant was persistent in the next growing season. The addition of red mud based passivator also reduced the exchangeable fraction of Cd in the soil and converted the exchangeable fraction into other unavailable fractions. This study demonstrated that the pH in acidic soil increased after the application of red mud based passivator. Furthermore, red mud based passivator had no effect on the concentrations of Olsen-K, Alkaline-N, Olsen-P in the soil, but increased rice grain yield. Overall, the results of this study indicated that the red mud based passivator at 0.6 kg m -2 could be a recommendation for Cd-polluted acidic paddy soil stabilization, and it would be a suitable method for remediation of Cd-polluted acidic paddy soil. Copyright © 2018 Elsevier B.V. All rights reserved.

Influence of the Drilling Mud Formulation Process on the Bacterial Communities in Thermogenic Natural Gas Wells of the Barnett Shale▿†

PubMed Central

Struchtemeyer, Christopher G.; Davis, James P.; Elshahed, Mostafa S.

2011-01-01

The Barnett Shale in north central Texas contains natural gas generated by high temperatures (120 to 150°C) during the Mississippian Period (300 to 350 million years ago). In spite of the thermogenic origin of this gas, biogenic sulfide production and microbiologically induced corrosion have been observed at several natural gas wells in this formation. It was hypothesized that microorganisms in drilling muds were responsible for these deleterious effects. Here we collected drilling water and drilling mud samples from seven wells in the Barnett Shale during the drilling process. Using quantitative real-time PCR and microbial enumerations, we show that the addition of mud components to drilling water increased total bacterial numbers, as well as the numbers of culturable aerobic heterotrophs, acid producers, and sulfate reducers. The addition of sterile drilling muds to microcosms that contained drilling water stimulated sulfide production. Pyrosequencing-based phylogenetic surveys of the microbial communities in drilling waters and drilling muds showed a marked transition from typical freshwater communities to less diverse communities dominated by Firmicutes and Gammaproteobacteria. The community shifts observed reflected changes in temperature, pH, oxygen availability, and concentrations of sulfate, sulfonate, and carbon additives associated with the mud formulation process. Finally, several of the phylotypes observed in drilling muds belonged to lineages that were thought to be indigenous to marine and terrestrial fossil fuel formations. Our results suggest a possible alternative exogenous origin of such phylotypes via enrichment and introduction to oil and natural gas reservoirs during the drilling process. PMID:21602366

Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale.

PubMed

Struchtemeyer, Christopher G; Davis, James P; Elshahed, Mostafa S

2011-07-01

The Barnett Shale in north central Texas contains natural gas generated by high temperatures (120 to 150°C) during the Mississippian Period (300 to 350 million years ago). In spite of the thermogenic origin of this gas, biogenic sulfide production and microbiologically induced corrosion have been observed at several natural gas wells in this formation. It was hypothesized that microorganisms in drilling muds were responsible for these deleterious effects. Here we collected drilling water and drilling mud samples from seven wells in the Barnett Shale during the drilling process. Using quantitative real-time PCR and microbial enumerations, we show that the addition of mud components to drilling water increased total bacterial numbers, as well as the numbers of culturable aerobic heterotrophs, acid producers, and sulfate reducers. The addition of sterile drilling muds to microcosms that contained drilling water stimulated sulfide production. Pyrosequencing-based phylogenetic surveys of the microbial communities in drilling waters and drilling muds showed a marked transition from typical freshwater communities to less diverse communities dominated by Firmicutes and Gammaproteobacteria. The community shifts observed reflected changes in temperature, pH, oxygen availability, and concentrations of sulfate, sulfonate, and carbon additives associated with the mud formulation process. Finally, several of the phylotypes observed in drilling muds belonged to lineages that were thought to be indigenous to marine and terrestrial fossil fuel formations. Our results suggest a possible alternative exogenous origin of such phylotypes via enrichment and introduction to oil and natural gas reservoirs during the drilling process.

Mapping of the minimal inorganic phosphate transporting unit of human PiT2 suggests a structure universal to PiT-related proteins from all kingdoms of life

PubMed Central

2011-01-01

Background The inorganic (Pi) phosphate transporter (PiT) family comprises known and putative Na+- or H+-dependent Pi-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with Pi to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na+-dependent Pi (NaPi) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins. Results We show that the human PiT2 histidine, H502, and the human PiT1 glutamate, E70, - both conserved in eukaryotic PiT family members - are critical for Pi transport function. Noticeably, human PiT2 H502 is located in the C-terminal PiT family signature sequence, and human PiT1 E70 is located in ProDom domains characteristic for all PiT family members. A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR254-V483), was found to be a fully functional Pi transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL183-V483) did also support Pi transport albeit at very low levels. Conclusions The results suggest that the overall structure of the Pi-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship. PMID:21586110

Mapping of the minimal inorganic phosphate transporting unit of human PiT2 suggests a structure universal to PiT-related proteins from all kingdoms of life.

PubMed

Bøttger, Pernille; Pedersen, Lene

2011-05-17

The inorganic (Pi) phosphate transporter (PiT) family comprises known and putative Na(+)- or H(+)-dependent Pi-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with Pi to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na(+)-dependent P(i) (NaP(i)) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins. We show that the human PiT2 histidine, H(502), and the human PiT1 glutamate, E(70),--both conserved in eukaryotic PiT family members--are critical for P(i) transport function. Noticeably, human PiT2 H(502) is located in the C-terminal PiT family signature sequence, and human PiT1 E(70) is located in ProDom domains characteristic for all PiT family members.A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR(254)-V(483)), was found to be a fully functional P(i) transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL(183)-V(483)) did also support P(i) transport albeit at very low levels. The results suggest that the overall structure of the P(i)-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship. © 2011 Bøttger and Pedersen; licensee BioMed Central Ltd.

A Broad-Spectrum Inhibitor of CRISPR-Cas9.

PubMed

Harrington, Lucas B; Doxzen, Kevin W; Ma, Enbo; Liu, Jun-Jie; Knott, Gavin J; Edraki, Alireza; Garcia, Bianca; Amrani, Nadia; Chen, Janice S; Cofsky, Joshua C; Kranzusch, Philip J; Sontheimer, Erik J; Davidson, Alan R; Maxwell, Karen L; Doudna, Jennifer A

2017-09-07

CRISPR-Cas9 proteins function within bacterial immune systems to target and destroy invasive DNA and have been harnessed as a robust technology for genome editing. Small bacteriophage-encoded anti-CRISPR proteins (Acrs) can inactivate Cas9, providing an efficient off switch for Cas9-based applications. Here, we show that two Acrs, AcrIIC1 and AcrIIC3, inhibit Cas9 by distinct strategies. AcrIIC1 is a broad-spectrum Cas9 inhibitor that prevents DNA cutting by multiple divergent Cas9 orthologs through direct binding to the conserved HNH catalytic domain of Cas9. A crystal structure of an AcrIIC1-Cas9 HNH domain complex shows how AcrIIC1 traps Cas9 in a DNA-bound but catalytically inactive state. By contrast, AcrIIC3 blocks activity of a single Cas9 ortholog and induces Cas9 dimerization while preventing binding to the target DNA. These two orthogonal mechanisms allow for separate control of Cas9 target binding and cleavage and suggest applications to allow DNA binding while preventing DNA cutting by Cas9. Copyright © 2017 Elsevier Inc. All rights reserved.

Sexual Risk-Taking in HIV-Negative Gay and Bisexual Men Increases with Depression: Results from a U.S. National Study

PubMed Central

Millar, Brett M.; Starks, Tyrel J.; Grov, Christian; Parsons, Jeffrey T.

2017-01-01

The link between depression and sexual risk-taking has received mixed findings in the literature. The current study analyzed the links between depression and recent condomless anal sex (CAS) with casual partners among 1033 HIV-negative, non-PrEP-using, gay and bisexual men. When CAS was dichotomized as either none or some, depression was not associated with the odds of CAS (with receptive and insertive combined) or insertive CAS only, but was positively associated with the odds of receptive CAS. When CAS was tallied as a count variable of events, depression was positively associated with total CAS, receptive CAS, and insertive CAS. With the addition of a quadratic term for depression, a positive quadratic effect was only found for total CAS and receptive CAS, but not for insertive CAS. These findings highlight the utility of using count data for CAS events and treating CAS separately with regard to receptive and insertive positioning when considering the role of depression among gay and bisexual men. PMID:27475943

POTENTIAL FOR INVASION OF UNDERGROUND SOURCES OF DRINKING WATER THROUGH MUD-PLUGGED WELLS: AN EXPERIMENTAL APPRAISAL

EPA Science Inventory

The main objective of the feasibility study described here was to test the hypothesis that properly plugged wells are effectively sealed by drilling mud. In The process of testing the hypothesis, evidence about dynamics of building mud cake on the wellbore-face was obtained, as ...

76 FR 61295 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-04

..., in the same column, in the ninth entry ``Tributary 11'' should read ``West Mud Creek Tributary 11... ``Tributary B'' should read ``West Mud Creek Tributary B''. 12. On the same page, in the same section, in the same table, in the same column, in the eleventh entry ``Tributary M-1'' should read ``West Mud Creek...

Clueless Newbies in the MUDs: An Introduction to Multiple-User Environments.

ERIC Educational Resources Information Center

LeNoir, W. David

1998-01-01

Describes Multiple-User Dungeons (MUDs), multiple-user computer programs that allow participants to interact with others in "real time" exchanges. Discusses their potential in the writing classroom and beyond, and notes their potential for faculty development activities. Offers a list of Internet resources, some actual MUD addresses, and other…

Programming for Fun: MUDs as a Context for Collaborative Learning.

ERIC Educational Resources Information Center

Bruckman, Amy

Multi-User Dungeons (MUDs), are text-based virtual reality environments in which participants separated by great physical distances can communicate and collaborate in programming. Most MUDs started out as adventure games but are quickly being adapted for more "serious" endeavors. This paper presents a case study of the experiences of a…

Differential proteomic analysis to identify proteins associated with quality traits of frozen mud shrimp (Solenocera melantho) using an iTRAQ-based strategy.

PubMed

Shi, Jing; Zhang, Longteng; Lei, Yutian; Shen, Huixing; Yu, Xunpei; Luo, Yongkang

2018-06-15

An iTRAQ-based strategy was applied to investigate proteome changes in mud shrimp during long-term frozen storage under different conditions. A total of 226 proteins was identified as differential abundance proteins (DAPs) in mud shrimp from two frozen treatment groups (-20 °C and -40 °C) compared with the fresh control group. The proteome changes in mud shrimp muscle stored under -20 °C was much greater than that under -40 °C. Correlation analysis between DAPs and quality traits of mud shrimp muscle showed that 12 proteins were correlated closely with color (L ∗ , a ∗ , and b ∗ value) and texture (hardness, elasticity, and chewiness). Bioinformatic analysis revealed that most of these proteins were involved in protein structure, metabolic enzymes, and protein turnover. Among them, several proteins might be potential protein markers for color, and some proteins are good candidate predictors for textural properties of mud shrimp muscle. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pilot-Scale Test of Dephosphorization in Steelmaking Using Red Mud-Based Flux

NASA Astrophysics Data System (ADS)

Li, Fengshan; Zhang, Yanling; Guo, Zhancheng

2017-09-01

Bayer red mud is characterized by its highly oxidizing nature and high alkalinity. It can act as an ideal flux and dephosphorizer in steelmaking. In this study, pilot-scale tests applying the Bayer red mud-based flux in steelmaking have been conducted in a 200-kg, medium-frequency induction furnace. Good slag fluidity and no rephosphorization phenomena are observed. High dephosphorization rates ( 90%) and low final [P] (<0.02%) are obtained in the situation of high [C] of 2.0-3.0%, which are of great importance for the production of clean steel. The P2O5 content in the P-rich phase in the red mud-based slag can reach as high as 34.05 wt.%, far higher than the 6.73 wt.% in ordinary industrial slag. This suggests that the Al2O3, TiO2 in Bayer red mud can enhance the solid solubility of phosphorus in the P-rich phase. The data obtained are important for promoting the large-scale application of red mud in steelmaking.

New discoveries of mud volcanoes on the Moroccan Atlantic continental margin (Gulf of Cádiz): morpho-structural characterization

NASA Astrophysics Data System (ADS)

León, Ricardo; Somoza, Luis; Medialdea, Teresa; Vázquez, Juan Tomás; González, Francisco Javier; López-González, Nieves; Casas, David; del Pilar Mata, María; del Fernández-Puga, María Carmen; Giménez-Moreno, Carmen Julia; Díaz-del-Río, Víctor

2012-12-01

During the MVSEIS-08 cruise of 2008, ten new mud volcanoes (MVs) were discovered on the offshore Moroccan continental margin (Gulf of Cádiz) at water depths between 750 and 1,600 m, using multibeam bathymetry, backscatter imagery, high-resolution seismic and gravity core data. Mud breccias were recovered in all cases, attesting to the nature of extrusion of these cones. The mud volcanoes are located in two fields: the MVSEIS, Moundforce, Pixie, Las Negras, Madrid, Guadix, Almanzor and El Cid MVs in the western Moroccan field, where mud volcanoes have long been suspected but to date not identified, and the Boabdil and Al Gacel MVs in the middle Moroccan field. Three main morphologies were observed: asymmetric, sub-circular and flat-topped cone-shaped types, this being the first report of asymmetric morphologies in the Gulf of Cádiz. Based on morpho-structural analysis, the features are interpreted to result from (1) repeated constructive (expulsion of fluid mud mixtures) and destructive (gravity-induced collapse and submarine landsliding) episodes and (2) interaction with bottom currents.

Hydration kinetics of cementitious materials composed of red mud and coal gangue

NASA Astrophysics Data System (ADS)

Zhang, Na; Li, Hong-xu; Liu, Xiao-ming

2016-10-01

To elucidate the intrinsic reaction mechanism of cementitious materials composed of red mud and coal gangue (RGC), the hydration kinetics of these cementitious materials at 20°C was investigated on the basis of the Krstulović-Dabić model. An isothermal calorimeter was used to characterize the hydration heat evolution. The results show that the hydration of RGC is controlled by the processes of nucleation and crystal growth (NG), interaction at phase boundaries (I), and diffusion (D) in order, and the pozzolanic reactions of slag and compound-activated red mud-coal gangue are mainly controlled by the I process. Slag accelerates the clinker hydration during NG process, whereas the compound-activated red mud-coal gangue retards the hydration of RGC and the time required for I process increases with increasing dosage of red mud-coal gangue in RGC.

A Volcano of Mud or Lava?

NASA Image and Video Library

2018-06-11

This image from NASA's Mars Reconnaissance Orbiter (MRO) shows a hill with a central crater. Such features have been interpreted as both mud volcanoes (really a sedimentary structure) and as actual volcanoes (the erupting lava kind). They occur on the floor of Valles Marineris below a closed topographic contour that could have held a lake, and the compaction of wet sediments may have created mud volcanoes. The fracture pattern of the bright flow unit surrounding the hill resembles mud cracks. However, there have also been observations from the CRISM instrument interpreted as high-temperature minerals, suggesting actual volcanism, although not necessarily at this location. Fine layers in the hill are consistent with either volcanism or mud flows. Either way, this activity is relatively recent in geologic time and may mark habitable subsurface environments. https://photojournal.jpl.nasa.gov/catalog/PIA22514

The three principles of action: a Pavlovian-instrumental transfer hypothesis

PubMed Central

Cartoni, Emilio; Puglisi-Allegra, Stefano; Baldassarre, Gianluca

2013-01-01

Pavlovian conditioned stimuli can influence instrumental responding, an effect called Pavlovian-instrumental transfer (PIT). During the last decade, PIT has been subdivided into two types: specific PIT and general PIT, each having its own neural substrates. Specific PIT happens when a conditioned stimulus (CS) associated with a reward enhances an instrumental response directed to the same reward. Under general PIT, instead, the CS enhances a response directed to a different reward. While important progress has been made into identifying the neural substrates, the function of specific and general PIT and how they interact with instrumental responses are still not clear. In the experimental paradigm that distinguishes specific and general PIT an effect of PIT inhibition has also been observed and is waiting for an explanation. Here we propose an hypothesis that links these three PIT effects (specific PIT, general PIT and PIT inhibition) to three aspects of action evaluation. These three aspects, which we call “principles of action”, are: context, efficacy, and utility. In goal-directed behavior, an agent has to evaluate if the context is suitable to accomplish the goal, the efficacy of his action in getting the goal, and the utility of the goal itself: we suggest that each of the three PIT effects is related to one of these aspects of action evaluation. In particular, we link specific PIT with the estimation of efficacy, general PIT with the evaluation of utility, and PIT inhibition with the adequacy of context. We also provide a latent cause Bayesian computational model that exemplifies this hypothesis. This hypothesis and the model provide a new framework and new predictions to advance knowledge about PIT functioning and its role in animal adaptation. PMID:24312025

The Totumo mud volcano and its near-shore marine sedimentological setting (North Colombia) - From sedimentary volcanism to epithermal mineralization

NASA Astrophysics Data System (ADS)

Dill, H. G.; Kaufhold, S.

2018-04-01

The Holocene mud volcano exposed at Totumo (younger than 4150 ± 50 yr BP) lines up together with some other landforms of its kind along the Caribbean Coast in northern Colombia. It currently vents a mud of the silicate-phosphate-bearing sulfur-sodium chloride type. The mud volcanoes evolved in an active continental margin setting of the South American Cordillera with high seismicity and affected by pervasive neotectonic structural disturbances. During the Neogene and Quaternary linear terrigenous shoreline sediments alternating with delta deposits evolved on this mobile crustal segment between the Andes and ancient Precambrian cratons. Meso- to microtidal sedimentary settings during transgression and progradation created meta- to instable sedimentary and petrophysical conditions (e.g. overpressure and gas-bearing bubble sands), favorable for the formation of mud volcanoes, whose lithofacies is subdivided into (1) footwall facies (detritus from metabasic, -pelitic source rocks), (2) mud volcano plus lateral facies (material from deep-seated hydrothermal sources, hydrocarbon plays, and brine reflux from the sea), (3) hanging wall facies, sand characterized by a strong longshore drift. The sedimentary volcanism in the area is characterized by different temperatures of formation: (1) pre-stage (<100 °C) and (2) recent stage (≈25 °C). Heavy (pyroxene, amphibole, epidote-clinozoisite, Fe-Ti silicates and oxides, garnet, alumosilicates, tourmaline, zircon, barite, Fe sulfides and -sulfates), light (Ca sulfates, calcite, quartz, feldspar) and clay minerals (kaolinite, mica, pyrophyllite, chlorite, vermiculite) are efficient tools to determine the source of mud, to subdivide the mud volcano system as to its facies and describe its physical-chemical regime as to the temperature of formation, pH and Eh values. The mud volcano system of Totumo bridges the gap between sedimentary "volcanism" and epithermal hot spring deposits of intermediate to high sulfidation and forms a useful "guide" to hydrocarbon accumulation.

Environmental impact of toxic elements in red mud studied by fractionation and speciation procedures.

PubMed

Milačič, Radmila; Zuliani, Tea; Ščančar, Janez

2012-06-01

Aluminum (Al) is mostly produced from bauxite ore, which contains up to 70% of Al(2)O(3) (alumina). Before alumina is refined to aluminum metal, it is purified by hot alkaline extraction. As a waste by-product red mud is formed. Due to its high alkalinity and large quantities, it represents a severe disposal problem. In Kidričevo (Slovenia), red mud was washed with water before disposal, and after drying, covered with soil. In Ajka (Hungary), the red mud slurry was collected directly in a containment structure, which burst caused a major accident in October 2010. In the present work the environmental impact of toxic elements in red mud from Kidričevo and Ajka were evaluated by applying a sequential extraction procedure and speciation analysis. The predominant red mud fraction was the insoluble residue; nevertheless, environmental concern was focused on the highly mobile water-soluble fraction of Al and Cr. Al in the water-soluble Ajka mud fraction was present exclusively in form of toxic [Al(OH)(4)](-), while Cr existed in its toxic hexavalent form. Comparative assessment to red mud from Kidričevo (Slovenia) with a lower alkalinity (pH 9) with that from Ajka demonstrated significantly lower Al solubility and the presence of only trace amounts of Cr(VI), confirming that disposal of neutralized mud is environmentally much more acceptable and carries a smaller risk of ecological accidents. Since during the Ajka accident huge amounts of biologically available Al and moderate Cr(VI) concentrations were released into the terrestrial and aquatic environments, monitoring of Al and Cr(VI) set free during remedial actions at the contaminated site is essential. Particular care should be taken to minimize the risk of release of soluble Al species and Cr(VI) into water supplies and surface waters. Copyright © 2012 Elsevier B.V. All rights reserved.

A probability distribution model of tooth pits for evaluating time-varying mesh stiffness of pitting gears

NASA Astrophysics Data System (ADS)

Lei, Yaguo; Liu, Zongyao; Wang, Delong; Yang, Xiao; Liu, Huan; Lin, Jing

2018-06-01

Tooth damage often causes a reduction in gear mesh stiffness. Thus time-varying mesh stiffness (TVMS) can be treated as an indication of gear health conditions. This study is devoted to investigating the mesh stiffness variations of a pair of external spur gears with tooth pitting, and proposes a new model for describing tooth pitting based on probability distribution. In the model, considering the appearance and development process of tooth pitting, we model the pitting on the surface of spur gear teeth as a series of pits with a uniform distribution in the direction of tooth width and a normal distribution in the direction of tooth height, respectively. In addition, four pitting degrees, from no pitting to severe pitting, are modeled. Finally, influences of tooth pitting on TVMS are analyzed in details and the proposed model is validated by comparing with a finite element model. The comparison results show that the proposed model is effective for the TVMS evaluations of pitting gears.

Support vector machine multiuser receiver for DS-CDMA signals in multipath channels.

PubMed

Chen, S; Samingan, A K; Hanzo, L

2001-01-01

The problem of constructing an adaptive multiuser detector (MUD) is considered for direct sequence code division multiple access (DS-CDMA) signals transmitted through multipath channels. The emerging learning technique, called support vector machines (SVM), is proposed as a method of obtaining a nonlinear MUD from a relatively small training data block. Computer simulation is used to study this SVM MUD, and the results show that it can closely match the performance of the optimal Bayesian one-shot detector. Comparisons with an adaptive radial basis function (RBF) MUD trained by an unsupervised clustering algorithm are discussed.

Influence of drilling operations on drilling mud gas monitoring during IODP Exp. 338 and 348

NASA Astrophysics Data System (ADS)

Hammerschmidt, Sebastian; Toczko, Sean; Kubo, Yusuke; Wiersberg, Thomas; Fuchida, Shigeshi; Kopf, Achim; Hirose, Takehiro; Saffer, Demian; Tobin, Harold; Expedition 348 Scientists, the

2014-05-01

The history of scientific ocean drilling has developed some new techniques and technologies for drilling science, dynamic positioning being one of the most famous. However, while industry has developed newer tools and techniques, only some of these have been used in scientific ocean drilling. The introduction of riser-drilling, which recirculates the drilling mud and returns to the platform solids and gases from the formation, to the International Ocean Drilling Program (IODP) through the launch of the Japan Agency of Marine Earth-Science and Technology (JAMSTEC) riser-drilling vessel D/V Chikyu, has made some of these techniques available to science. IODP Expedition 319 (NanTroSEIZE Stage 2: riser/riserless observatory) was the first such attempt, and among the tools and techniques used was drilling mud gas analysis. While industry regularly conducts drilling mud gas logging for safety concerns and reservoir evaluation, science is more interested in other components (e.g He, 222Rn) that are beyond the scope of typical mud logging services. Drilling mud gas logging simply examines the gases released into the drilling mud as part of the drilling process; the bit breaks and grinds the formation, releasing any trapped gases. These then circulate within the "closed circuit" mud-flow back to the drilling rig, where a degasser extracts these gases and passes them on to a dedicated mud gas logging unit. The unit contains gas chromatographs, mass spectrometers, spectral analyzers, radon gas analyzers, and a methane carbon isotope analyzer. Data are collected and stored in a database, together with several drilling parameters (rate of penetration, mud density, etc.). This initial attempt was further refined during IODP Expeditions 337 (Deep Coalbed Biosphere off Shimokita), 338 (NanTroSEIZE Stage 3: NanTroSEIZE Plate Boundary Deep Riser 2) and finally 348 (NanTroSEIZE Stage 3: NanTroSEIZE Plate Boundary Deep Riser 3). Although still in its development stage for scientific application, this technique can provide a valuable suite of measurements to complement more traditional IODP shipboard measurements. Here we present unpublished data from IODP Expeditions 338 and 348, penetrating the Nankai Accretionary wedge to 3058.5 meters below seafloor. Increasing mud density decreased degasser efficiency, especially for higher hydrocarbons. Blurring of the relative variations in total gas by depth was observed, and confirmed with comparison to headspace gas concentrations from the cored interval. Theoretically, overpressured zones in the formation can be identified through C2/C3 ratios, but these ratios are highly affected by changing drilling parameters. Proper mud gas evaluations will need to carefully consider the effects of variable drilling parameters when designing experiments and interpreting the data.

A Cas9 transgenic Plasmodium yoelii parasite for efficient gene editing.

PubMed

Qian, Pengge; Wang, Xu; Yang, Zhenke; Li, Zhenkui; Gao, Han; Su, Xin-Zhuan; Cui, Huiting; Yuan, Jing

2018-06-01

The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P. yoelii. The resulted PyCas9ki parasite displays normal progression during the whole life cycle and possesses the Cas9 protein expression in asexual blood stage. By introducing the plasmid (pYCs) containing only sgRNA and homologous template elements, we successfully achieved both deletion and tagging modifications for different endogenous genes in the genome of PyCas9ki parasite. This cas9-knockin PyCas9ki parasite provides a new platform facilitating gene functions study in the rodent malaria parasite P. yoelii. Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluation of blends bauxite-calcination-method red mud with other industrial wastes as a cementitious material: properties and hydration characteristics.

PubMed

Zhang, Na; Liu, Xiaoming; Sun, Henghu; Li, Longtu

2011-01-15

Red mud is generated from alumina production, and its disposal is currently a worldwide problem. In China, large quantities of red mud derived from bauxite calcination method are being discharged annually, and its utilization has been an urgent topic. This experimental research was to evaluate the feasibility of blends red mud derived from bauxite calcination method with other industrial wastes for use as a cementitious material. The developed cementitious material containing 30% of the bauxite-calcination-method red mud possessed compressive strength properties at a level similar to normal Portland cement, in the range of 45.3-49.5 MPa. Best compressive strength values were demonstrated by the specimen RSFC2 containing 30% bauxite-calcination-method red mud, 21% blast-furnace slag, 10% fly ash, 30% clinker, 8% gypsum and 1% compound agent. The mechanical and physical properties confirm the usefulness of RSFC2. The hydration characteristics of RSFC2 were characterized by XRD, FTIR, (27)Al MAS-NMR and SEM. As predominant hydration products, ettringite and amorphous C-S-H gel are principally responsible for the strength development of RSFC2. Comparing with the traditional production for ordinary Portland cement, this green technology is easier to be implemented and energy saving. This paper provides a key solution to effectively utilize bauxite-calcination-method red mud. Copyright © 2010 Elsevier B.V. All rights reserved.

Molecular Simulation Study on Modification Mechanism of Red Mud Modified Asphalt

NASA Astrophysics Data System (ADS)

Tao, FU; Hui-ming, BAO; xing-xing, Duan

2017-12-01

This article used red mud, the aluminum industrial wastes, as modified asphalt material, through the study of the routine test of modified asphalt properties, and the micro test of electron microscope scanning, infrared spectrum and differential scanning calorimetry analysis etc. to discuss its performance and modification mechanism . The test results show that after mixing red mud, asphalt’s penetration index and 15 °C ductility reduced, softening point enhanced, thus the temperature sensitivity and high temperature stability of asphalt improved; Red mud after mixing the matrix asphalt, can form a uniform, stable and matrix asphalt blending system, and improve the asphalt’s thermal stability. Using molecular simulation technology to analyze the asphalt with the temperature change of energy and find in the process of asphalt melting, the largest is the key to influence on bituminous, and van der waals energy is small. It concludes that red mud -modified asphalt material is mainly controlled by bond energy, in order to obtain its favorable property of modification mechanism, red mud of senior activation and molecular bond energy of asphalt is needed to be enhanced.The results of molecular simulation show that the main component of hematite in red mud is the most adsorbed in the asphalt, the asphaltene is the second, the colloid is the worst, but the adsorption capacity of the colloid is the highest.

Alkaline Pretreatment of Sugarcane Bagasse and Filter Mud Codigested to Improve Biomethane Production

PubMed Central

Mehryar, Esmaeil; Bi, Jinhua

2016-01-01

To enhance the codigestion of degradation and improve biomethane production potential, sugarcane bagasse and filter mud were pretreated by sodium hydroxide NaOH 1 N at 100°C for 15, 30, and 45 minutes, respectively. Biomethane generation from 1-liter batch reactor was studied at mesophilic temperature (37 ± 1)°C, solid concentrations of 6%, and five levels of mixing proportion with and without pretreatment. The results demonstrate that codigestion of filter mud with bagasse produces more biomethane than fermentation of filter mud as single substrate; even codigested substrate composition presented a better balance of nutrients (C/N ratio of 24.70) when codigestion ratio between filter mud and bagasse was 25 : 75 in comparison to filter mud as single substrate (C/N ratio 9.68). All the pretreatments tested led to solubilization of the organic matter, with a maximum lignin reduction of 86.27% and cumulative yield of biomethane (195.8 mL·gVS−1, digestion of pretreated bagasse as single substrate) obtained after 45 minutes of cooking by NaOH 1 N at 100°C. Under this pretreatment condition, significant increase in cumulative methane yield was observed (126.2 mL·gVS−1) at codigestion ratio of 25 : 75 between filter mud and bagasse by increase of 81.20% from untreated composition. PMID:27738635

Large historical eruptions at subaerial mud volcanoes, Italy

NASA Astrophysics Data System (ADS)

Manga, M.; Bonini, M.

2012-11-01

Active mud volcanoes in the northern Apennines, Italy, currently have gentle eruptions. There are, however, historical accounts of violent eruptions and outbursts. Evidence for large past eruptions is also recorded by large decimeter rock clasts preserved in erupted mud. We measured the rheological properties of mud currently being erupted in order to evaluate the conditions needed to transport such large clasts to the surface. The mud is well-characterized by the Herschel-Bulkley model, with yield stresses between 4 and 8 Pa. Yield stresses of this magnitude can support the weight of particles with diameters up to several mm. At present, particles larger than this size are not being carried to the surface. The transport of larger clasts to the surface requires ascent speeds greater than their settling speed in the mud. We use a model for the settling of particles and rheological parameters from laboratory measurements to show that the eruption of large clasts requires ascent velocities > 1 m s-1, at least three orders of magnitude greater than during the present, comparatively quiescent, activity. After regional earthquakes on 20 May and 29 May 2012, discharge also increased at locations where the stress changes produced by the earthquakes would have unclamped feeder dikes below the mud volcanoes. The magnitude of increased discharge, however, is less than that inferred from the large clasts. Both historical accounts and erupted deposits are consistent in recording episodic large eruptions.

Effects of thermal treatments on the characterisation and utilisation of red mud with sawdust additive.

PubMed

Liu, Yanju; Naidu, Ravi; Ming, Hui; Dharmarajan, Rajarathnam; Du, Jianhua

2016-06-01

Extremely large amounts of red mud (bauxite residue) are generated globally every year from alumina refining industries, which are being disposed of on engineered landfills. The objective of this study is to investigate the effects of thermal treatments on red mud for development of utilisation strategies. Thermal treatments of red mud samples and their characterisations were investigated under inert (N2) and oxidative (air) conditions with and without sawdust addition at 200-600°C. After calcination, the resulting samples were analysed using thermogravimetric-infrared spectroscopy (TG-IR) for functional group transformations, thermogravimetric analysis (TGA) for thermal loss profiles and X-ray diffraction (XRD) for mineral transformations. The characterisation results showed that in N2 environment, boehmite in red mud was transferred to transition alumina at around 400°C while losing water from structural components. The addition of sawdust for incubation and calcination of red mud in air increased the surface area, whereas that in nitrogen atmosphere lead to reduction of hematite to magnetite at around 500°C. The incorporated carbon materials played a major role in increasing the surface area especially for pore size less than 2.5 nm. This treated red mud with altered mineral composition and improved properties for binding contaminants can be used for environmental remediation and in the process of metal recovery such as iron. © The Author(s) 2016.

Alkaline Pretreatment of Sugarcane Bagasse and Filter Mud Codigested to Improve Biomethane Production.

PubMed

Talha, Zahir; Ding, Weimin; Mehryar, Esmaeil; Hassan, Muhammad; Bi, Jinhua

2016-01-01

To enhance the codigestion of degradation and improve biomethane production potential, sugarcane bagasse and filter mud were pretreated by sodium hydroxide NaOH 1 N at 100°C for 15, 30, and 45 minutes, respectively. Biomethane generation from 1-liter batch reactor was studied at mesophilic temperature (37 ± 1)°C, solid concentrations of 6%, and five levels of mixing proportion with and without pretreatment. The results demonstrate that codigestion of filter mud with bagasse produces more biomethane than fermentation of filter mud as single substrate; even codigested substrate composition presented a better balance of nutrients (C/N ratio of 24.70) when codigestion ratio between filter mud and bagasse was 25 : 75 in comparison to filter mud as single substrate (C/N ratio 9.68). All the pretreatments tested led to solubilization of the organic matter, with a maximum lignin reduction of 86.27% and cumulative yield of biomethane (195.8 mL·gVS -1 , digestion of pretreated bagasse as single substrate) obtained after 45 minutes of cooking by NaOH 1 N at 100°C. Under this pretreatment condition, significant increase in cumulative methane yield was observed (126.2 mL·gVS -1 ) at codigestion ratio of 25 : 75 between filter mud and bagasse by increase of 81.20% from untreated composition.

Experimental Study of Goaf Filling Materials Based on Red Mud

NASA Astrophysics Data System (ADS)

Mu, Mangen; Gao, Xiaozhen; Guo, Taoming; Hu, Xinping

2018-01-01

Red mud as soild waste is difficult to treatment. Goaf filling materials can make a large use of red mud. By the experimental study,we find that the red mud, fly ash, ground slag and desulfida-tion gypsum can be used to make goaf filling materials based on the principle of alkali excitation and metalion stability.Through the control variable method, we find that the optimal proportion of goaf filling materials based on red mud is red mud 55%, fly ash 30%, cement 7.5%, fly ash 2.5%, desulfurization gypsum 5%, admixture 1%, and water solid ratio=1:1.2.The 28days final material strength was 2.0 MPa,which achives the technical specification requirements.Through the test of SEM, XRD and IR, it is indicated that the strength formation of goaf filling material based on red mud is from the unformed linking hydration products of amorphous alkali excitation system. With curing time from 3 to 7 days, the unformed linking hydration products grown a lot of vitreous hydration products. When hydration reaction basicly finished after 28 days, the hydration products have developed into a large volume of massive vitreous with an extremely dense structure. The Ca2SiO3 mineral phase is significantly reduced, which is participate in hydration reactions. The decrease of Ca2SiO3 indicates that the Si-O bond in the system have been ruptured and reorganized.

Automatic mouse ultrasound detector (A-MUD): A new tool for processing rodent vocalizations

PubMed Central

Reitschmidt, Doris; Noll, Anton; Balazs, Peter; Penn, Dustin J.

2017-01-01

House mice (Mus musculus) emit complex ultrasonic vocalizations (USVs) during social and sexual interactions, which have features similar to bird song (i.e., they are composed of several different types of syllables, uttered in succession over time to form a pattern of sequences). Manually processing complex vocalization data is time-consuming and potentially subjective, and therefore, we developed an algorithm that automatically detects mouse ultrasonic vocalizations (Automatic Mouse Ultrasound Detector or A-MUD). A-MUD is a script that runs on STx acoustic software (S_TOOLS-STx version 4.2.2), which is free for scientific use. This algorithm improved the efficiency of processing USV files, as it was 4–12 times faster than manual segmentation, depending upon the size of the file. We evaluated A-MUD error rates using manually segmented sound files as a ‘gold standard’ reference, and compared them to a commercially available program. A-MUD had lower error rates than the commercial software, as it detected significantly more correct positives, and fewer false positives and false negatives. The errors generated by A-MUD were mainly false negatives, rather than false positives. This study is the first to systematically compare error rates for automatic ultrasonic vocalization detection methods, and A-MUD and subsequent versions will be made available for the scientific community. PMID:28727808

A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) in Haloferax volcanii*

PubMed Central

Brendel, Jutta; Stoll, Britta; Lange, Sita J.; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A.; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

2014-01-01

The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA. PMID:24459147

A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii.

PubMed

Brendel, Jutta; Stoll, Britta; Lange, Sita J; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

2014-03-07

The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1-8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.

Beta-carbonic anhydrases play a role in fruiting body development and ascospore germination in the filamentous fungus Sordaria macrospora.

PubMed

Elleuche, Skander; Pöggeler, Stefanie

2009-01-01

Carbon dioxide (CO(2)) is among the most important gases for all organisms. Its reversible interconversion to bicarbonate (HCO(3) (-)) reaches equilibrium spontaneously, but slowly, and can be accelerated by a ubiquitous group of enzymes called carbonic anhydrases (CAs). These enzymes are grouped by their distinct structural features into alpha-, beta-, gamma-, delta- and zeta-classes. While physiological functions of mammalian, prokaryotic, plant and algal CAs have been extensively studied over the past years, the role of beta-CAs in yeasts and the human pathogen Cryptococcus neoformans has been elucidated only recently, and the function of CAs in multicellular filamentous ascomycetes is mostly unknown. To assess the role of CAs in the development of filamentous ascomycetes, the function of three genes, cas1, cas2 and cas3 (carbonic anhydrase of Sordaria) encoding beta-class carbonic anhydrases was characterized in the filamentous ascomycetous fungus Sordaria macrospora. Fluorescence microscopy was used to determine the localization of GFP- and DsRED-tagged CAs. While CAS1 and CAS3 are cytoplasmic enzymes, CAS2 is localized to the mitochondria. To assess the function of the three isoenzymes, we generated knock-out strains for all three cas genes (Deltacas1, Deltacas2, and Deltacas3) as well as all combinations of double mutants. No effect on vegetative growth, fruiting-body and ascospore development was seen in the single mutant strains lacking cas1 or cas3, while single mutant Deltacas2 was affected in vegetative growth, fruiting-body development and ascospore germination, and the double mutant strain Deltacas1/2 was completely sterile. Defects caused by the lack of cas2 could be partially complemented by elevated CO(2) levels or overexpression of cas1, cas3, or a non-mitochondrial cas2 variant. The results suggest that CAs are required for sexual reproduction in filamentous ascomycetes and that the multiplicity of isoforms results in redundancy of specific and non-specific functions.

NIR detection of pits and pit fragments in fresh cherries (abstract)

USDA-ARS?s Scientific Manuscript database

The feasibility of using near infrared (NIR) diffuse reflectance spectroscopy for the detection of pits and pit fragments in cherries was demonstrated. For detection of whole pits, 300 cherries were obtained locally and pits were removed from half. NIR reflectance spectra were obtained in triplicate...

7 CFR 52.779 - Freedom from pits.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Freedom from pits. 52.779 Section 52.779 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Freedom from pits. (a) General. The factor of freedom from pits refers to the incidence of pits and pit...

The effects of pitting on fatigue crack nucleation in 7075-T6 aluminum alloy

NASA Technical Reports Server (NTRS)

Ma, LI; Hoeppner, David W.

1994-01-01

A high-strength aluminum alloy, 7075-T6, was studied to quantitatively evaluate chemical pitting effects of its corrosion fatigue life. The study focused on pit nucleation, pit growth, and fatigue crack nucleation. Pitting corrosion fatigue experiments were conducted in 3.5 percent NaCl aqueous solution under constant amplitude sinusoidal loading at two frequencies, 5 and 20 Hz. Smooth and unnotched specimens were used in this investigation. A video recording system was developed to allow in situ observation of the surface changes of the specimens during testing. The results indicated that pitting corrosion considerably reduces the fatigue strength by accelerating fatigue crack nucleation. A metallographic examination was conducted on the specimens to evaluate the nature of corrosion pits. First, the actual shapes of the corrosion pits were evaluated by cross-sectioning the pits. Secondly, the relation between corrosion pits and microstructure was also investigated. Finally, the possibility of another corrosion mechanism that might be involved in pitting was explored in this investigation. The fractography of the tested specimens showed that corner corrosion pits were responsible for fatigue crack nucleation in the material due to the associated stress concentration. The pits exhibited variance of morphology. Fatigue life for the experimental conditions appeared to be strongly dependent on pitting kinetics and the crack nucleation stage.

The role of Cas8 in type I CRISPR interference.

PubMed

Cass, Simon D B; Haas, Karina A; Stoll, Britta; Alkhnbashi, Omer S; Sharma, Kundan; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita; Bolt, Edward L

2015-05-05

CRISPR (clustered regularly interspaced short palindromic repeat) systems provide bacteria and archaea with adaptive immunity to repel invasive genetic elements. Type I systems use 'cascade' [CRISPR-associated (Cas) complex for antiviral defence] ribonucleoprotein complexes to target invader DNA, by base pairing CRISPR RNA (crRNA) to protospacers. Cascade identifies PAMs (protospacer adjacent motifs) on invader DNA, triggering R-loop formation and subsequent DNA degradation by Cas3. Cas8 is a candidate PAM recognition factor in some cascades. We analysed Cas8 homologues from type IB CRISPR systems in archaea Haloferax volcanii (Hvo) and Methanothermobacter thermautotrophicus (Mth). Cas8 was essential for CRISPR interference in Hvo and purified Mth Cas8 protein responded to PAM sequence when binding to nucleic acids. Cas8 interacted physically with Cas5-Cas7-crRNA complex, stimulating binding to PAM containing substrates. Mutation of conserved Cas8 amino acid residues abolished interference in vivo and altered catalytic activity of Cas8 protein in vitro. This is experimental evidence that Cas8 is important for targeting Cascade to invader DNA. © 2015 Authors.

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation.

PubMed

Kieper, Sebastian N; Almendros, Cristóbal; Behler, Juliane; McKenzie, Rebecca E; Nobrega, Franklin L; Haagsma, Anna C; Vink, Jochem N A; Hess, Wolfgang R; Brouns, Stan J J

2018-03-27

CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Differential InSAR Monitoring of the Lampur Sidoarjo Mud Volcano (Java, Indonesia) Using ALOS PALSAR Imagery

NASA Astrophysics Data System (ADS)

Thomas, Adam; Holley, Rachel; Burren, Richard; Meikle, Chris; Shilston, David

2010-03-01

The Lampur Sidoarjo mud volcano (Java, Indonesia), colloquially called LUSI, first appeared in May 2006. Its cause, whether the result of natural or anthropogenic activities (or a combination of both), is still being debated within the academic, engineering and political communities.The mud volcano expels up to 150,000 m3 of mud per day; and over time, this large volume of mud has had a major environmental and economic impact on the region. The mud flow from LUSI has now covered 6 km2 to depths some tens of metres, displacing approximately 30,000 residents; and continues to threaten local communities, businesses and industry. With such a large volume of mud being expelled each day it is inevitable (as with onshore oil and gas production fields) that there will be some ground surface movement and instability issues at the mud source (the main vent), and in the vicinity of the mud volcano footprint.Due to the dynamic ground surface conditions, engineers and academics alike have found it difficult to reliably monitor ground surface movements within the effected region using conventional surveying techniques. Consequently, engineers responsible for the risk assessment of ground surface instabilities within the proximity of LUSI have called upon the use of satellite interferometry to continually monitor the hazard.The Advanced Land Observing Satellite (ALOS), launched on 24th January 2006, carries onboard an L- band Synthetic Aperture Radar (SAR) instrument called PALSAR (Phased Array type L-band Synthetic Aperture Radar). In contrast to established C-band (5.6cm wavelength) SAR instruments onboard ERS-1 & -2, Envisat, Radarsat-1, and the recently launched Radarsat-2 satellite, PALSAR's (L-band/23.8cm wavelength) instrument presents a number of advantages, including the ability to map larger-scale ground motions, over relatively short timeframes, in tropical environments, without suffering as significantly from signal decorrelation associated with C-band imagery.This paper presents the results of a 2-year ALOS PALSAR Differential Interferometric (DifSAR) monitoring campaign across the LUSI mud volcano. DifSAR processing was applied to a sequence of images acquired on a 3 to 6-month basis between May 2006 and May 2008. The results highlight the capability of ALOS PALSAR in detecting decimetres of coherent ground subsidence to assist engineers in their analysis of the structure, dynamics and overall stability of the mud volcano and the surrounding region.

Naturally Occurring Off-Switches for CRISPR-Cas9.

PubMed

Pawluk, April; Amrani, Nadia; Zhang, Yan; Garcia, Bianca; Hidalgo-Reyes, Yurima; Lee, Jooyoung; Edraki, Alireza; Shah, Megha; Sontheimer, Erik J; Maxwell, Karen L; Davidson, Alan R

2016-12-15

CRISPR-Cas9 technology would be enhanced by the ability to inhibit Cas9 function spatially, temporally, or conditionally. Previously, we discovered small proteins encoded by bacteriophages that inhibit the CRISPR-Cas systems of their host bacteria. These "anti-CRISPRs" were specific to type I CRISPR-Cas systems that do not employ the Cas9 protein. We posited that nature would also yield Cas9 inhibitors in response to the evolutionary arms race between bacteriophages and their hosts. Here, we report the discovery of three distinct families of anti-CRISPRs that specifically inhibit the CRISPR-Cas9 system of Neisseria meningitidis. We show that these proteins bind directly to N. meningitidis Cas9 (NmeCas9) and can be used as potent inhibitors of genome editing by this system in human cells. These anti-CRISPR proteins now enable "off-switches" for CRISPR-Cas9 activity and provide a genetically encodable means to inhibit CRISPR-Cas9 genome editing in eukaryotes. VIDEO ABSTRACT. Copyright © 2016 Elsevier Inc. All rights reserved.

Naturally occurring off-switches for CRISPR-Cas9

PubMed Central

Pawluk, April; Amrani, Nadia; Zhang, Yan; Garcia, Bianca; Hidalgo-Reyes, Yurima; Lee, Jooyoung; Edraki, Alireza; Shah, Megha; Sontheimer, Erik J.; Maxwell, Karen L.; Davidson, Alan R.

2017-01-01

Summary CRISPR-Cas9 technology would be enhanced by the ability to inhibit Cas9 function spatially, temporally, or conditionally. Previously, we discovered small proteins encoded by bacteriophages that inhibit the CRISPR-Cas systems of their host bacteria. These “anti-CRISPRs” were specific to type I CRISPR-Cas systems that do not employ the Cas9 protein. We posited that nature would also yield Cas9 inhibitors in response to the evolutionary arms race between bacteriophages and their hosts. Here, we report the discovery of three distinct families of anti-CRISPRs that specifically inhibit the CRISPR-Cas9 system of Neisseria meningitidis. We show that these proteins bind directly to N. meningitidis Cas9 (NmeCas9), and can be used as potent inhibitors of genome editing by this system in human cells. These anti-CRISPR proteins now enable “off-switches” for CRISPR-Cas9 activity, and provide a genetically-encodable means to inhibit CRISPR-Cas9 genome editing in eukaryotes. PMID:27984730

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit.

PubMed

Murugan, Karthik; Babu, Kesavan; Sundaresan, Ramya; Rajan, Rakhi; Sashital, Dipali G

2017-10-05

CRISPR-Cas systems defend prokaryotes against bacteriophages and mobile genetic elements and serve as the basis for revolutionary tools for genetic engineering. Class 2 CRISPR-Cas systems use single Cas endonucleases paired with guide RNAs to cleave complementary nucleic acid targets, enabling programmable sequence-specific targeting with minimal machinery. Recent discoveries of previously unidentified CRISPR-Cas systems have uncovered a deep reservoir of potential biotechnological tools beyond the well-characterized Type II Cas9 systems. Here we review the current mechanistic understanding of newly discovered single-protein Cas endonucleases. Comparison of these Cas effectors reveals substantial mechanistic diversity, underscoring the phylogenetic divergence of related CRISPR-Cas systems. This diversity has enabled further expansion of CRISPR-Cas biotechnological toolkits, with wide-ranging applications from genome editing to diagnostic tools based on various Cas endonuclease activities. These advances highlight the exciting prospects for future tools based on the continually expanding set of CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

A comparative study of mud-like and coralliform calcium carbonate gallbladder stones.

PubMed

Ma, Rui-Hong; Luo, Xiao-Bing; Wang, Xiao-Feng; Qiao, Tie; Huang, Hai-Yi; Zhong, Hai-Qiang

2017-07-01

To gain insight to underlying mechanism of the formation of calcium carbonate (CaCO 3 ) gallbladder stones, we did comparative study of stones with mud appearance and those with coralliform appearance. A total of 93 gallbladder stones with mud appearance and 50 stones with coralliform appearance were analyzed. The appearance, color, texture, and the detection of Clonorchis sinensis eggs by microscopic examination were compared between the two groups. Then, the material compositions of stones were analyzed using Fourier Transform Infrared spectroscopy and the spectrogram characteristics were compared. Moreover, microstructure characteristics of the two kinds of stones were observed and compared with Scanning Electron Microscopy. Mud-like gallbladder stones were mainly earthy yellow or brown with brittle or soft texture, while coralliform stones were mainly black with extremely hard texture, the differences between the two groups was significant (p < .05). The analytic results of FTIR spectroscopy showed that 95.7% (89/93) of the mud-like gallbladder stones were CaCO 3 stones, and mainly aragonite; while all of the coralliform stones were CaCO 3 stones, and mainly calcite (p < .05). Meanwhile, microscopic examination indicated that the detection rate of Clonorchis sinensis eggs in mud-like CaCO 3 stones was lower than that in coralliform CaCO 3 stones (p < .05), and that in aragonite CaCO 3 stones was lower than that in calcite CaCO 3 stones(p < .05). Mud-like CaCO 3 stones mainly happened to patients with cystic duct obstruction. Clonorchis sinensis infection was mainly associated with coralliform (calcite) CaCO 3 stones. Cystic duct obstruction was mainly associated with mud-like (aragonite) CaCO 3 stones. © 2017 Wiley Periodicals, Inc.

Wave climate, sediment supply and the depth of the sand-mud transition: A global survey

USGS Publications Warehouse

George, D.A.; Hill, P.S.

2008-01-01

The influences of wave climate and sediment supply on the depths of sand-mud transitions (hSMT) are investigated. Depths of sand-mud transitions (SMT) are based on published granulometric data from surface samples gathered from 14 sites in different wave-dominated coastal environments with fluvial input, including high energy (Columbia, Eel, Russian, San Lorenzo, Copper, and Nepean rivers), moderate energy (Ebro, Nile, Santa Clara, Tseng-wen and Kao-ping rivers), and low energy (Po, Pescara and Tronto rivers) regimes. Geometric mean diameter (GMD) and mud percent are compiled from samples along shore-normal transects, and significant correlation is found between these two textural descriptors. Nominally, the SMT is defined as the transition from GMD > 63????m to 25% mud. This dual definition is applied to the 14 systems, and hSMT is tabulated for each system. Correlation is found between hSMT and the depth at which wave-induced bottom shear stress equals the critical erosion shear stress of the largest mud particles and also between hSMT and significant wave height. Lack of correlation between hSMT and sediment load of nearby rivers indicates either that the influence of sediment supply on depth of the sand-mud transition is small or is not adequately represented in this study. Shelf width and slope do not correlate with residuals from a formalized linear relationship between hSMT and significant wave height. The relationship between hSMT and wave climate is useful for calibration of numerical models of erosion and deposition in wave-dominated coastal environments, for prediction of seabed properties in remote or inaccessible areas, and for reconstruction of paleodepth based on facies changes from sand to mud in ancient rocks. ?? 2008.

Matched sibling versus matched unrelated allogeneic hematopoietic stem cell transplantation in children with severe acquired aplastic anemia: experience of the polish pediatric group for hematopoietic stem cell transplantation.

PubMed

Szpecht, Dawid; Gorczyńska, Ewa; Kałwak, Krzysztof; Owoc-Lempach, Joanna; Choma, Marta; Styczyński, Jan; Goździk, Jolanta; Dłużniewska, Agnieszka; Wysocki, Mariusz; Kowalczyk, Jerzy R; Chybicka, Alicja; Pieczonka, Anna; Wachowiak, Jacek

2012-06-01

In the study, 48 children with severe acquired aplastic anemia (SAA) transplanted from matched sibling donor (MSD) between 1991 and 2009, and 38 children with SAA transplanted from matched unrelated donor (MUD) between 2000 and 2009 were evaluated. Engraftment was achieved in 45 (93.75 %) patients after MSD-hematopoietic stem cell transplantation (HSCT) and in 33 (86.8 %) after MUD-HSCT. Transplant-related mortality rate after MSD-HSCT was 8 %, while 37 % after MUD-HSCT. After MSD-HSCT 44 (91.7 %) patients are alive for 1-216 months (median: 85 months), while after MUD-HSCT 24 (63.2 %) patients for 1-84 months (median: 16 months). The 5-year probability of event-free survival after MSD-HSCT and MUD-HSCT was 87 and 53 %, respectively, while 5 years of overall survival was 91 and 64 %, respectively. It was concluded that MSD-HSCT as the first line treatment for children with SAA is a safe therapeutic approach with a low rate of treatment failures and excellent outcome. Results of MUD-HSCT in pediatric patients with SAA who failed to respond to immunosuppressive therapy are still inferior than those of MSD-HSCT. Treatment failures of MUD-HSCT are mainly related to infectious complications and graft failure. It seems, however, that HLA-matching of unrelated donors at allelic level along with early MUD-HSCT after FCA (FLUDA, low-dose cyclophosphamide, and anti-thymocyte globulin) conditioning, perhaps using lower Thymoglobulin dose could enable further improvement of long-term results in children with SAA who lack MSD.

The effects of the Yogyakarta earthquake at LUSI mud volcano, Indonesia

NASA Astrophysics Data System (ADS)

Lupi, M.; Saenger, E. H.; Fuchs, F.; Miller, S. A.

2013-12-01

The M6.3 Yogyakarta earthquake shook Central Java on May 27th, 2006. Forty seven hours later, hot mud outburst at the surface near Sidoarjo, approximately 250 km from the earthquake epicentre. The mud eruption continued and originated LUSI, the youngest mud volcanic system on earth. Since the beginning of the eruption, approximately 30,000 people lost their homes and 13 people died due to the mud flooding. The causes that initiated the eruption are still debated and are based on different geological observations. The earthquake-triggering hypothesis is supported by the evidence that at the time of the earthquake ongoing drilling operations experienced a loss of the drilling mud downhole. In addition, the eruption of the mud began only 47 hours after the Yogyakarta earthquake and the mud reached the surface at different locations aligned along the Watukosek fault, a strike-slip fault upon which LUSI resides. Moreover, the Yogyakarta earthquake also affected the volcanic activity of Mt. Semeru, located as far as Lusi from the epicentre of the earthquake. However, the drilling-triggering hypothesis points out that the earthquake was too far from LUSI for inducing relevant stress changes at depth and highlight how upwelling fluids that reached the surface first emerged only 200 m far from the drilling rig that was operative at the time. Hence, was LUSI triggered by the earthquake or by drilling operations? We conducted a seismic wave propagation study on a geological model based on vp, vs, and density values for the different lithologies and seismic profiles of the crust beneath LUSI. Our analysis shows compelling evidence for the effects produced by the passage of seismic waves through the geological formations and highlights the importance of the overall geological structure that focused and reflected incoming seismic energy.

Cellular immune responses and phagocytic activity of fishes exposed to pollution of volcano mud.

PubMed

Risjani, Yenny; Yunianta; Couteau, Jerome; Minier, Christophe

2014-05-01

Since May 29, 2006, a mud volcano in the Brantas Delta of the Sidoarjo district has emitted mud that has inundated nearby villages. Pollution in this area has been implicated in detrimental effects on fish health. In fishes, leukocyte and phagocytic cells play a vital role in body defenses. We report for the first time the effect of "LUSI" volcano mud on the immune systems of fish in the Brantas Delta. The aim of this study was to find biomarkers to allow the evaluation of the effects of volcanic mud and anthropogenic pollution on fish health in the Brantas Delta. The study took places at the Brantas Delta, which was polluted by volcano mud, and at reference sites in Karangkates and Pasuruan. Leukocyte numbers were determined using a Neubauer hemocytometer and a light microscope. Differential leukocyte counts were determined using blood smears stained with May Grunwald-Giemsa, providing neutrophil, lymphocyte and monocyte counts. Macrophages were taken from fish kidney, and their phagocytic activity was measured. In vitro analyses revealed that leukocyte and differential leukocyte counts (DLC) were higher in Channa striata and Chanos chanos caught from the polluted area. Macrophage numbers were higher in Oreochromis mossambicus than in the other species, indicating that this species is more sensitive to pollution. In areas close to volcanic mud eruption, all specimens had lower phagocytic activity. Our results show that immune cells were changed and phagocytic activity was reduced in the polluted area indicating cytotoxicity and alteration of the innate immune system in fishes exposed to LUSI volcano mud and anthropogenic pollution. Copyright © 2014 Elsevier Ltd. All rights reserved.

How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.

PubMed

Xiao, Yibei; Ng, Sherwin; Nam, Ki Hyun; Ke, Ailong

2017-10-05

CRISPR (clustered regularly interspaced short palindromic repeats) and the nearby Cas (CRISPR-associated) operon establish an RNA-based adaptive immunity system in prokaryotes. Molecular memory is created when a short foreign DNA-derived prespacer is integrated into the CRISPR array as a new spacer. Whereas the RNA-guided CRISPR interference mechanism varies widely among CRISPR-Cas systems, the spacer integration mechanism is essentially identical. The conserved Cas1 and Cas2 proteins form an integrase complex consisting of two distal Cas1 dimers bridged by a Cas2 dimer. The prespacer is bound by Cas1-Cas2 as a dual-forked DNA, and the terminal 3'-OH of each 3' overhang serves as an attacking nucleophile during integration. The prespacer is preferentially integrated into the leader-proximal region of the CRISPR array, guided by the leader sequence and a pair of inverted repeats inside the CRISPR repeat. Spacer integration in the well-studied Escherichia coli type I-E CRISPR system also relies on the bacterial integration host factor. In type II-A CRISPR, however, Cas1-Cas2 alone integrates spacers efficiently in vitro; other Cas proteins (such as Cas9 and Csn2) have accessory roles in the biogenesis phase of prespacers. Here we present four structural snapshots from the type II-A system of Enterococcus faecalis Cas1 and Cas2 during spacer integration. Enterococcus faecalis Cas1-Cas2 selectively binds to a splayed 30-base-pair prespacer bearing 4-nucleotide 3' overhangs. Three molecular events take place upon encountering a target: first, the Cas1-Cas2-prespacer complex searches for half-sites stochastically, then it preferentially interacts with the leader-side CRISPR repeat, and finally, it catalyses a nucleophilic attack that connects one strand of the leader-proximal repeat to the prespacer 3' overhang. Recognition of the spacer half-site requires DNA bending and leads to full integration. We derive a mechanistic framework to explain the stepwise spacer integration process and the leader-proximal preference.

How Type II CRISPR-Cas establish immunity through Cas1-Cas2 mediated spacer integration

PubMed Central

Xiao, Yibei; Ng, Sherwin; Nam, Ki Hyun; Ke, Ailong

2017-01-01

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the nearby cas (CRISPR-associated) operon establish an RNA-based adaptive immunity system in prokaryotes1–5. Molecular memory is created when a short foreign DNA-derived prespacer is integrated into the CRISPR array as a new spacer6–9. Whereas the RNA-guided CRISPR interference mechanism varies widely among CRISPR-Cas systems, the spacer integration mechanism is essentially identical7–9. The conserved Cas1 and Cas2 proteins form an integrase complex consisting two distal Cas1 dimers bridged by a Cas2 dimer in the middle6,10. The prespacer is bound by Cas1-Cas2 as a dual forked DNA, and the terminal 3′-OH of each 3′-overhang serves as an attacking nucleophile during integration11–14. Importantly, the prespacer is preferentially integrated into the leader-proximal region of the CRISPR array1,7,10,15, guided by the leader sequence and a pair of inverted repeats (IRs) inside the CRISPR repeat7,15–20. Spacer integration in the most well-studied Escherichia coli Type I-E CRISPR system further relies on the bacterial Integration Host Factor (IHF)21,22. In Type II-A CRISPR, however, Cas1-Cas2 alone integrates spacer efficiently in vitro18; other Cas proteins (Cas9 and Csn2) play accessory roles in prespacer biogenesis17,23. Focusing on the Enterococcus faecalis Type II-A system24, here we report four structure snapshots of Cas1-Cas2 during spacer integration. EfaCas1-Cas2 selectively binds to a splayed 30-bp prespacer bearing 4-nt 3′-overhangs. Three molecular events take place upon encountering a target: Cas1-Cas2/prespacer first searches for half-sites stochastically, then preferentially interacts with the leader-side CRISPR repeat and catalyzes a nucleophilic attack that connects one strand of the leader-proximal repeat to the prespacer 3′-overhang. Recognition of the spacer half-site requires DNA bending and leads to full integration. We derive a mechanistic framework explaining the stepwise spacer integration process and the leader-proximal preference. PMID:28869593

The effect of mud therapy on pain relief in patients with knee osteoarthritis: a meta-analysis of randomized controlled trials.

PubMed

Liu, Hua; Zeng, Chao; Gao, Shu-guang; Yang, Tuo; Luo, Wei; Li, Yu-sheng; Xiong, Yi-lin; Sun, Jin-peng; Lei, Guang-hua

2013-10-01

A meta-analysis was conducted to examine the effect of mud therapy on pain relief in patients with knee osteoarthritis (OA). A detailed search of PubMed®/MEDLINE® was undertaken to identify randomized controlled trials and prospective comparative studies published before 9 March 2013 that compared mud therapy with control group treatments in patients with knee OA. A quantitative meta-analysis of seven studies (410 patients) was performed. There was a significant difference between the groups in the visual analogue scale pain score (standardized mean difference [SMD] -0.73) and Western Ontario and McMaster Universities Osteoarthritis Index pain score (SMD -0.30), with differences in favour of mud therapy. Mud therapy is a favourable option for pain relief in patients with knee OA. Additional high-quality randomized controlled trials need to be conducted to explore this issue further and to confirm this conclusion.

Radioactivity of peat mud used in therapy.

PubMed

Karpińska, Maria; Mnich, Krystian; Kapała, Jacek; Bielawska, Agnieszka; Kulesza, Grzegorz; Mnich, Stanisław

2016-02-01

The aim of the study was to determine the contents of natural and artificial isotopes in peat mud and to estimate the radiation dose absorbed via skin in patients during standard peat mud treatment. The analysis included 37 samples collected from 8 spas in Poland. The measurements of isotope concentration activity were conducted with the use of gamma spectrometry methods. The skin dose in a standard peat mud bath therapy is approximately 300 nSv. The effective dose of such therapy is considered to be 22 nSv. The doses absorbed during peat mud therapy are 5 orders of magnitude lower than effective annual dose absorbed from the natural radiation background by a statistical Pole (3.5 mSv). Neither therapeutic nor harmful effect is probable in case of such a small dose of ionising radiation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Red mud application in construction industry: review of benefits and possibilities

NASA Astrophysics Data System (ADS)

Lima, M. S. S.; Thives, L. P.; Haritonovs, V.; Bajars, K.

2017-10-01

Red mud is a waste originated in the processing of bauxite into aluminium, which properties of high alkalinity make it cumulatively stored, occupying increasing deforested areas. Annually, it is estimated that approximately 117 million tons of red mud are generated in the world, with no prospect of use, what represents an imminent risk of pollution prone to contamination. Nevertheless, environmental liabilities caused by red mud affect not only the environment, but also the companies responsible for the waste, which will be subject to highest fee payments. Although there are studies that prove the feasibility of using this solid waste in the constitution of ceramic materials, there are no large-scale applications. This study seeks to evaluate the possibilities of red mud application in construction industry, focusing into two main areas: cement production/ceramic material and road construction. Backgrounds from other researchers were taken into consideration and analysed according environmental, economic and technical feasibilities.

The wister mud pot lineament: Southeastward extension or abandoned strand of the San Andreas fault?

USGS Publications Warehouse

Lynch, D.K.; Hudnut, K.W.

2008-01-01

We present the results of a survey of mud pots in the Wister Unit of the Imperial Wildlife Area. Thirty-three mud pots, pot clusters, or related geothermal vents (hundreds of pots in all) were identified, and most were found to cluster along a northwest-trending line that is more or less coincident with the postulated Sand Hills fault. An extrapolation of the trace of the San Andreas fault southeastward from its accepted terminus north of Bombay Beach very nearly coincides with the mud pot lineament and may represent a surface manifestation of the San Andreas fault southeast of the Salton Sea. Additionally, a recent survey of vents near Mullet Island in the Salton Sea revealed eight areas along a northwest-striking line where gas was bubbling up through the water and in two cases hot mud and water were being violently ejected.

Effect of eight outer continental shelf drilling muds on the calcification rate and free amino acid pool of the coral Acropora cervicornis

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

Powell, E.N.; Kendall, J.J. Jr.; Connor, S.J.

1984-09-01

During most offshore drilling operations, drilling muds are routinely discharged into surrounding waters. Because corals are relatively sensitive to many environmental perturbations and can be adversely affected by offshore drilling operations, the effects of drilling muds on corals have received considerable attention. Because drilling muds are discharged intermittently, only periodic exposures of short duration should impact nearby coral reefs. To fully assess the impact of a drilling mud discharge on corals requires an assessment of the capacity for corals to recover from short-term exposure. The purpose of this study was to assess the relative toxicity of a number of mudsmore » that were slated for marine disposal for the coral Acropora cervicornis after a 48-hr recovery period. Calcification rate and free amino acid pool were investigated.« less

A non-inheritable maternal Cas9-based multiple-gene editing system in mice.

PubMed

Sakurai, Takayuki; Kamiyoshi, Akiko; Kawate, Hisaka; Mori, Chie; Watanabe, Satoshi; Tanaka, Megumu; Uetake, Ryuichi; Sato, Masahiro; Shindo, Takayuki

2016-01-28

The CRISPR/Cas9 system is capable of editing multiple genes through one-step zygote injection. The preexisting method is largely based on the co-injection of Cas9 DNA (or mRNA) and guide RNAs (gRNAs); however, it is unclear how many genes can be simultaneously edited by this method, and a reliable means to generate transgenic (Tg) animals with multiple gene editing has yet to be developed. Here, we employed non-inheritable maternal Cas9 (maCas9) protein derived from Tg mice with systemic Cas9 overexpression (Cas9 mice). The maCas9 protein in zygotes derived from mating or in vitro fertilization of Tg/+ oocytes and +/+ sperm could successfully edit the target genome. The efficiency of such maCas9-based genome editing was comparable to that of zygote microinjection-based genome editing widely used at present. Furthermore, we demonstrated a novel approach to create "Cas9 transgene-free" gene-modified mice using non-Tg (+/+) zygotes carrying maCas9. The maCas9 protein in mouse zygotes edited nine target loci simultaneously after injection with nine different gRNAs alone. Cas9 mouse-derived zygotes have the potential to facilitate the creation of genetically modified animals carrying the Cas9 transgene, enabling repeatable genome engineering and the production of Cas9 transgene-free mice.

Dose-Dependent Dual Role of PIT-1 (POU1F1) in Somatolactotroph Cell Proliferation and Apoptosis

PubMed Central

Jullien, Nicolas; Roche, Catherine; Brue, Thierry; Figarella-Branger, Dominique; Graillon, Thomas; Barlier, Anne; Herman, Jean-Paul

2015-01-01

To test the role of wtPIT-1 (PITWT) or PIT-1 (R271W) (PIT271) in somatolactotroph cells, we established, using inducible lentiviral vectors, sublines of GH4C1 somatotroph cells that allow the blockade of the expression of endogenous PIT-1 and/or the expression of PITWT or PIT271, a dominant negative mutant of PIT-1 responsible for Combined Pituitary Hormone Deficiency in patients. Blocking expression of endogenous PIT-1 induced a marked decrease of cell proliferation. Overexpressing PITWT twofold led also to a dose-dependent decrease of cell proliferation that was accompanied by cell death. Expression of PIT271 induced a strong dose-dependent decrease of cell proliferation accompanied by a very pronounced cell death. These actions of PIT271 are independent of its interaction/competition with endogenous PIT-1, as they were unchanged when expression of endogenous PIT-1 was blocked. All these actions are specific for somatolactotroph cells, and could not be observed in heterologous cells. Cell death induced by PITWT or by PIT271 was accompanied by DNA fragmentation, but was not inhibited by inhibitors of caspases, autophagy or necrosis, suggesting that this cell death is a caspase-independent apoptosis. Altogether, our results indicate that under normal conditions PIT-1 is important for the maintenance of cell proliferation, while when expressed at supra-normal levels it induces cell death. Through this dual action, PIT-1 may play a role in the expansion/regression cycles of pituitary lactotroph population during and after lactation. Our results also demonstrate that the so-called “dominant-negative” action of PIT271 is independent of its competition with PIT-1 or a blockade of the actions of the latter, and are actions specific to this mutant variant of PIT-1. PMID:25822178

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing.

PubMed

Swarts, Daan C; Jinek, Martin

2018-05-22

Cas9 and Cas12a are multidomain CRISPR-associated nucleases that can be programmed with a guide RNA to bind and cleave complementary DNA targets. The guide RNA sequence can be varied, making these effector enzymes versatile tools for genome editing and gene regulation applications. While Cas9 is currently the best-characterized and most widely used nuclease for such purposes, Cas12a (previously named Cpf1) has recently emerged as an alternative for Cas9. Cas9 and Cas12a have distinct evolutionary origins and exhibit different structural architectures, resulting in distinct molecular mechanisms. Here we compare the structural and mechanistic features that distinguish Cas9 and Cas12a, and describe how these features modulate their activity. We discuss implications for genome editing, and how they may influence the choice of Cas9 or Cas12a for specific applications. Finally, we review recent studies in which Cas12a has been utilized as a genome editing tool. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes. © 2018 Wiley Periodicals, Inc.

[Clustered regularly interspaced short palindromic repeat associated protein genes cas1 and cas2 in Shigella].

PubMed

Xue, Zerun; Wang, Yingfang; Duan, Guangcai; Wang, Pengfei; Wang, Linlin; Guo, Xiangjiao; Xi, Yuanlin

2014-05-01

To detect the distribution of clustered regularly interspaced short palindromic repeat (CRISPR) associated protein genes cas1 and cas2 in Shigella and to understand the characteristics of CRISPR with relationship between CRISPR and related characteristics on drug resistance. CRISPR associated protein genes cas1 and cas2 in Shigella were detected by PCR, with its products sequenced and compared. The CRISPR-associated protein genes cas1 and cas2 were found in all the 196 Shigella isolates which were isolated at different times and locations in China. Consistencies showed through related sequencing appeared as follows: cas2, cas1 (a) and cas1 (b) were 96.44%, 97.61% and 96.97%, respectively. There were two mutations including 3177129 site(C→G)and 3177126 site (G→C) of cas1 (b) gene in 2003135 strain which were not found in the corresponding sites of Z23 and 2008113. showed that in terms of both susceptibility and antibiotic-resistance, strain 2003135 was stronger than Z23 and 2008113. CRISPR system widely existed in Shigella, with the level of drug resistance in cas1 (b) gene mutant strains higher than in wild strains. Cas1 (b) gene mutation might be one of the reasons causing the different levels of resistance.

Rain Erosion Studies of Sapphire, Aluminum Oxynitride, Spinel, Lanthana- Doped Yttria, and TAF Glass

DTIC Science & Technology

1990-07-01

small , there is little change in average scatter for any material in any test. CONCLUSIONS AND DISCUSSION The principal conclusions are 1. ALON...20 Sample broke erosion damage 10 Slight pitting, 20 No change erosion damage 15 Pitting, cratering, 20 Small surface pits erosion damage 15 Pitting...Sample broke 10 No damage 15 Sample pitted, small edge fracture 15 Slight pitting, 1 crater, 20 Sample pitted, erosion damage small edge fracture 15 SUght

Expression of MdCAS1 and MdCAS2, encoding apple beta-cyanoalanine synthase homologs, is concomitantly induced during ripening and implicates MdCASs in the possible role of the cyanide detoxification in Fuji apple (Malus domestica Borkh.) fruits.

PubMed

Han, Sang Eun; Seo, Young Sam; Kim, Daeil; Sung, Soon-Kee; Kim, Woo Taek

2007-08-01

Fruit ripening involves complex biochemical and physiological changes. Ethylene is an essential hormone for the ripening of climacteric fruits. In the process of ethylene biosynthesis, cyanide (HCN), an extremely toxic compound, is produced as a co-product. Thus, most cyanide produced during fruit ripening should be detoxified rapidly by fruit cells. In higher plants, the key enzyme involved in the detoxification of HCN is beta-cyanoalanine synthase (beta-CAS). As little is known about the molecular function of beta-CAS genes in climacteric fruits, we identified two homologous genes, MdCAS1 and MdCAS2, encoding Fuji apple beta-CAS homologs. The structural features of the predicted polypeptides as well as an in vitro enzyme activity assay with bacterially expressed recombinant proteins indicated that MdCAS1 and MdCAS2 may indeed function as beta-CAS isozymes in apple fruits. RNA gel-blot studies revealed that both MdCAS1 and MdCAS2 mRNAs were coordinately induced during the ripening process of apple fruits in an expression pattern comparable with that of ACC oxidase and ethylene production. The MdCAS genes were also activated effectively by exogenous ethylene treatment and mechanical wounding. Thus, it seems like that, in ripening apple fruits, expression of MdCAS1 and MdCAS2 genes is intimately correlated with a climacteric ethylene production and ACC oxidase activity. In addition, beta-CAS enzyme activity was also enhanced as the fruit ripened, although this increase was not as dramatic as the mRNA induction pattern. Overall, these results suggest that MdCAS may play a role in cyanide detoxification in ripening apple fruits.

Drilling mud additives

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

Roemer, P.; Downhour, R. Jr.

1970-06-30

A drilling mud additive prepared from farinaceous material contains relatively high gluten and fat contents and has between 30 and 40% water soluble solids on a dry basis. The product is particularly useful in rotary drilling as an additive to the drilling mud to inhibit water loss. The key to achieving the desired product is pretreatment of the raw flour and control of moisture. (2 claims)

30 CFR 250.1722 - If I install a subsea protective device, what requirements must I meet?

Code of Federal Regulations, 2010 CFR

2010-07-01

... protective covering, the casing stub or mud line suspension equipment, or the trawl, and a discussion of any... subsea wellheads, casing stubs, mud line suspensions, or other obstructions in water depths less than 300... reveals that a casing stub or mud line suspension is no longer properly protected, or if the trawl does...

THE "MUD VOLCANO," A STINKY THERMAL FEATURE ON THE GRAND ...

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

THE "MUD VOLCANO," A STINKY THERMAL FEATURE ON THE GRAND LOOP ROAD. ACIDIC HOT SPRINGS HAVE REDUCED THE UNDERLYING LAVA TO A FINE CLAY, PRODUCING AN AREA OF BOILING MUD. THE ODOR OF ROTTEN EGGS IS FROM HYDROGEN SULFIDE GAS. - Grand Loop Road, Forming circuit between Mammoth Hot Springs, Norris Junction, Madison Junction, Old Faithful, Mammoth, Park County, WY

Mud Volcanoes as Exploration Targets on Mars

NASA Technical Reports Server (NTRS)

Allen, Carlton C.; Oehler, Dorothy Z.

2010-01-01

Tens of thousands of high-albedo mounds occur across the southern part of the Acidalia impact basin on Mars. These structures have geologic, physical, mineralogic, and morphologic characteristics consistent with an origin from a sedimentary process similar to terrestrial mud volcanism. The potential for mud volcanism in the Northern Plains of Mars has been recognized for some time, with candidate mud volcanoes reported from Utopia, Isidis, northern Borealis, Scandia, and the Chryse-Acidalia region. We have proposed that the profusion of mounds in Acidalia is a consequence of this basin's unique geologic setting as the depocenter for the tune fraction of sediments delivered by the outflow channels from the highlands.

Sequential activities of Dynein, Mud and Asp in centrosome-spindle coupling maintain centrosome number upon mitosis.

PubMed

Bosveld, Floris; Ainslie, Anna; Bellaïche, Yohanns

2017-10-15

Centrosomes nucleate microtubules and are tightly coupled to the bipolar spindle to ensure genome integrity, cell division orientation and centrosome segregation. While the mechanisms of centrosome-dependent microtubule nucleation and bipolar spindle assembly have been the focus of numerous works, less is known about the mechanisms ensuring the centrosome-spindle coupling. The conserved NuMA protein (Mud in Drosophila ) is best known for its role in spindle orientation. Here, we analyzed the role of Mud and two of its interactors, Asp and Dynein, in the regulation of centrosome numbers in Drosophila epithelial cells. We found that Dynein and Mud mainly initiate centrosome-spindle coupling prior to nuclear envelope breakdown (NEB) by promoting correct centrosome positioning or separation, while Asp acts largely independently of Dynein and Mud to maintain centrosome-spindle coupling. Failure in the centrosome-spindle coupling leads to mis-segregation of the two centrosomes into one daughter cell, resulting in cells with supernumerary centrosomes during subsequent divisions. Altogether, we propose that Dynein, Mud and Asp operate sequentially during the cell cycle to ensure efficient centrosome-spindle coupling in mitosis, thereby preventing centrosome mis-segregation to maintain centrosome number. © 2017. Published by The Company of Biologists Ltd.

Surface electrochemical properties of red mud (bauxite residue): zeta potential and surface charge density.

PubMed

Liu, Yanju; Naidu, Ravendra; Ming, Hui

2013-03-15

The surface electrochemical properties of red mud (bauxite residue) from different alumina refineries in Australia and China were studied by electrophoresis and measuring surface charge density obtained from acid/base potentiometric titrations. The electrophoretic properties were measured from zeta potentials obtained in the presence of 0.01 and 0.001 M KNO(3) over a wide pH range (3.5-10) by titration. The isoelectric point (IEP) values were found to vary from 6.35 to 8.70 for the red mud samples. Further investigation into the surface charge density of one sample (RRM) by acid/base potentiometric titration showed similar results for pH(PZC) with pH(IEP) obtained from electrokinetic measurements. The pH(IEP) determined from zeta potential measurements can be used as a characteristic property of red mud. The minerals contained in red mud contributed to the different values of pH(IEP) of samples obtained from different refineries. Different relationships of pH(IEP) with Al/Fe and Al/Si ratios (molar basis) were also found for different red mud samples. Copyright © 2012 Elsevier Inc. All rights reserved.

Effects of mud sedimentation on lugworm ecosystem engineering

NASA Astrophysics Data System (ADS)

Montserrat, F.; Suykerbuyk, W.; Al-Busaidi, R.; Bouma, T. J.; van der Wal, D.; Herman, P. M. J.

2011-01-01

Benthic ecosystem engineering organisms attenuate hydrodynamic or biogeochemical stress to ameliorate living conditions. Bioturbating infauna, like the lugworm Arenicola marina, determine intertidal process dynamics by maintaining the sediment oxygenated and sandy. Maintaining the permeability of the surrounding sediment enables them to pump water through the interstitial spaces, greatly increasing the oxygen availability. In a field experiment, both lugworm presence and siltation regime were manipulated to investigate to what extent lugworms are able to cope with sedimentation of increasing mud percentage and how this would affect its ecosystem engineering. Fluorescent tracers were added to experimentally deposited mud to visualise bioturbation effects on fine sediment fractions. Lugworm densities were not affected by an increasing mud percentage in experimentally deposited sediment. Negative effects are expected to occur under deposition with significantly higher mud percentages. Surface chlorophyll a content was a function of experimental mud percentage, with no effect of lugworm bioturbation. Surface roughness and sediment permeability clearly increased by lugworm presence, whereas sediment erosion threshold was not significantly affected by lugworms. The general idea that A. marina removes fine sediment fractions from the bed could not be confirmed. Rather, the main ecosystem engineering effect of A. marina is hydraulic destabilisation of the sediment matrix.

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems.

PubMed

Yamada, Mari; Watanabe, Yuto; Gootenberg, Jonathan S; Hirano, Hisato; Ran, F Ann; Nakane, Takanori; Ishitani, Ryuichiro; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2017-03-16

The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems. The CjCas9 guide RNA contains a triple-helix structure, which is distinct from known RNA triple helices, thereby expanding the natural repertoire of RNA triple helices. Furthermore, unlike the other Cas9 orthologs, CjCas9 contacts the nucleotide sequences in both the target and non-target DNA strands and recognizes the 5'-NNNVRYM-3' as the protospacer-adjacent motif. Collectively, these findings improve our mechanistic understanding of the CRISPR-Cas9 systems and may facilitate Cas9 engineering. Copyright © 2017 Elsevier Inc. All rights reserved.

Phosphate (Pi)-regulated heterodimerization of the high-affinity sodium-dependent Pi transporters PiT1/Slc20a1 and PiT2/Slc20a2 underlies extracellular Pi sensing independently of Pi uptake.

PubMed

Bon, Nina; Couasnay, Greig; Bourgine, Annabelle; Sourice, Sophie; Beck-Cormier, Sarah; Guicheux, Jérôme; Beck, Laurent

2018-02-09

Extracellular phosphate (P i ) can act as a signaling molecule that directly alters gene expression and cellular physiology. The ability of cells or organisms to detect changes in extracellular P i levels implies the existence of a P i -sensing mechanism that signals to the body or individual cell. However, unlike in prokaryotes, yeasts, and plants, the molecular players involved in P i sensing in mammals remain unknown. In this study, we investigated the involvement of the high-affinity, sodium-dependent P i transporters PiT1 and PiT2 in mediating P i signaling in skeletal cells. We found that deletion of PiT1 or PiT2 blunted the P i -dependent ERK1/2-mediated phosphorylation and subsequent gene up-regulation of the mineralization inhibitors matrix Gla protein and osteopontin. This result suggested that both PiTs are necessary for P i signaling. Moreover, the ERK1/2 phosphorylation could be rescued by overexpressing P i transport-deficient PiT mutants. Using cross-linking and bioluminescence resonance energy transfer approaches, we found that PiT1 and PiT2 form high-abundance homodimers and P i -regulated low-abundance heterodimers. Interestingly, in the absence of sodium-dependent P i transport activity, the PiT1-PiT2 heterodimerization was still regulated by extracellular P i levels. Of note, when two putative P i -binding residues, Ser-128 (in PiT1) and Ser-113 (in PiT2), were substituted with alanine, the PiT1-PiT2 heterodimerization was no longer regulated by extracellular P i These observations suggested that P i binding rather than P i uptake may be the key factor in mediating P i signaling through the PiT proteins. Taken together, these results demonstrate that P i -regulated PiT1-PiT2 heterodimerization mediates P i sensing independently of P i uptake. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure and function of bordered pits: new discoveries and impacts on whole-plant hydraulic function.

PubMed

Choat, Brendan; Cobb, Alexander R; Jansen, Steven

2008-01-01

Bordered pits are cavities in the lignified cell walls of xylem conduits (vessels and tracheids) that are essential components in the water-transport system of higher plants. The pit membrane, which lies in the center of each pit, allows water to pass between xylem conduits but limits the spread of embolism and vascular pathogens in the xylem. Averaged across a wide range of species, pits account for > 50% of total xylem hydraulic resistance, indicating that they are an important factor in the overall hydraulic efficiency of plants. The structure of pits varies dramatically across species, with large differences evident in the porosity and thickness of pit membranes. Because greater porosity reduces hydraulic resistance but increases vulnerability to embolism, differences in pit structure are expected to correlate with trade-offs between efficiency and safety of water transport. However, trade-offs in hydraulic function are influenced both by pit-level differences in structure (e.g. average porosity of pit membranes) and by tissue-level changes in conduit allometry (average length, diameter) and the total surface area of pit membranes that connects vessels. In this review we address the impact of variation in pit structure on water transport in plants from the level of individual pits to the whole plant.

Structure and Engineering of Francisella novicida Cas9

PubMed Central

Hirano, Hisato; Gootenberg, Jonathan S.; Horii, Takuro; Abudayyeh, Omar O.; Kimura, Mika; Hsu, Patrick D.; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2016-01-01

Summary The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA, and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5′-NGG-3′ PAM, and used the structural information to create a variant that can recognize the more relaxed 5′-YG-3′ PAM. Furthermore, we demonstrated that pre-assembled FnCas9 ribonucleoprotein complexes can be microinjected into mouse zygotes to edit endogenous sites with the 5′-YG-3′ PAMs, thus expanding the target space of the CRISPR-Cas9 toolbox. PMID:26875867

The Impact of DNA Topology and Guide Length on Target Selection by a Cytosine-Specific Cas9.

PubMed

Tsui, Tsz Kin Martin; Hand, Travis H; Duboy, Emily C; Li, Hong

2017-06-16

Cas9 is an RNA-guided DNA cleavage enzyme being actively developed for genome editing and gene regulation. To be cleaved by Cas9, a double stranded DNA, or the protospacer, must be complementary to the guide region, typically 20-nucleotides in length, of the Cas9-bound guide RNA, and adjacent to a short Cas9-specific element called Protospacer Adjacent Motif (PAM). Understanding the correct juxtaposition of the protospacer- and PAM-interaction with Cas9 will enable development of versatile and safe Cas9-based technology. We report identification and biochemical characterization of Cas9 from Acidothermus cellulolyticus (AceCas9). AceCas9 depends on a 5'-NNNCC-3' PAM and is more efficient in cleaving negative supercoils than relaxed DNA. Kinetic as well as in vivo activity assays reveal that AceCas9 achieves optimal activity when combined with a guide RNA containing a 24-nucleotide complementarity region. The cytosine-specific, DNA topology-sensitive, and extended guide-dependent properties of AceCas9 may be explored for specific genome editing applications.

Structure and Engineering of Francisella novicida Cas9.

PubMed

Hirano, Hisato; Gootenberg, Jonathan S; Horii, Takuro; Abudayyeh, Omar O; Kimura, Mika; Hsu, Patrick D; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2016-02-25

The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5'-NGG-3' PAM, and used the structural information to create a variant that can recognize the more relaxed 5'-YG-3' PAM. Furthermore, we demonstrated that the FnCas9-ribonucleoprotein complex can be microinjected into mouse zygotes to edit endogenous sites with the 5'-YG-3' PAM, thus expanding the target space of the CRISPR-Cas9 toolbox. Copyright © 2016 Elsevier Inc. All rights reserved.

Cas9 in Genetically Modified Food Is Unlikely to Cause Food Allergy.

PubMed

Nakajima, Osamu; Nishimaki-Mogami, Tomoko; Kondo, Kazunari

2016-01-01

Genome editing has undergone rapid development during the last three years. It is anticipated that genetically modified organisms (GMOs) for food purposes will be widely produced using the clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR)/Cas9 system in the near future. However, the Cas9 gene may then enter the genomes of GMOs for food if the breeding process is not strictly managed, which could lead to the Cas9 protein or associated peptides being produced within these organisms. A variety of peptides could theoretically be produced from the Cas9 gene by using open reading frames different from that of Cas9 in the GMOs. In this study, Cas9 and the peptides potentially encoded by Cas9 genes were studied regarding their immunogenicity, in terms of the digestibility of Cas9 and the homology of the peptides to food allergens. First, the digestibility and thermal stability of Cas9 were studied. Digestibility was tested with natural or heat-denatured Cas9 in simulated gastric fluid in vitro. The two types of Cas9 were digested rapidly. Cas9 was also gradually degraded during heat treatment. Second, the peptides potentially encoded by Cas9 genes were examined for their homology to food allergens. Specifically, an 8-mer exact match search and a sliding 80-mer window search were performed using allergen databases. One of the peptides was found to have homology with a food allergen.

Green preparation of a novel red mud@carbon composite and its application for adsorption of 2,4-dichlorophenoxyacetic acid from aqueous solution.

PubMed

Kazak, Omer; Eker, Yasin Ramazan; Akin, Ilker; Bingol, Haluk; Tor, Ali

2017-10-01

This study reports the eco-friendly preparation of a novel composite material consisting of red mud and carbon spheres, denoted as red mud@C composite, and its application for the removal of 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) from aqueous solution. The preparation route has a green approach because it follows the low-energy consuming one-step hydrothermal process by using starch as a renewable carbon precursor and red mud as a waste from aluminum production industry. Characterization of the red mud@C composite was performed by FT-IR, TGA, SEM, TEM, BET, XRD, and Raman microscopy analyses. The batch adsorption studies revealed that the red mud@C composite has higher 2,4-D adsorption efficiency than those of the red mud and the naked carbon spheres. The maximum removal at initial pH of 3.0 is explained by considering the pKa of 2,4-D and pH of point of zero charge (pH pzc ) of the composite material. The adsorption equilibrium time was 60 min, which followed the pseudo-second-order kinetic model together with intra-particle diffusion model. The isotherm analysis indicated that Freundlich isotherm model better represented the adsorption data, with isotherm parameters of k [15.849 (mg/g) (mg/L) -1/n ] and n (2.985). The prepared composite is reusable at least 5 cycles of adsorption-desorption with no significant decrease in the adsorption capacity.

Dead Sea mud packs for chronic low back pain.

PubMed

Abu-Shakra, Mahmoud; Mayer, Amit; Friger, Michael; Harari, Marco

2014-09-01

Low back pain (LBP) is chronic disease without a curative therapy. Alternative and complementary therapies are widely used in the management of this condition. To evaluate the efficacy of home application of Dead Sea mud compresses to the back of patients with chronic LBP. Forty-six consecutive patients suffering from chronic LBP were recruited. All patients were followed at the Soroka University Rheumatic Diseases Unit. The patients were randomized into two groups: one group was treated with mineral-rich mud compresses, and the other with mineral-depleted compresses. Mud compresses were applied five times a week for 3 consecutive weeks. The primary outcome was the patient's assessment of the overall back pain severity. The score of the Ronald & Morris questionnaire served as a secondary outcome. Forty-four patients completed the therapy and the follow-up assessments: 32 were treated with real mud packs and 12 used the mineral-depleted packs. A significant decrease in intensity of pain, as described by the patients, was observed only in the treatment group. In this group, clinical improvement was clearly seen at completion of therapy and was sustained a month later. Significant improvement in the scores of the Roland & Morris questionnaire was observed in both groups. The data suggest that pain severity was reduced in patients treated with mineral-rich mud compresses compared with those treated with mineral-depleted compresses. Whether this modest effect is the result of a "true" mud effect or other causes can not be determined in this study.

Gas hydrates and active mud volcanism on the South Shetland continental margin, Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Tinivella, U.; Accaino, F.; Della Vedova, B.

2008-04-01

During the Antarctic summer of 2003 2004, new geophysical data were acquired from aboard the R/V OGS Explora in the BSR-rich area discovered in 1996 1997 along the South Shetland continental margin off the Antarctic Peninsula. The objective of the research program, supported by the Italian National Antarctic Program (PNRA), was to verify the existence of a potential gas hydrate reservoir and to reconstruct the tectonic setting of the margin, which probably controls the extent and character of the diffused and discontinuous bottom simulating reflections. The new dataset, i.e. multibeam bathymetry, seismic profiles (airgun and chirp), and two gravity cores analysed by computer-aided tomography as well as for gas composition and content, clearly shows active mud volcanism sustained by hydrocarbon venting in the region: several vents, located mainly close to mud volcanoes, were imaged during the cruise and their occurrence identified in the sediment samples. Mud volcanoes, vents and recent slides border the gas hydrate reservoir discovered in 1996 1997. The cores are composed of stiff silty mud. In core GC01, collected in the proximity of a mud volcano ridge, the following gases were identified (maximum contents in brackets): methane (46 μg/kg), pentane (45), ethane (35), propane (34), hexane (29) and butane (28). In core GC02, collected on the flank of the Vualt mud volcano, the corresponding data are methane (0 μg/kg), pentane (45), ethane (22), propane (0), hexane (27) and butane (25).

Childhood adversities and first onset of psychiatric disorders in a national sample of adolescents

PubMed Central

McLaughlin, Katie A.; Green, Jennifer Greif; Gruber, Michael J.; Sampson, Nancy A.; Zaslavsky, Alan M.; Kessler, Ronald C.

2012-01-01

Context Although childhood adversities (CAs) are known to be highly co-occurring, most research examines their associations with mental disorders one at a time. Recent evidence from adult studies suggests, though, that the associations of multiple CAs with mental disorders are non-additive, arguing for the importance of multivariate analysis of multiple CAs. No attempt has yet been made to carry out a similar kind of analysis among children or adolescents. Objective To examine the multivariate associations of 12 CAs with first onset of mental disorders in a national sample of US adolescents. Design US national survey of adolescents (ages 13–17) assessing DSM-IV anxiety, mood, behavior, and substance disorders and CAs. The CAs include parental loss (death, divorce, other separations), maltreatment (physical, sexual, and emotional abuse, neglect), parental maladjustment (psychopathology, substance abuse, criminality, violence) and economic adversity. Setting Dual-frame household-school samples. Participants 6,483 adolescents-parent pairs. Main outcome measure Lifetime DSM-IV disorders assessed with the WHO Composite International Diagnostic Interview. Results 58.3% of adolescents reported at least one CA, among whom 59.7% reported multiple CAs. CAs reflecting maladaptive family functioning (MFF) were more strongly associated than other CAs with disorder onsets. The best-fitting model included terms for type and number of CAs and distinguished between MFF and Other CAs. CAs predicted behavior disorders most strongly and fear disorders least strongly. The joint associations of multiple CAs were sub-additive. The population-attributable risk proportions for disorder classes ranged from 15.7% for fear disorders to 40.7% for behavior disorders. CAs were associated with 28.2% of all onsets. Conclusions CAs are common, highly co-occurring, and strongly associated with onset of mental disorders among US adolescents. The sub-additive multivariate associations of CAs with disorder onsets have implications for targeting interventions to reduce exposure to CAs and to mitigate the harmful effects of CAs to improve population mental health. PMID:23117636

PitScan: Computer-Assisted Feature Detection

NASA Astrophysics Data System (ADS)

Wagner, R. V.; Robinson, M. S.

2018-04-01

We developed PitScan to assist in searching the very large LROC image dataset for pits — unusual <200m wide vertical-walled holes in the Moon's surface. PitScan reduces analysts' workload by pre-filtering images to identify possible pits.

Quantitative Correlation of 7B04 Aluminum Alloys Pitting Corrosion Morphology Characteristics with Stress Concentration Factor

NASA Astrophysics Data System (ADS)

Liu, Zhiguo; Yan, Guangyao; Mu, Zhitao; Li, Xudong

2018-01-01

The accelerated pitting corrosion test of 7B04 aluminum alloy specimen was carried out according to the spectrum which simulated airport environment, and the corresponding pitting corrosion damage was obtained and was defined through three parameters A and B and C which respectively denoted the corrosion pit surface length and width and corrosion pit depth. The ratio between three parameters could determine the morphology characteristics of corrosion pits. On this basis the stress concentration factor of typical corrosion pit morphology under certain load conditions was quantitatively analyzed. The research shows that the corrosion pits gradually incline to be ellipse in surface and moderate in depth, and most value of B/A and C/A lies in 1 between 4 and few maximum exceeds 4; The stress concentration factor Kf of corrosion pits is obviously affected by the its morphology, the value of Kf increases with corrosion pits depth increasement under certain corrosion pits surface geometry. Also, the value of Kf decreases with surface width increasement under certain corrosion pits depth. The research conclusion can set theory basis for corrosion fatigue life analysis of aircraft aluminum alloy structure.

All-in-One CRISPR-Cas9/FokI-dCas9 Vector-Mediated Multiplex Genome Engineering in Cultured Cells.

PubMed

Sakuma, Tetsushi; Sakamoto, Takuya; Yamamoto, Takashi

2017-01-01

CRISPR-Cas9 enables highly convenient multiplex genome engineering in cultured cells, because it utilizes generic Cas9 nuclease and an easily customizable single-guide RNA (sgRNA) for site-specific DNA double-strand break induction. We previously established a multiplex CRISPR-Cas9 assembly system for constructing an all-in-one vector simultaneously expressing multiple sgRNAs and Cas9 nuclease or other Cas9 variants including FokI-dCas9, which supersedes the wild-type Cas9 with regard to high specificity. In this chapter, we describe a streamlined protocol to design and construct multiplex CRISPR-Cas9 or FokI-dCas9 vectors, to introduce them into cultured cells by lipofection or electroporation, to enrich the genomically edited cells with a transient puromycin selection, to validate the mutation efficiency by Surveyor nuclease assay, and to perform off-target analyses. We show that our protocol enables highly efficient multiplex genome engineering even in hard-to-transfect HepG2 cells.

Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility.

PubMed

Peddinti, Divyaswetha; Nanduri, Bindu; Kaya, Abdullah; Feugang, Jean M; Burgess, Shane C; Memili, Erdogan

2008-02-22

Male infertility is a major problem for mammalian reproduction. However, molecular details including the underlying mechanisms of male fertility are still not known. A thorough understanding of these mechanisms is essential for obtaining consistently high reproductive efficiency and to ensure lower cost and time-loss by breeder. Using high and low fertility bull spermatozoa, here we employed differential detergent fractionation multidimensional protein identification technology (DDF-Mud PIT) and identified 125 putative biomarkers of fertility. We next used quantitative Systems Biology modeling and canonical protein interaction pathways and networks to show that high fertility spermatozoa differ from low fertility spermatozoa in four main ways. Compared to sperm from low fertility bulls, sperm from high fertility bulls have higher expression of proteins involved in: energy metabolism, cell communication, spermatogenesis, and cell motility. Our data also suggests a hypothesis that low fertility sperm DNA integrity may be compromised because cell cycle: G2/M DNA damage checkpoint regulation was most significant signaling pathway identified in low fertility spermatozoa. This is the first comprehensive description of the bovine spermatozoa proteome. Comparative proteomic analysis of high fertility and low fertility bulls, in the context of protein interaction networks identified putative molecular markers associated with high fertility phenotype.

Characterization of Breast Cancer Interstitial Fluids by TmT Labeling, LTQ-Orbitrap Velos Mass Spectrometry and Pathway Analysis

PubMed Central

Cinzia, Raso; Carlo, Cosentino; Marco, Gaspari; Natalia, Malara; Xuemei, Han; Daniel, McClatchy; Kyu, Park Sung; Maria, Renne; Nuria, Vadalà; Ubaldo, Prati; Giovanni, Cuda; Vincenzo, Mollace; Francesco, Amato; Yates, John R.

2012-01-01

Cancer is currently considered as the end point of numerous genomic and epigenomic mutations and as the result of the interaction of transformed cells within the stromal microenvironment. The present work focuses on breast cancer, one of the most common malignancies affecting the female population in industrialized countries. In this study we perform a proteomic analysis of bioptic samples from human breast cancer, namely interstitial fluids and primary cells, normal vs disease tissues, using Tandem mass Tags (TmT) quantitative mass spectrometry combined with the MudPIT technique. To the best of our knowledge this work, with over 1700 proteins identified, represents the most comprehensive characterization of the breast cancer interstitial fluid proteome to date. Network analysis was used to identify functionally active networks in the breast cancer associated samples. From the list of differentially expressed genes we have retrieved the associated functional interaction networks. Many different signaling pathways were found activated, strongly linked to invasion, metastasis development, proliferation and with a significant cross-talking rate. This pilot study presents evidence that the proposed quantitative proteomic approach can be applied to discriminate between normal and tumoral samples and for the discovery of yet unknown carcinogenesis mechanisms and therapeutic strategies. PMID:22563702

Physiological and molecular alterations promoted by Schizotetranychus oryzae mite infestation in rice leaves

PubMed Central

Buffon, Giseli; Blasi, Édina A. R.; Adamski, Janete M.; Ferla, Noeli J.; Berger, Markus; Santi, Lucélia; Lavallée-Adam, Mathieu; Yates, John R.; Beys-da-Silva, Walter O.; Sperotto, Raul A.

2016-01-01

Infestation of phytophagous mite Schizotetranychus oryzae in rice causes critical yield losses. To better understand this interaction, we employed Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We detected 18 unique proteins in control and 872 in infested leaves, respectively, along with 32 proteins more abundant in control leaves. S. oryzae infestation caused decreased abundance of proteins related to photosynthesis (mostly photosystem II-related), carbon assimilation and energy production, chloroplast detoxification, defense, fatty acid and gibberellin synthesis. On the other hand, infestation caused increased abundance of proteins involved in protein modification and degradation, gene expression at the translation level, protein partitioning to different organelles, lipid metabolism, actin cytoskeleton remodeling, and synthesis of jasmonate, amino acid and molecular chaperones. Our results also suggest that S. oryzae infestation promotes cell wall remodeling and interferes with ethylene biosynthesis in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of infested rice leaves, and suggest that the acceptor side of PSII is probably the major damaged target in the photosynthetic apparatus. These data will be useful in future biotechnological approaches aiming to induce phytophagous mite resistance in rice. PMID:26667653

Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility

PubMed Central

Peddinti, Divyaswetha; Nanduri, Bindu; Kaya, Abdullah; Feugang, Jean M; Burgess, Shane C; Memili, Erdogan

2008-01-01

Background Male infertility is a major problem for mammalian reproduction. However, molecular details including the underlying mechanisms of male fertility are still not known. A thorough understanding of these mechanisms is essential for obtaining consistently high reproductive efficiency and to ensure lower cost and time-loss by breeder. Results Using high and low fertility bull spermatozoa, here we employed differential detergent fractionation multidimensional protein identification technology (DDF-Mud PIT) and identified 125 putative biomarkers of fertility. We next used quantitative Systems Biology modeling and canonical protein interaction pathways and networks to show that high fertility spermatozoa differ from low fertility spermatozoa in four main ways. Compared to sperm from low fertility bulls, sperm from high fertility bulls have higher expression of proteins involved in: energy metabolism, cell communication, spermatogenesis, and cell motility. Our data also suggests a hypothesis that low fertility sperm DNA integrity may be compromised because cell cycle: G2/M DNA damage checkpoint regulation was most significant signaling pathway identified in low fertility spermatozoa. Conclusion This is the first comprehensive description of the bovine spermatozoa proteome. Comparative proteomic analysis of high fertility and low fertility bulls, in the context of protein interaction networks identified putative molecular markers associated with high fertility phenotype. PMID:18294385

Alterations in the Rat Serum Proteome Induced by Prepubertal Exposure to Bisphenol A and Genistein

PubMed Central

2015-01-01

Humans are exposed to an array of chemicals via the food, drink and air, including a significant number that can mimic endogenous hormones. One such chemical is Bisphenol A (BPA), a synthetic chemical that has been shown to cause developmental alterations and to predispose for mammary cancer in rodent models. In contrast, the phytochemical genistein has been reported to suppress chemically induced mammary cancer in rodents, and Asians ingesting a diet high in soy containing genistein have lower incidence of breast and prostate cancers. In this study, we sought to: (1) identify protein biomarkers of susceptibility from blood sera of rats exposed prepubertally to BPA or genistein using Isobaric Tandem Mass Tags quantitative mass spectrometry (TMT-MS) combined with MudPIT technology and, (2) explore the relevance of these proteins to carcinogenesis. Prepubertal exposures to BPA and genistein resulted in altered expression of 63 and 28 proteins in rat sera at postnatal day (PND) 21, and of 9 and 18 proteins in sera at PND35, respectively. This study demonstrates the value of using quantitative proteomic techniques to explore the effect of chemical exposure on the rat serum proteome and its potential for unraveling cellular targets altered by BPA and genistein involved in carcinogenesis. PMID:24552547

Structures of Bordered Pits Potentially Contributing to Isolation of a Refilled Vessel from Negative Xylem Pressure in Stems of Morus australis Poir.: Testing of the Pit Membrane Osmosis and Pit Valve Hypotheses.

PubMed

Ooeda, Hiroki; Terashima, Ichiro; Taneda, Haruhiko

2017-02-01

Two hypotheses have been proposed to explain the mechanism preventing the refilling vessel water from being drained to the neighboring functional vessels under negative pressure. The pit membrane osmosis hypothesis proposes that the xylem parenchyma cells release polysaccharides that are impermeable to the intervessel pit membranes into the refilling vessel; this osmotically counteracts the negative pressure, thereby allowing the vessel to refill. The pit valve hypothesis proposes that gas trapped within intervessel bordered pits isolates the refilling vessel water from the surrounding functional vessels. Here, using the single-vessel method, we assessed these hypotheses in shoots of mulberry (Morus australis Poir.). First, we confirmed the occurrence of xylem refilling under negative pressure in the potted mulberry saplings. To examine the pit membrane osmosis hypothesis, we estimated the semi-permeability of pit membranes for molecules of various sizes and found that the pit membranes were not semi-permeable to polyethylene glycol of molecular mass <20,000. For the pit valve hypothesis, we formed pit valves in the intervessel pits in the short stem segments and measured the maximum liquid pressure up to which gases in bordered pits were retained. The threshold pressure ranged from 0.025 to 0.10 MPa. These values matched the theoretical value calculated from the geometry of the pit chamber (0.0692-0.101 MPa). Our results suggest that gas in the pits is retained by surface tension, even under substantial positive pressure to resolve gases in the refilling vessel, whereas the molecule size required for the pit membrane osmosis mechanism in mulberry would be unrealistically large. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field.

PubMed

He, Zhi-Yao; Men, Ke; Qin, Zhou; Yang, Yang; Xu, Ting; Wei, Yu-Quan

2017-05-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies. Moreover, CRISPR-Cas9 systems have been used to partially or completely alleviate disease symptoms by mutating or correcting related genes. However, the efficient transfer of CRISPR-Cas9 system into cells and target organs remains a challenge that affects the robust and precise genome editing activity. The current review focuses on delivery systems for Cas9 mRNA, Cas9 protein, or vectors encoding the Cas9 gene and corresponding sgRNA. Non-viral delivery of Cas9 appears to help Cas9 maintain its on-target effect and reduce off-target effects, and viral vectors for sgRNA and donor template can improve the efficacy of genome editing and homology-directed repair. Safe, efficient, and producible delivery systems will promote the application of CRISPR-Cas9 technology in human gene therapy.

Interactions between iron(III)-hydroxide polymaltose complex and commonly used medications / laboratory studies in rats.

PubMed

Funk, Felix; Canclini, Camillo; Geisser, Peter

2007-01-01

Simple iron salts, such as iron sulphate, often interact with food and other medications reducing bioavailability and tolerability. Iron(III)-hydroxide polymaltose complex (IPC, Maltofer) provides a soluble form of non-ionic iron, making it an ideal form of oral iron supplementation. The physicochemical properties of IPC predict a low potential for interactions. The effects of co-administration with aluminium hydroxide (CAS 21645-51-2), acetylsalicylic acid (CAS 50-78-2), bromazepam (CAS 1812-30-2), calcium acetate (CAS 62-54-4), calcium carbonate (CAS 471-34-1), auranofin (CAS 34031-32-8), magnesium-L-aspartate hydrochloride (CAS 28184-71-6), methyldopa sesquihydrate (CAS 41372-08-1), paracetamol (CAS 103-90-2), penicillamine (CAS 52-67-5), sulfasalazine (CAS 599-79-1), tetracycline hydrochloride (CAS 64-75-5), calcium phosphate (CAS 7757-93-9) in combination with vitamin D3 (CAS 67-97-0), and a multi-vitamin preparation were tested in rats fed an iron-deficient diet. Uptake of iron from radiolabelled IPC with and without concomitant medications was compared. None of the medicines tested had a significant effect on iron uptake. Iron-59 retrieval from blood and major storage organs was 64-76% for IPC alone compared with 59-85% following co-administration with other medications. It is concluded that, under normal clinical conditions, IPC does not interact with these medications.

Acquired pit of the optic nerve: a risk factor for progression of glaucoma.

PubMed

Ugurlu, S; Weitzman, M; Nduaguba, C; Caprioli, J

1998-04-01

To examine acquired pit of the optic nerve as a risk factor for progression of glaucoma. In a retrospective longitudinal study, 25 open-angle glaucoma patients with acquired pit of the optic nerve were compared with a group of 24 open-angle glaucoma patients without acquired pit of the optic nerve. The patients were matched for age, mean intraocular pressure, baseline ratio of neuroretinal rim area to disk area, visual field damage, and duration of follow-up. Serial optic disk photographs and visual fields of both groups were evaluated by three independent observers for glaucomatous progression. Of 46 acquired pits of the optic nerve in 37 eyes of 25 patients, 36 pits were located inferiorly (76%) and 11 superiorly (24%; P < .001). Progression of optic disk damage occurred in 16 patients (64%) in the group with acquired pit and in three patients (12.5%) in the group without acquired pit (P < .001). Progression of visual field loss occurred in 14 patients (56%) in the group with acquired pit and in six (25%) in the group without pit (P=.04). Bilateral acquired pit of the optic nerve was present in 12 patients (48%). Disk hemorrhages were observed more frequently in the group with acquired pit (10 eyes, 40%) compared with the group without pit (two eyes, 8%; P=.02). Among patients with glaucoma, patients with acquired pit of the optic nerve represent a subgroup who are at increased risk for progressive optic disk damage and visual field loss.

Parturition pit: the bony imprint of vaginal birth.

PubMed

McArthur, Tatum A; Meyer, Isuzu; Jackson, Bradford; Pitt, Michael J; Larrison, Matthew C

2016-09-01

To retrospectively evaluate for pits along the dorsum of the pubic body in females and compare the presence/absence of these pits to vaginal birth data. We retrospectively reviewed females with vaginal birth data who underwent pelvic CT. The presence of pits along the dorsum of the pubic body, pit grade (0 = not present; 1 = faintly imperceptible; 2 = present; 3 = prominent), and the presence of osteitis condensans ilii, preauricular sulcus, and sacroiliac joint vacuum phenomenon were assessed on imaging. Musculoskeletal radiologists who were blinded to the birth data evaluated the CTs. 48 males were also evaluated for the presence of pits. 482 female patients underwent CT pelvis and 171 were excluded due to lack of vaginal birth data. Of the 311 study patients, 262 had prior vaginal birth(s) and 194 had pits on CT. Only 7 of the 49 patients without prior vaginal birth had pits. There was a statistically significant association between vaginal birth and presence of pits (p < 0.0001). Patients with more prominent pits (grades 2/3) had a greater number of vaginal births. As vaginal deliveries increased, the odds of having parturition pits greatly increased, adjusting for age and race at CT (p < 0.0001). No males had pits. Our study indicates that parturition pits are associated with prior vaginal birth and should be considered a characteristic of the female pelvis. The lytic appearance of prominent pits on imaging can simulate disease and create a diagnostic dilemma for interpreting radiologists.

Parturition Pit: The Bony Imprint of Vaginal Birth

PubMed Central

Meyer, Isuzu; Jackson, Bradford; Pitt, Michael J.; Larrison, Matthew C.

2017-01-01

Purpose To retrospectively evaluate for pits along the dorsum of the pubic body in females and compare the presence/absence of these pits to vaginal birth data. Materials and Methods We retrospectively reviewed females with vaginal birth data who underwent pelvic CT. The presence of pits along the dorsum of the pubic body, pit grade (0 = not present; 1 = faintly imperceptible; 2 = present; 3 = prominent), and the presence of osteitis condensans ilii, preauricular sulcus, and sacroiliac joint vacuum phenomenon were assessed on imaging. Musculoskeletal radiologists who were blinded to the birth data evaluated the CTs. 48 males were also evaluated for the presence of pits. Results 482 female patients underwent CT pelvis and 171 were excluded due to lack of vaginal birth data. Of the 311 study patients, 262 had prior vaginal birth(s) and 194 had pits on CT. Only 7 of the 49 patients without prior vaginal birth had pits. There was a statistically significant association between vaginal birth and presence of pits (p<0.0001). Patients with more prominent pits (grades 2/3) had a greater number of vaginal births. As vaginal deliveries increased, the odds of having parturition pits greatly increased, adjusting for age and race at CT (p<0.0001). No males had pits. Conclusion Our study indicates that parturition pits are associated prior vaginal birth and should be considered a characteristic of the female pelvis. The lytic appearance of prominent pits on imaging can simulate disease and create a diagnostic dilemma for interpreting radiologists. PMID:27270921

The effect of normal pulsed Nd-YAG laser irradiation on pits and fissures in human teeth.

PubMed

Bahar, A; Tagomori, S

1994-01-01

The effects of normal pulsed Nd-YAG laser irradiation on the acid resistance of human dental enamel of pits and fissures, the cleaning of the pit and fissure contents and fluoride uptake into deep pits and fissures were examined. The acid resistance of the pit and fissure enamel was evaluated by the amount of dissolved calcium per square millimeter of the surface area. The pit and fissure enamel treated with laser irradiation obtained an acid resistance 30% higher than that of the unlased controls. The cleaning effect of laser irradiation on the pit and fissure contents was compared with chemicomechanical and mechanical methods. The laser irradiation was found to clean the pits and fissures to a greater depth without alterating the shape of pits and fissures, compared with the other two methods. The distribution of calcium, phosphorus and fluoride in the enamel of the pits and fissures was then measured by electron probe microanalyzer. At the entrance and in the deep part of the pits and fissures, the fluoride content of the enamel treated with acidulated phosphate fluoride after laser irradiation was higher than that of the enamel treated with acidulated phosphate fluoride alone. These results thus suggest that Nd-YAG laser irradiation might be effective in increasing the acid resistance of the pit and fissure enamel, while removing the pit and fissure debris contents and increasing the fluoride uptake into the pit and fissure enamel.

30 CFR 250.1721 - If I temporarily abandon a well that I plan to re-enter, what must I do?

Code of Federal Regulations, 2010 CFR

2010-07-01

... or cement plug must be no more than 1,000 feet below the mud line. MMS may consider approving..., or other obstructions that extend above the mud line according to U.S. Coast Guard (USCG) requirements; and (f) Except in water depths greater than 300 feet, protect subsea wellheads, casing stubs, mud...

Genome Editing with CRISPR-Cas9: Can It Get Any Better?

PubMed Central

Haeussler, Maximilian; Concordet, Jean-Paul

2017-01-01

The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo. At the same time, the on-target activity of thousands of guides has been determined. These data have led to numerous online tools that facilitate the selection of guide RNAs in target sequences. It appears that for most basic research applications, cleavage activity can be maximized and off-targets minimized by carefully choosing guide RNAs based on computational predictions. Moreover, recent studies of Cas proteins have further improved the flexibility and precision of the CRISPR-Cas toolkit for genome editing. Inspired by the crystal structure of the complex of sgRNA-SpCas9 bound to target DNA, several variants of SpCas9 have recently been engineered, either with novel protospacer adjacent motifs (PAMs) or with drastically reduced off-targets. Novel Cas9 and Cas9-like proteins called Cpf1 have also been characterized from other bacteria and will benefit from the insights obtained from SpCas9. Genome editing with CRISPR-Cas9 may also progress with better understanding and control of cellular DNA repair pathways activated after Cas9-induced DNA cleavage. PMID:27210042

Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and Cas9 mRNA for Genome Editing in Zebrafish

PubMed Central

Hu, Peinan; Zhao, Xueying; Zhang, Qinghua; Li, Weiming; Zu, Yao

2018-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N-, C-, or both the N- and C-termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish. Phenotypic analysis revealed that all types of Cas9 led to hypopigmentation in similar proportions of injected embryos. Genome analysis by T7 Endonuclease I (T7E1) assays demonstrated that all types of Cas9 similarly induced mutagenesis in four target sites. Sequencing results further confirmed that a high frequency of indels occurred in the target sites (tyr1 > 66%, tyr2 > 73%, gol1 > 50%, and gol2 > 35%), as well as various types (more than six) of indel mutations observed in all four types of Cas9-injected embryos. Furthermore, all types of Cas9 showed efficient targeted mutagenesis on multiplex genome editing, resulting in multiple phenotypes simultaneously. Collectively, we conclude that various NLS-fused Cas9 proteins and Cas9 mRNAs have similar genome editing efficiencies on targeting single or multiple genes, suggesting that the efficiency of CRISPR/Cas9 genome editing is highly dependent on guide RNAs (gRNAs) and gene loci. These findings may help to simplify the selection of Cas9 for gene editing using the CRISPR/Cas9 system. PMID:29295818

CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.

PubMed

Hochstrasser, Megan L; Taylor, David W; Bhat, Prashant; Guegler, Chantal K; Sternberg, Samuel H; Nogales, Eva; Doudna, Jennifer A

2014-05-06

In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) DNA-targeting complex Cascade (CRISPR-associated complex for antiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets at sites adjacent to a trinucleotide signature sequence called the protospacer adjacent motif (PAM). The Cascade complex then recruits Cas3, a nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded DNA (dsDNA) bearing a sequence matching that of the crRNA. Cascade comprises the CasA-E proteins and one crRNA, forming a structure that binds and unwinds dsDNA to form an R loop in which the target strand of the DNA base pairs with the 32-nt RNA guide sequence. Single-particle electron microscopy reconstructions of dsDNA-bound Cascade with and without Cas3 reveal that Cascade positions the PAM-proximal end of the DNA duplex at the CasA subunit and near the site of Cas3 association. The finding that the DNA target and Cas3 colocalize with CasA implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the PAM region is unnecessary for target binding but critical for Cas3-mediated degradation. In addition, the L1 loop of CasA, previously implicated in PAM recognition, is essential for Cas3 activation following target binding by Cascade. Together, these data show that the CasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage.

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.

PubMed

Lin, Feng-Jiau; Liu, Yuan; Sha, Zhongli; Tsang, Ling Ming; Chu, Ka Hou; Chan, Tin-Yam; Liu, Ruiyu; Cui, Zhaoxia

2012-11-16

The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

[Situation and assessment of heavy metal pollution in river and mud in one city in Henan Province].

PubMed

Xi, Jingzhuan; Li, Cuimei; Wang, Shouying; Jiang, Zhigang; Zhang, Miaomiao; Han, Guangliang

2010-11-01

To study the heavy metal contamination status in river water and mud in the suburb of a city in Henan Province. Typical sampling method is used to select a farmland irrigation river of the suburb of a city. Use the atomic absorption spectrophotometry, and measure the heavy metal cadmium (Cd), copper (Cu), lead (Pb) in the river water samples and mud samples by graphite furnace method and flame method, respectively. The results of water were compared with GB 3838-2002, Environmental Quality Standards for Surface Water, and GB 5084-2005, Standards for Irrigation Water Quality. The results of mud were compared with national soil background value. The contents of Cu and Cd in the river samples do not exceed the standard, and that of Pb is 3 to 6 times higher than the standard. According to the single factor pollution index method, the single factor pollution indice of Cu, and Cd in the river are less than 0.2 and are of clean level, while that of Pb reaches 6.84, indicating the Pb pollution in river water is severe. Cu in mud is more than 4 times of the soil background value, and that of Cd is more than 69 times of the soil background value, and that of Pb is more than 2 times of the soil background value. The single item pollution index indicates, in mud, the pollution index of Pb is 2.5, medium level pollution. The pollution indice of Cu and Cd in mud are more than 3, is severe pollution, and the Cd pollution is especially heavy, and the single pollution index reaches 67.76. The comprehensive pollution indice of the river and the mud are 5.346 and 84.115, respectively, indicating that both are at heavy pollution level. The main pollution source of the river originates from Pb, and that of the mud is from Cd and it is required to take measure and control as early as possible.

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes

PubMed Central

2012-01-01

Background The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. Results We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Conclusions Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda. PMID:23153176

Rational Design of Mini-Cas9 for Transcriptional Activation.

PubMed

Ma, Dacheng; Peng, Shuguang; Huang, Weiren; Cai, Zhiming; Xie, Zhen

2018-04-20

Nuclease dead Cas9 (dCas9) has been widely used for modulating gene expression by fusing with different activation or repression domains. However, delivery of the CRISPR/Cas system fused with various effector domains in a single adeno-associated virus (AAV) remains challenging due to the payload limit. Here, we engineered a set of downsized variants of Cas9 including Staphylococcus aureus Cas9 (SaCas9) that retained DNA binding activity by deleting conserved functional domains. We demonstrated that fusing FokI nuclease domain to the N-terminal of the minimal SaCas9 (mini-SaCas9) or to the middle of the split mini-SaCas9 can trigger efficient DNA cleavage. In addition, we constructed a set of compact transactivation domains based on the tripartite VPR activation domain and self-assembled arrays of split SpyTag:SpyCatch peptides, which are suitable for fusing to the mini-SaCas9. Lastly, we produced a single AAV containing the mini-SaCas9 fused with a downsized transactivation domain along with an optimized gRNA expression cassette, which showed efficient transactivation activity. Our results highlighted a practical approach to generate down-sized CRISPR/Cas9 and gene activation systems for in vivo applications.

Pitting Corrosion Behaviour of New Corrosion-Resistant Reinforcement Bars in Chloride-Containing Concrete Pore Solution

PubMed Central

Liu, Yao; Chu, Hong-yan; Wang, Danqian; Ma, Han; Sun, Wei

2017-01-01

In this study, the pitting behaviour of a new corrosion-resistant alloy steel (CR) is compared to that of low-carbon steel (LC) in a simulated concrete pore solution with a chloride concentration of 5 mol/L. The electrochemical behaviour of the bars was characterised using linear polarisation resistance (LPR) and electrochemical impedance spectroscopy (EIS). The pitting profiles were detected by reflective digital holographic microscopy (DHM), scanning electron microscopy (SEM), and the chemical components produced in the pitting process were analysed by X-ray energy dispersive spectroscopy (EDS). The results show that the CR bars have a higher resistance to pitting corrosion than the LC bars. This is primarily because of the periodic occurrence of metastable pitting during pitting development. Compared to the pitting process in the LC bars, the pitting depth grows slowly in the CR bars, which greatly reduces the risk of pitting. The possible reason for this result is that the capability of the CR bars to heal the passivation film helps to restore the metastable pits to the passivation state. PMID:28777327

Pitting corrosion as a mixed system: coupled deterministic-probabilistic simulation of pit growth

NASA Astrophysics Data System (ADS)

Ibrahim, Israr B. M.; Fonna, S.; Pidaparti, R.

2018-05-01

Stochastic behavior of pitting corrosion poses a unique challenge in its computational analysis. However, it also stems from electrochemical activity causing general corrosion. In this paper, a framework for corrosion pit growth simulation based on the coupling of the Cellular Automaton (CA) and Boundary Element Methods (BEM) is presented. The framework assumes that pitting corrosion is controlled by electrochemical activity inside the pit cavity. The BEM provides the prediction of electrochemical activity given the geometrical data and polarization curves, while the CA is used to simulate the evolution of pit shapes based on electrochemical activity provided by BEM. To demonstrate the methodology, a sample case of local corrosion cells formed in pitting corrosion with varied dimensions and polarization functions is considered. Results show certain shapes tend to grow in certain types of environments. Some pit shapes appear to pose a higher risk by being potentially significant stress raisers or potentially increasing the rate of corrosion under the surface. Furthermore, these pits are comparable to commonly observed pit shapes in general corrosion environments.

Experimental research on micro-pit defects of SUS 430 stainless steel strip in cold rolling process

NASA Astrophysics Data System (ADS)

Li, Changsheng; Li, Miao; Zhu, Tao; Huo, Gang

2013-05-01

In order to improve surface glossiness of stainless steel strip in tandem cold rolling, experimental research on micro-pit defects of SUS 430 ferrite stainless steel was investigated in laboratory. The surface morphology of micro-pit defects was observed by SEM. The effects of micro-pit defects on rolling reduction, roll surface roughness and emulsion parameters were analyzed. With the pass number increasing, the quantity and surface of micro-pit defects were reduced, uneven peak was decreased and gently along rolling direction, micro-pit defects had equally distributed tendency along tranverse direction. The micro-pit defects were increased with the roll surface roughness increase. The defects ratio was declined with larger gradient at pass number 1 to 3, but gentle slope at pass number 4 to 5. The effects of temperature 55° and 63°, concentration 3% and 6% of emulsion on micro-pit effects had not obvious difference. Maintain of micro-pit was effected by rolling oil or air in the micro-pit, the quality of oil was much more than the air in the micro-pit in lubrication rolling.

Distribution, morphology, and origins of Martian pit crater chains

NASA Astrophysics Data System (ADS)

Wyrick, Danielle; Ferrill, David A.; Morris, Alan P.; Colton, Shannon L.; Sims, Darrell W.

2004-06-01

Pit craters are circular to elliptical depressions found in alignments (chains), which in many cases coalesce into linear troughs. They are common on the surface of Mars and similar to features observed on Earth and other terrestrial bodies. Pit craters lack an elevated rim, ejecta deposits, or lava flows that are associated with impact craters or calderas. It is generally agreed that the pits are formed by collapse into a subsurface cavity or explosive eruption. Hypotheses regarding the formation of pit crater chains require development of a substantial subsurface void to accommodate collapse of the overlying material. Suggested mechanisms of formation include: collapsed lava tubes, dike swarms, collapsed magma chamber, substrate dissolution (analogous to terrestrial karst), fissuring beneath loose material, and dilational faulting. The research described here is intended to constrain current interpretations of pit crater chain formation by analyzing their distribution and morphology. The western hemisphere of Mars was systematically mapped using Mars Orbiter Camera (MOC) images to generate ArcView™ Geographic Information System (GIS) coverages. All visible pit crater chains were mapped, including their orientations and associations with other structures. We found that pit chains commonly occur in areas that show regional extension or local fissuring. There is a strong correlation between pit chains and fault-bounded grabens. Frequently, there are transitions along strike from (1) visible faulting to (2) faults and pits to (3) pits alone. We performed a detailed quantitative analysis of pit crater morphology using MOC narrow angle images, Thermal Emission Imaging System (THEMIS) visual images, and Mars Orbiter Laser Altimeter (MOLA) data. This allowed us to determine a pattern of pit chain evolution and calculate pit depth, slope, and volume. Volumes of approximately 150 pits from five areas were calculated to determine volume size distribution and regional trends. The information collected in the study was then compared with non-Martian examples of pit chains and physical analog models. We evaluated the various mechanisms for pit chain development based on the data collected and conclude that dilational normal faulting and sub-vertical fissuring provide the simplest and most comprehensive mechanisms to explain the regional associations, detailed geometry, and progression of pit chain development.

A probable martian analogue in muttom in southern india

NASA Astrophysics Data System (ADS)

Wankhede, Tushar; Rajesh, V. J.; Charri, Abhishek

2012-07-01

Mars, a terrestrial planet fourth from the Sun in the solar system, is widely known as the red planet. The iron oxide sand/dust is predominant on its surface and gives the reddish appearance. Recent explorations have exposed abundance of haematite-rich loose materials in the surface of Mars especially at Meridiani Planum. Sedimentary structures like bedding, cross-bedding, ripple marks, gullies, mud cracks etc. are identified in this area. It is essential to look for some terrestrial analogues for the iron oxide rich sand/dust in order to explore their genetic mechanisms in Martian surface. Red sand beds occur above the crystalline basement or younger calcareous sandstone/limestone as isolated patches of partly indurated or unindurated dunes and sheets fringing the south western coastal lands of Tamil Nadu. Calcretes, source of carbonates, also occur at places within these red sand beds. Muttom soils are dark red in color on fresh surfaces. The red sand beds are dominated by iron-bearing minerals such as hematite and ilmenite. Local patches of heavy mineral deposition by the action of wind and water were also observed in the Muttom area. Preliminary spectral analyses confirmed the presence of iron bearing minerals like hematite and ilmenite which are also present in Mars. Many sedimentary structures like gullies, channels, polygonal mud cracks, erosion pits and dunes were present in Muttom area similar to those observed on Martian surface. Meridiani planum outcrops are composed of some siliciclastics grains, and hematite, and only few deposits on Earth match this description. The siliciclastics grains are primarily quartz grain coated with hematite. Quartz is also found in Muttom which, may have been transported by the action of wind while in the Mars siliciclastics is the alteration product of basalt. The structures are more or less similar to those observed at Meridiani Planum. Previous workers interpreted these red sands as `unique' formed either by a mixed beach and dune environment, or as similar to colluvium (formed by mass wasting and fluvial processes). Comparative studies between the red sand beds formations on Martian surface and southern Tamil Nadu can provide valuable insights on the origin, weathering pattern, tectonics and depositional environment of red sand beds in Mars.

Sedimentation rates in the marshes of Sand Lake National Wildlife Refuge

USGS Publications Warehouse

Gleason, R.A.; Euliss, N.H.; Holmes, C.W.

2003-01-01

Impoundments located within river systems in the Northern Great Plains are vulnerable to sediment inputs because intensive agriculture in watersheds has increased soil erosion and sediments in rivers. At the request of the U.S. Fish and Wildlife Service (FWS), we evaluated the vertical accretion of sediment in the Mud Lake impoundment of Sand Lake National Wildlife Refuge (NWR), Brown County, South Dakota. The Mud Lake impoundment was created in 1936 by constructing a low-head dam across the James River. We collected sediment cores from the Mud Lake impoundment during August 2000 for determination of vertical accretion rates. Accretion rates were estimated using cesium-13 7 and lead-210 isotopic dating techniques to estimate sediment accretion over the past 100 years. Accretion rates were greatest near the dam (1.3 cm yr-1) with less accretion (0.2 cm yr-1) occurring in the upper reaches of Mud Lake. As expected, accretion was highest near the dam where water velocities and greater water depth facilitates sediment deposition. Higher rates of sedimentation (accretion> 2.0 cm year-1) occurred during the 1990s when river flows were especially high. Since 1959, sediment accretion has reduced maximum pool depth of Mud Lake near the dam by 55 cm. Assuming that sediment accretion rates remain the same in the future, we project Mud Lake will have a maximum pool depth of 77 and 51 cm by 2020 and 2040, respectively. Over this same time frame, water depths in the upper reaches of Mud Lake would be reduced to< 2 cm. Projected future loss of water depth will severely limit the ability of managers to manipulate pool levels in Mud Lake to cycle vegetation and create interspersion of cover and water to meet current wildlife habitat management objectives. As predicted for major dams constructed on rivers throughout the world, Mud Lake will have a finite life span. Our data suggests that the functional life span of Mud Lake since construction will be < 100 years. We anticipate that over the next 20 years, sediments entering Mud Lake will reduce water depths to the point that current wildlife management objectives cannot be achieved through customary water-level manipulations. Sedimentation impacts are not unique to the Sand Lake NWR. It is widely accepted that impoundments trap sediments and shallow impoundments, such as those managed by the FWS, are especially vulnerable. Given the ecological impacts associated with loss of water depths, we recommend that managers begin evaluating the long-term wildlife management goals for the refuge relative to associated costs and feasibility of options available to enhance and maximize the life span of existing impoundments, including upper watershed management.

Corrosion behavior of binary titanium aluminide intermetallics

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

Saffarian, H.M.; Gan, Q.; Hadkar, R.

1996-08-01

The corrosion behavior of arc-melted binary titanium aluminide intermetallics TiAl, Ti{sub 2}Al, and TiAl{sub 3} in aqueous sodium sulfate and sodium chloride solutions was measured and compared to that of pure Ti and Al. Effects of electrolyte composition (e.g., sulfate [0.25 M SO{sub 4}{sup 2}{sup {minus}}], chloride [0.1 to 1.0 M Cl{sup {minus}}], and pH [3 to 10]) were examined. Anodic polarization of titanium aluminides in aqueous SO{sub 4}{sup 2}{sup {minus}} solutions was similar (showing passive behavior), but no pitting or pitting potential (E{sub pit}) was observed. In aqueous NaCl, however, titanium aluminides were susceptible to pitting, and E{sub pit}more » decreased with increasing Al content (i.e., Ti{sub 3}Al had the highest E{sub pit} and, therefore, a greater resistance to pitting, followed by TiAl and TiAl{sub 3}). For TiAl, E{sub pit} was slightly dependent upon pH or Cl{sup {minus}} concentration. Pit morphology and E{sub pit} values were quite different for TiAl compared to Ti{sub 3}Al. TiAl showed numerous small pits, whereas Ti{sub 3}Al exhibited fewer but larger and deeper pits. The larger pit density for TiAl was associated with Al-rich interdendrite regions. One interesting feature of the anodic polarization curves for Ti{sub 3}Al was a small anodic peak frequently observed at {approximately}1.4 V{sub SCE} to 1.8 V{sub SCE}. Results suggested this peak was associated with pit initiation, since pitting initiated concurrently with the peak or immediately afterward.« less

Investigating pitting in X65 carbon steel using potentiostatic polarisation

NASA Astrophysics Data System (ADS)

Mohammed, Sikiru; Hua, Yong; Barker, R.; Neville, A.

2017-11-01

Although pitting corrosion in passive materials is generally well understood, the growth of surface pits in actively-corroding materials has received much less attention to date and remains poorly understood. One of the key challenges which exists is repeatedly and reliably generating surface pits in a practical time-frame in the absence of deformation and/or residual stress so that studies on pit propagation and healing can be performed. Another pertinent issue is how to evaluate pitting while addressing general corrosion in low carbon steel. In this work, potentiostatic polarisation was employed to induce corrosion pits (free from deformation or residual stress) on actively corroding X65 carbon steel. The influence of applied potential (50 mV, 100 mV and 150 mV vs open circuit potential) was investigated over 24 h in a CO2-saturated, 3.5 wt.% NaCl solution at 30 °C and pH 3.8. Scanning electron microscopy (SEM) was utilised to examine pits, while surface profilometry was conducted to measure pit depth as a function of applied potential over the range considered. Analyses of light pitting (up to 120 μm) revealed that pit depth increased linearly with increase in applied potential. This paper relates total pit volume (measured using white light interferometry) to dissipated charge or total mass loss (using the current response for potentiostatic polarisation in conjunction with Faraday's law). By controlling the potential of the surface (anodic) the extent of pitting and general corrosion could be controlled. This allowed pits to be evaluated for their ability to continue to propagate after the potentiostatic technique was employed. Linear growth from a depth of 70 μm at pH 3.8, 80 °C was demonstrated. The technique offers promise for the study of inhibition of pitting.

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

USDA-ARS?s Scientific Manuscript database

The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. | Office of Cancer Genomics

Cancer.gov

The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter.

Cas9, Cpf1 and C2c1/2/3―What's next?

PubMed Central

Yamamoto, Takashi; Sakuma, Tetsushi

2017-01-01

ABSTRACT Since the rapid emergence of clustered regulatory interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system, developed as a genome engineering tool in 2012–2013, most researchers in the life science field have had a fixated interest in this fascinating technology. CRISPR-Cas9 is an RNA-guided DNA endonuclease system, which consists of Cas9 nuclease defining a few targeting base via protospacer adjacent motif complexed with easily customizable single guide RNA targeting around 20-bp genomic sequence. Although Streptococcus pyogenes Cas9 (SpCas9), one of the Cas9 proteins that applications in genome engineering were first demonstrated, still has wide usage because of its high nuclease activity and broad targeting range, there are several limitations such as large molecular weight and potential off-target effect. In this commentary, we describe various improvements and alternatives of CRISPR-Cas systems, including engineered Cas9 variants, Cas9 homologs, and novel Cas proteins other than Cas9. These variations enable flexible genome engineering with high efficiency and specificity, orthogonal genetic control at multiple gene loci, gene knockdown, or fluorescence imaging of transcripts mediated by RNA targeting, and beyond. PMID:28140746

Cell-type-specific genome editing with a microRNA-responsive CRISPR–Cas9 switch

PubMed Central

Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J. C.; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut

2017-01-01

Abstract The CRISPR–Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR–Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. PMID:28525578

Cas9, Cpf1 and C2c1/2/3-What's next?

PubMed

Nakade, Shota; Yamamoto, Takashi; Sakuma, Tetsushi

2017-05-04

Since the rapid emergence of clustered regulatory interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system, developed as a genome engineering tool in 2012-2013, most researchers in the life science field have had a fixated interest in this fascinating technology. CRISPR-Cas9 is an RNA-guided DNA endonuclease system, which consists of Cas9 nuclease defining a few targeting base via protospacer adjacent motif complexed with easily customizable single guide RNA targeting around 20-bp genomic sequence. Although Streptococcus pyogenes Cas9 (SpCas9), one of the Cas9 proteins that applications in genome engineering were first demonstrated, still has wide usage because of its high nuclease activity and broad targeting range, there are several limitations such as large molecular weight and potential off-target effect. In this commentary, we describe various improvements and alternatives of CRISPR-Cas systems, including engineered Cas9 variants, Cas9 homologs, and novel Cas proteins other than Cas9. These variations enable flexible genome engineering with high efficiency and specificity, orthogonal genetic control at multiple gene loci, gene knockdown, or fluorescence imaging of transcripts mediated by RNA targeting, and beyond.

Organic chemical composition of mud from the LUSI mud volcano, Sidoarjo, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Rosenbauer, R. J.; Campbell, P.; Lam, A.

2009-12-01

Sidoarjo, East Java, Indonesia is the site of LUSI, a terrestrial mud volcano that has been erupting since May 29, 2006. In response to a U.S. Department of State request, the U.S. Geological Survey has been assisting the Indonesian Government to describe the geological and geochemical aspects and potential health risk of the mud eruption. We report here on the organic chemical composition of the mud. Organic chemical analyses were carried out by gas chromatography/mass spectroscopy following organic extraction by microwave-assisted solvent extraction and compound fractionation by adsorption chromatography. There is a petroliferous component in the mud that is fresh, immature, and nonbiodegraded. There is a complete suite of n-alkanes with a bell-shaped pattern typical of fresh petroleum with a Cmax around C20. The alkane content ranges from 0.12 to 1.01 mg/kg dry mud. The presence of certain hopanes (i.e. 17 α,21β(H)-30-norhopane and 17α,21β(H)-hopane) is also indicative of the presence of oil. The proportions of other biomarker compounds (pristane/phytane = 2.4) and the dominance of the C27 sterane (5α(H),14α(H),17α(H)-chlolestane) suggest that oil formed under oxic conditions and has a likely coastal marine or terrigenous source. The presence of oleanane indicates a Cretaceous or younger age for the petrogenic material. These geochemical parameters are consistent with Indonesian oil derived from Tertiary marlstone source rocks that contained kerogen deposited under oxic conditions, probably the upper Miocene Klasafet Formation. Polycyclic aromatic hydrocarbons (PAHs) are present and range in content from 0.1 to 2.2 mg/kg dry mud. The low molecular weight (LMW) PAHs, in particular, naphthalene and methyl-naphthalene are dominant except for perylene which is ubiquitous in the environment. The presence of both parent and higher homologue PAHs indicate a petrogenic rather than combustion source. PAHs are known carcinogens but toxicity data in sediments are sparse and often qualitative, depending on the PAH matrix and thus bioavailability. The distribution and content of PAHs measured in the LUSI mud do exceed USEPA recommended interim sediment quality criteria. In addition, judging sediment toxicity on the basis of single PAH compounds risks underestimating effects because mixtures of PAHs tend to aggregate toxicity. Further studies are needed to determine whether or not PAHs are present in levels that exceed soil remediation or aquatic guidelines. The mud contains low levels (tens of ppb) of the higher plant sterols including stigmasterol and β-sitosterol. Also, 22-dehydrocholesterol (generally ascribed to algal material) is present at 39 ppb. These compounds are derived from natural sources, are non-hazardous, and were likely entrained in the mud during ascent to the surface or mixed with the mud post-eruption. The organic compounds identified to date will exhibit a variety of environmental behaviors and effects. Some compounds will volatilize and photo-oxidize or biodegrade relatively quickly (i.e. n-alkanes), and are relatively nontoxic. LMW PAHs are sparingly soluble in water but heavier PAHs will likely persist in the environment and represent potential toxicity to biota because PAHs are bio-accumulative. But the overall toxicity of the mud appears low.

Morphology and Evolution of Sublimation Pits on Pluto

NASA Astrophysics Data System (ADS)

Abu-Hashmeh, N.; Conrad, J. W.; Nimmo, F.; Moore, J. M.; Stern, A.; Olkin, C.; Weaver, H. A., Jr.; Ennico Smith, K.; Young, L. A.

2017-12-01

Pluto's Sputnik Planitia region hosts a geologically young surface of nitrogen ice that exhibits striking pitted terrain (Moore et al., Science 351, 2016). These pits are most likely formed by sublimation due to incident sunlight, similar to the southern polar cap of Mars (Byrne and Ingersoll, Science 299, 2003); however, their evolution over time has resulted in unique morphological characteristics. Motivated by this, we used the high-resolution mosaic strips captured by New Horizons' Long Range Reconnaissance Imager (LORRI) to map sublimation pits in the southernmost region of Sputnik Planitia. Statistical data shows pit orientations appearing North-South dominant; their morphology also indicates extensional evolution along the major axis caused by further sublimation and contact-coalescence processes. Qualitative analysis of the region yielded indications of an evolutionary path for individual pits that coalesce into each other and exhibit an elongated end-stage. Additionally, densely-pitted regions generally appear to correlate with regions containing longer pits, implying that coalescence may be an important process for elongation. We also model the evolution geometry through competing effects of diffusion (viscous relaxation) and retreat (sublimation) (Buhler and Ingersoll, LPSC Abstract #1746, 2017). The model demonstrates single-pit and coalescing-pit evolutions that influence overall length, as well as a potential ability for the pit center to move in space while the pit morphology evolves.

Erosion properties of cohesive sediments in the Colorado River in Grand Canyon

USGS Publications Warehouse

Akahori, R.; Schmeeckle, M.W.; Topping, D.J.; Melis, T.S.

2008-01-01

Cohesive sediment deposits characterized by a high fraction of mud (silt plus clay) significantly affect the morphology and ecosystem of rivers. Potentially cohesive sediment samples were collected from deposits in the Colorado River in Marble and Grand Canyons. The erosion velocities of these samples were measured in a laboratory flume under varying boundary shear stresses. The non-dimensional boundary shear stress at which erosion commenced showed a systematic deviation from that of non-cohesive sediments at mud fractions greater than 0.2. An empirical relation for the boundary shear stress threshold of erosion as a function of mud fraction was proposed. The mass erosion rate was modelled using the Ariathurai-Partheniades equation. The erosion rate parameter of this equation was found to be a strong function of mud fraction. Under similar boundary shear stress and sediment supply conditions in the Colorado River, cohesive lateral eddy deposits formed of mud fractions in excess of 0.2 will erode less rapidly than non-cohesive deposits. Copyright ?? 2008 John Wiley & Sons, Ltd.

Radioactivity of natural medicinal preparations contained extracts from peat mud available in retail trade used externally.

PubMed

Karpińska, Maria; Kapała, Jacek; Raciborska, Agnieszka; Kulesza, Grzegorz; Milewska, Anna; Mnich, Stanisław

2017-08-01

In this work were identified and measured the activity of radioactive isotopes present in medicinal preparations from peat mud and estimated the doses obtained from them during therapy. Radioactivity of 22 preparations from peat mud and 20 water samples from water of the North-East region of Poland was studied. The median of the total activity was 24.8 Bq kg -1 . Total maximal isotope activity was observed in the Iwonicka Cube 146 Bq kg -1 while considerable amounts of isotopes were found in the Kolobrzeska Peat Mud Paste 112 Bq kg -1 . The doses obtained during therapy were within the range of 11 nSv-13 μSv depending on extracts of medicinal preparations from peat mud. The probability that such a small dose would stimulate biological effects is low. However, some clinicians believe that one of the possible therapeutic mechanisms in the treatment of rheumatoid disorders is the induction of immune response by ionising radiation.

Biostratinomic processes for the development of mud-cast logs in Carboniferous and Holocene swamps

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

Gastaldo, R.A.; Demko, T.M.; Liu, Yuejin

1989-08-01

Prostrate trees are common features of fossil forest litters, and are frequently preserved as mud-casts. Specimens of Carboniferous mud-cast trees and a mud-filled incipient cast of a Holocene Taxodium have been investigated to determine the biostratinomic processes responsible for their formation. These processes are complex. Hollowing of tree trunks may take place during life or by degradation after death. Once the trunk has fallen, the hollow cavity is supported by surrounding wood and/or bark tissues and acts as a conduit for sediment-laden waters. Leaf litter may be preserved on bedding surfaces. The infilling sequence of horizontal, parallel bedded, fine-grained sedimentmore » is deposited from suspended load during multiple overbank flooding events. These results differ from experimentally produced pith casts in which the sediment grain size is of fine sand. In Holocene specimens, alluvial mud within the log may provide a substrate for infaunal invertebrates. No evidence of infaunal burrowing in Carboniferous analogues exists.« less

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins.

PubMed

Rauch, Benjamin J; Silvis, Melanie R; Hultquist, Judd F; Waters, Christopher S; McGregor, Michael J; Krogan, Nevan J; Bondy-Denomy, Joseph

2017-01-12

Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a countermeasure, numerous phages are known that produce proteins to block the function of class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages. More than half of L. monocytogenes strains with cas9 contain at least one prophage-encoded inhibitor, suggesting widespread CRISPR-Cas9 inactivation. Two of these inhibitors also blocked the widely used Streptococcus pyogenes Cas9 when assayed in Escherichia coli and human cells. These natural Cas9-specific "anti-CRISPRs" present tools that can be used to regulate the genome engineering activities of CRISPR-Cas9. Copyright © 2017 Elsevier Inc. All rights reserved.

Cas9 specifies functional viral targets during CRISPR-Cas adaptation.

PubMed

Heler, Robert; Samai, Poulami; Modell, Joshua W; Weiner, Catherine; Goldberg, Gregory W; Bikard, David; Marraffini, Luciano A

2015-03-12

Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their associated (Cas) proteins provide adaptive immunity against viral infection in prokaryotes. Upon infection, short phage sequences known as spacers integrate between CRISPR repeats and are transcribed into small RNA molecules that guide the Cas9 nuclease to the viral targets (protospacers). Streptococcus pyogenes Cas9 cleavage of the viral genome requires the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) sequence immediately downstream of the viral target. It is not known whether and how viral sequences flanked by the correct PAM are chosen as new spacers. Here we show that Cas9 selects functional spacers by recognizing their PAM during spacer acquisition. The replacement of cas9 with alleles that lack the PAM recognition motif or recognize an NGGNG PAM eliminated or changed PAM specificity during spacer acquisition, respectively. Cas9 associates with other proteins of the acquisition machinery (Cas1, Cas2 and Csn2), presumably to provide PAM-specificity to this process. These results establish a new function for Cas9 in the genesis of prokaryotic immunological memory.

Mud Volcanoes - A New Class of Sites for Geological and Astrobiological Exploration of Mars

NASA Technical Reports Server (NTRS)

Allen, C.C.; Oehler, D.Z.; Baker, D.M.

2009-01-01

Mud volcanoes provide a unique low-temperature window into the Earth s subsurface - including the deep biosphere - and may prove to be significant sources of atmospheric methane. The identification of analogous features on Mars would provide an important new class of sites for geological and astrobiological exploration. We report new work suggesting that features in Acidalia Planitia are most consistent with their being mud volcanoes.

Recycling of red muds with the extraction of metals and special additions to cement

NASA Astrophysics Data System (ADS)

Zinoveev, D. V.; Diubanov, V. G.; Shutova, A. V.; Ziniaeva, M. V.

2015-01-01

The liquid-phase reduction of iron oxides from red mud is experimentally studied. It is shown that, in addition to a metal, a slag suitable for utilization in the construction industry can be produced as a result of pyrometallurgical processing of red mud. Portland cement is shown to be produced from this slag with mineral additions and a high-aluminate expansion addition to cement.

The biomechanics of burrowing and boring.

PubMed

Dorgan, Kelly M

2015-01-15

Burrowers and borers are ecosystem engineers that alter their physical environments through bioturbation, bioirrigation and bioerosion. The mechanisms of moving through solid substrata by burrowing or boring depend on the mechanical properties of the medium and the size and morphology of the organism. For burrowing animals, mud differs mechanically from sand; in mud, sediment grains are suspended in an organic matrix that fails by fracture. Macrofauna extend burrows through this elastic mud by fracture. Sand is granular and non-cohesive, enabling grains to more easily move relative to each other, and macrofaunal burrowers use fluidization or plastic rearrangement of grains. In both sand and mud, peristaltic movements apply normal forces and reduce shear. Excavation and localized grain compaction are mechanisms that plastically deform sediments and are effective in both mud and sand, with bulk excavation being used by larger organisms and localized compaction by smaller organisms. Mechanical boring of hard substrata is an extreme form of excavation in which no compaction of burrow walls occurs and grains are abraded with rigid, hard structures. Chemical boring involves secretion to dissolve or soften generally carbonate substrata. Despite substantial differences in the mechanics of the media, similar burrowing behaviors are effective in mud and sand. © 2015. Published by The Company of Biologists Ltd.

OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE - A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING

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

Arnis Judzis

2002-10-01

This document details the progress to date on the OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE -- A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING contract for the quarter starting July 2002 through September 2002. Even though we are awaiting the optimization portion of the testing program, accomplishments include the following: (1) Smith International agreed to participate in the DOE Mud Hammer program. (2) Smith International chromed collars for upcoming benchmark tests at TerraTek, now scheduled for 4Q 2002. (3) ConocoPhillips had a field trial of the Smith fluid hammer offshore Vietnam. The hammer functioned properly, though themore » well encountered hole conditions and reaming problems. ConocoPhillips plan another field trial as a result. (4) DOE/NETL extended the contract for the fluid hammer program to allow Novatek to ''optimize'' their much delayed tool to 2003 and to allow Smith International to add ''benchmarking'' tests in light of SDS Digger Tools' current financial inability to participate. (5) ConocoPhillips joined the Industry Advisors for the mud hammer program. (6) TerraTek acknowledges Smith International, BP America, PDVSA, and ConocoPhillips for cost-sharing the Smith benchmarking tests allowing extension of the contract to complete the optimizations.« less

Suppression of HBV replication by the expression of nickase- and nuclease dead-Cas9.

PubMed

Kurihara, Takeshi; Fukuhara, Takasuke; Ono, Chikako; Yamamoto, Satomi; Uemura, Kentaro; Okamoto, Toru; Sugiyama, Masaya; Motooka, Daisuke; Nakamura, Shota; Ikawa, Masato; Mizokami, Masashi; Maehara, Yoshihiko; Matsuura, Yoshiharu

2017-07-21

Complete removal of hepatitis B virus (HBV) DNA from nuclei is difficult by the current therapies. Recent reports have shown that a novel genome-editing tool using Cas9 with a single-guide RNA (sgRNA) system can cleave the HBV genome in vitro and in vivo. However, induction of a double-strand break (DSB) on the targeted genome by Cas9 risks undesirable off-target cleavage on the host genome. Nickase-Cas9 cleaves a single strand of DNA, and thereby two sgRNAs are required for inducing DSBs. To avoid Cas9-induced off-target mutagenesis, we examined the effects of the expressions of nickase-Cas9 and nuclease dead Cas9 (d-Cas9) with sgRNAs on HBV replication. The expression of nickase-Cas9 with a pair of sgRNAs cleaved the target HBV genome and suppressed the viral-protein expression and HBV replication in vitro. Moreover, nickase-Cas9 with the sgRNA pair cleaved the targeted HBV genome in mouse liver. Interestingly, d-Cas9 expression with the sgRNAs also suppressed HBV replication in vitro without cleaving the HBV genome. These results suggest the possible use of nickase-Cas9 and d-Cas9 with a pair of sgRNAs for eliminating HBV DNA from the livers of chronic hepatitis B patients with low risk of undesirable off-target mutation on the host genome.

Tuffaceous Mud is a Volumetrically Important Volcaniclastic Facies of Reararc Submarine Volcanism

NASA Astrophysics Data System (ADS)

Gill, J. B.; Bongiolo, E.; Miyazaki, T.; Hamelin, C.; Jutzeler, M.

2016-12-01

Unexpectedly, about 2/3 of the 1806 m of rock drilled during IODP Exp 350 on the flank of an Upper Miocene andesitic seamount in the Izu reararc was tuffaceous mud and tuffaceous mudstone that accumulated at high carbonate-free sedimentation rates (60-120 m/MY). This rate is several times faster than at adjacent sites in the forearc or incoming plate. Most tuffaceous muds contain <1% <2 mm-sized fragments of glass shards and plag±cpx crystals. Most muds are dacitic in bulk composition on an anhydrous, carbonate-free basis. They are intercalated with thin ash or tuff beds. The trace element and Sr-Nd-Hf-Pb isotope geochemistry of carbonate-free tuffaceous mud and mudstone indicates that >70% and often >90% of them consist of local volcanic materials that range from basalt to rhyolite. Most exceptions were deposited during Pleistocene glacial intervals. Consequently, tuffaceous mud is an important submarine volcaniclastic facies destined to become shale or slate in the geological record while retaining geochemical information about its provenance. Even though the drill site was <10 km from the summit of a 2-km-high and at times subaerially exposed seamount, and the sedimentation rate exceeded that in the adjacent forearc, tuffaceous mud was the principal reararc volcaniclastic facies. To explain this fine grain size, we infer that much of the submarine volcanism was explosive despite water depths approaching 2 km. The resulting very fine glass quickly becomes clay or is too small to be recognized in thin section or smear slides, and can be sampled only in sediment cores.

A dimensional approach to understanding severity estimates and risk correlates of marijuana abuse and dependence in adults

PubMed Central

WU, LI-TZY; WOODY, GEORGE E.; YANG, CHONGMING; PAN, JENG-JONG; REEVE, BRYCE B.; BLAZER, DAN G.

2012-01-01

While item response theory (IRT) research shows a latent severity trait underlying response patterns of substance abuse and dependence symptoms, little is known about IRT-based severity estimates in relation to clinically relevant measures. In response to increased prevalences of marijuana-related treatment admissions, an elevated level of marijuana potency, and the debate on medical marijuana use, we applied dimensional approaches to understand IRT-based severity estimates for marijuana use disorders (MUDs) and their correlates while simultaneously considering gender- and race/ethnicity-related differential item functioning (DIF). Using adult data from the 2008 National Survey on Drug Use and Health (N=37,897), DSM-IV criteria for MUDs among past-year marijuana users were examined by IRT, logistic regression, and multiple indicators–multiple causes (MIMIC) approaches. Among 6,917 marijuana users, 15% met criteria for a MUD; another 24% exhibited subthreshold dependence. Abuse criteria were highly correlated with dependence criteria (correlation=0.90), indicating unidimensionality; item information curves revealed redundancy in multiple criteria. MIMIC analyses showed that MUD criteria were positively associated with weekly marijuana use, early marijuana use, other substance use disorders, substance abuse treatment, and serious psychological distress. African Americans and Hispanics showed higher levels of MUDs than whites, even after adjusting for race/ethnicity-related DIF. The redundancy in multiple criteria suggests an opportunity to improve efficiency in measuring symptom-level manifestations by removing low-informative criteria. Elevated rates of MUDs among African Americans and Hispanics require research to elucidate risk factors and improve assessments of MUDs for different racial/ethnic groups. PMID:22351489

Potential risks of the residue from Samarco's mine dam burst (Bento Rodrigues, Brazil).

PubMed

Segura, Fabiana Roberta; Nunes, Emilene Arusievicz; Paniz, Fernanda Pollo; Paulelli, Ana Carolina Cavalheiro; Rodrigues, Gabriela Braga; Braga, Gilberto Úbida Leite; Dos Reis Pedreira Filho, Walter; Barbosa, Fernando; Cerchiaro, Giselle; Silva, Fábio Ferreira; Batista, Bruno Lemos

2016-11-01

On November 5th, 2015, Samarco's iron mine dam - called Fundão - spilled 50-60 million m 3 of mud into Gualaxo do Norte, a river that belongs to Rio Doce Basin. Approximately 15 km 2 were flooded along the rivers Gualaxo do Norte, Carmo and Doce, reaching the Atlantic Ocean on November 22nd, 2015. Six days after, our group collected mud, soil and water samples in Bento Rodrigues (Minas Gerais, Brazil), which was the first impacted area. Overall, the results, water samples - potable and surface water from river - presented chemical elements concentration according to Brazilian environmental legislations, except silver concentration in surface water that ranged from 1.5 to 1087 μg L -1 . In addition, water mud-containing presented Fe and Mn concentrations approximately 4-fold higher than the maximum limit for water bodies quality assessment, according to Brazilian laws. Mud particle size ranged from 1 to 200 μm. SEM-EDS spot provided us some semi quantitative data. Leaching/extraction tests suggested that Ba, Pb, As, Sr, Fe, Mn and Al have high potential mobilization from mud to water. Low microbial diversity in mud samples compared to background soil samples. Toxicological bioassays (HepG2 and Allium cepa) indicated potential risks of cytotoxicity and DNA damage in mud and soil samples used in both assays. The present study provides preliminary information aiming to collaborate to the development of future works for monitoring and risk assessment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium.

PubMed Central

Higgins, N P; Yang, X; Fu, Q; Roth, J R

1996-01-01

A genetic system was developed to investigate the supercoil structure of bacterial chromosomes. New res-carrying transposons were derived from MudI1734 (MudJr1 and MudJr2) and Tn10 (Tn10dGn). The MudJr1 and MudJr2 elements each have a res site in opposite orientation so that when paired with a Tn10dGn element in the same chromosome, one MudJr res site will be ordered as a direct repeat. Deletion formation was studied in a nonessential region (approximately 100 kb) that extends from the his operon through the cob operon. Strains with a MudJr insertion in the cobT gene at the 5' end of the cob operon plus a Tn10dGn insertion positioned either clockwise or counterclockwise from cobT were exposed to a burst of RES protein. Following a pulse of resolvase expression, deletion formation was monitored by scoring the loss of the Lac+ phenotype or by loss of tetracycline resistance. In exponentially growing populations, deletion products appeared quickly in some cells (in 10 min) but also occurred more than an hour after RES induction. The frequency of deletion (y) diminished with increasing distance (x) between res sites. Results from 15 deletion intervals fit the exponential equation y = 120 . 10(-0.02x). We found that res sites can be plectonemically interwound over long distances ( > 100 kb) and that barriers to supercoil diffusion are placed stochastically within the 43- to 45-min region of the chromosome. PMID:8631670

Timing and mechanisms for the deposition of the glaciomarine mud in and around the Gulf of Maine: A discussion of alternative models

USGS Publications Warehouse

Oldale, Robert N.

1989-01-01

Glaciomarine mud in the Gulf of Maine, characterized by rhythmic seismic layers that mimic the morphology of the underlying surface, is composed of subequal amounts of silt and clay, variable amounts of sand, and sparse gravel-sized clasts. The mud is Wisconsinan in age and was deposited during the retreat of the last ice sheet. A beginning date of 38 ka, proposed by King and Fader (1986) in their chronology of the last deglaciation, is considered too old. An alternative chronology, more consistent with the continental record to the west, is proposed here. ln this interpretation, deposition ofglaciomarine mud began about 18 ka when the late Wisconsinan ice retreated from Georges Bank, Great South Channel, and Northeast Channel and ended around 11 ka, when meltwater ceased to enter the Gulf of Maine. Basal-till melt-out from an ice shelf and bergs as the source of the glaciomarine mud, also proposed by King and Fader (1986), is thought to be inconsistent with the volume, widespread rhythmic bedding, and low stone content of the deposit. More likely the source of the glaciomarine mud was rock-flour-laden meltwater that entered the sea along the grounding line of a calving glacier or by way of subaerial meltwater streams. The rock flour was then dispersed by sediment plumes and was deposited when the sediment fell to the sea floor, aided by flocculation and biological agglutination. Rhythmic layers within the glaciomarine mud could represent annual cyclic sedimentation (varves) or cyclic events of lesser duration.

Fragmentation of the CRISPR-Cas Type I-B signature protein Cas8b.

PubMed

Richter, Hagen; Rompf, Judith; Wiegel, Julia; Rau, Kristina; Randau, Lennart

2017-11-01

CRISPR arrays are transcribed into long precursor RNA species, which are further processed into mature CRISPR RNAs (crRNAs). Cas proteins utilize these crRNAs, which contain spacer sequences that can be derived from mobile genetic elements, to mediate immunity during a reoccurring virus infection. Type I CRISPR-Cas systems are defined by the presence of different Cascade interference complexes containing large and small subunits that play major roles during target DNA selection. Here, we produce the protein and crRNA components of the Type I-B CRISPR-Cas complex of Clostridium thermocellum and Methanococcus maripaludis. The C. thermocellum Cascade complexes were reconstituted and analyzed via size-exclusion chromatography. Activity of the heterologous M. maripaludis CRISPR-Cas system was followed using phage lambda plaques assays. The reconstituted Type-I-B Cascade complex contains Cas7, Cas5, Cas6b and the large subunit Cas8b. Cas6b can be omitted from the reconstitution protocol. The large subunit Cas8b was found to be represented by two tightly associated protein fragments and a small C-terminal Cas8b segment was identified in recombinant complexes and C. thermocellum cell lysate. Production of Cas8b generates a small C-terminal fragment, which is suggested to fulfill the role of the missing small subunit. A heterologous, synthetic M. maripaludis Type I-B system is active in E. coli against phage lambda, highlighting a potential for genome editing using endogenous Type-I-B CRISPR-Cas machineries. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal structures of two tetrameric β-carbonic anhydrases from the filamentous ascomycete Sordaria macrospora.

PubMed

Lehneck, Ronny; Neumann, Piotr; Vullo, Daniela; Elleuche, Skander; Supuran, Claudiu T; Ficner, Ralf; Pöggeler, Stefanie

2014-04-01

Carbonic anhydrases (CAs) are metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate (hydrogen carbonate) and protons. CAs have been identified in archaea, bacteria and eukaryotes and can be classified into five groups (α, β, γ, δ, ζ) that are unrelated in sequence and structure. The fungal β-class has only recently attracted attention. In the present study, we investigated the structure and function of the plant-like β-CA proteins CAS1 and CAS2 from the filamentous ascomycete Sordaria macrospora. We demonstrated that both proteins can substitute for the Saccharomyces cerevisiae β-CA Nce103 and exhibit an in vitro CO2 hydration activity (kcat /Km of CAS1: 1.30 × 10(6) m(-1) ·s(-1) ; CAS2: 1.21 × 10(6 ) m(-1) ·s(-1) ). To further investigate the structural properties of CAS1 and CAS2, we determined their crystal structures to a resolution of 2.7 Å and 1.8 Å, respectively. The oligomeric state of both proteins is tetrameric. With the exception of the active site composition, no further major differences have been found. In both enzymes, the Zn(2) (+) -ion is tetrahedrally coordinated; in CAS1 by Cys45, His101 and Cys104 and a water molecule and in CAS2 by the side chains of four residues (Cys56, His112, Cys115 and Asp58). Both CAs are only weakly inhibited by anions, making them good candidates for industrial applications. CAS1 and CAS2 bind by x-ray crystallography (View interaction) Structural data have been deposited in the Protein Data Bank database under accession numbers 4O1J for CAS1 and 4O1K for CAS2. © 2014 FEBS.

Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system.

PubMed

Koo, Yoon; Ka, Donghyun; Kim, Eun-Jin; Suh, Nayoung; Bae, Euiyoung

2013-10-23

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form an RNA-mediated microbial immune system against invading foreign genetic elements. Cas5 proteins constitute one of the most prevalent Cas protein families in CRISPR-Cas systems and are predicted to have RNA recognition motif (RRM) domains. Cas5d is a subtype I-C-specific Cas5 protein that can be divided into two distinct subgroups, one of which has extra C-terminal residues while the other contains a longer insertion in the middle of its N-terminal RRM domain. Here, we report crystal structures of Cas5d from Streptococcus pyogenes and Xanthomonas oryzae, which respectively represent the two Cas5d subgroups. Despite a common domain architecture consisting of an N-terminal RRM domain and a C-terminal β-sheet domain, the structural differences between the two Cas5d proteins are highlighted by the presence of a unique extended helical region protruding from the N-terminal RRM domain of X. oryzae Cas5d. We also demonstrate that Cas5d proteins possess not only specific endoribonuclease activity for CRISPR RNAs but also nonspecific double-stranded DNA binding affinity. These findings suggest that Cas5d may play multiple roles in CRISPR-mediated immunity. Furthermore, the specific RNA processing was also observed between S. pyogenes Cas5d protein and X. oryzae CRISPR RNA and vice versa. This cross-species activity of Cas5d provides a special opportunity for elucidating conserved features of the CRISPR RNA processing event. Copyright © 2013 Elsevier Ltd. All rights reserved.

Initation of pitting corrosion in martensitic stainless steels. [17-4PH; 13-8Mo; Custom 450

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

Cieslak, W.R.; Semarge, R.E.; Bovard, F.S.

1986-01-01

The form of localized corrosion known as pitting often initiates preferentially at microstructural inhomogeneities. The pit initiation resistance, therefore, is controlled by the characteristics of the initiation sites, rather than by the bulk material composition. This investigation correlates the pit initiation resistance, as measured by critical pitting potentials, with preferred pit initiation sites for 3 martensitic stainless steels. Pit initiation sites are determined by secondary electron (SE) and backscattered electron (BSE) imaging and energy dispersive and wavelength dispersive spectrometries (EDS and WDS) with a scalling electron microscope (SEM) and an electron probe microanalyzer (EPMA).

Burn Pit Emissions Exposure and Respiratory and Cardiovascular Conditions Among Airborne Hazards and Open Burn Pit Registry Participants.

PubMed

Liu, Jason; Lezama, Nicholas; Gasper, Joseph; Kawata, Jennifer; Morley, Sybil; Helmer, Drew; Ciminera, Paul

2016-07-01

The aim of this study was to determine how burn pit emissions exposure is associated with the incidence of respiratory and cardiovascular conditions. We examined the associations between assumed geographic and self-reported burn pit emissions exposure and respiratory and cardiovascular outcomes in participants of the Airborne Hazards and Open Burn Pit Registry. We found significant dose-response associations for higher risk of self-reported emphysema, chronic bronchitis, or chronic obstructive pulmonary disease with increased days of deployment within 2 miles of selected burn pits (P-trend = 0.01) and self-reported burn pit smoke exposure (P-trend = 0.0005). We found associations between burn pit emissions exposure and higher incidence of post-deployment self-reported respiratory and cardiovascular conditions, but these findings should be interpreted with caution because the surrogate measurements of burn pit emissions exposure in this analysis may not reflect individual exposure levels.

Pitted terrains on (1) Ceres and implications for shallow subsurface volatile distribution

PubMed Central

Platz, T.; Schorghofer, N.; Prettyman, T. H.; De Sanctis, M. C.; Crown, D. A.; Schmedemann, N.; Neesemann, A.; Kneissl, T.; Marchi, S.; Schenk, P. M.; Bland, M. T.; Schmidt, B. E.; Hughson, K. H. G.; Tosi, F.; Zambon, F.; Mest, S. C.; Yingst, R. A.; Williams, D. A.; Russell, C. T.; Raymond, C. A.

2017-01-01

Abstract Prior to the arrival of the Dawn spacecraft at Ceres, the dwarf planet was anticipated to be ice‐rich. Searches for morphological features related to ice have been ongoing during Dawn's mission at Ceres. Here we report the identification of pitted terrains associated with fresh Cerean impact craters. The Cerean pitted terrains exhibit strong morphological similarities to pitted materials previously identified on Mars (where ice is implicated in pit development) and Vesta (where the presence of ice is debated). We employ numerical models to investigate the formation of pitted materials on Ceres and discuss the relative importance of water ice and other volatiles in pit development there. We conclude that water ice likely plays an important role in pit development on Ceres. Similar pitted terrains may be common in the asteroid belt and may be of interest to future missions motivated by both astrobiology and in situ resource utilization. PMID:28989206

Pitted terrains on (1) Ceres and implications for shallow subsurface volatile distribution.

PubMed

Sizemore, H G; Platz, T; Schorghofer, N; Prettyman, T H; De Sanctis, M C; Crown, D A; Schmedemann, N; Neesemann, A; Kneissl, T; Marchi, S; Schenk, P M; Bland, M T; Schmidt, B E; Hughson, K H G; Tosi, F; Zambon, F; Mest, S C; Yingst, R A; Williams, D A; Russell, C T; Raymond, C A

2017-07-16

Prior to the arrival of the Dawn spacecraft at Ceres, the dwarf planet was anticipated to be ice-rich. Searches for morphological features related to ice have been ongoing during Dawn's mission at Ceres. Here we report the identification of pitted terrains associated with fresh Cerean impact craters. The Cerean pitted terrains exhibit strong morphological similarities to pitted materials previously identified on Mars (where ice is implicated in pit development) and Vesta (where the presence of ice is debated). We employ numerical models to investigate the formation of pitted materials on Ceres and discuss the relative importance of water ice and other volatiles in pit development there. We conclude that water ice likely plays an important role in pit development on Ceres. Similar pitted terrains may be common in the asteroid belt and may be of interest to future missions motivated by both astrobiology and in situ resource utilization.

Pitted terrains on (1) Ceres and implications for shallow subsurface volatile distribution

USGS Publications Warehouse

Sizemore, H.G.; Platz, Thomas; Schorghofer, Norbert; Prettyman, Thomas; De Sanctis, Maria Christina; Crown, David A.; Schmedemann, Nico; Nessemann, Andeas; Kneissl, Thomas; Simone Marchi,; Schenk, Paul M.; Bland, Michael T.; Schmidt, B.E.; Hughson, Kynan H.G.; Tosi, F.; Zambon, F; Mest, S.C.; Yingst, R.A.; Williams, D.A.; Russell, C.T.; Raymond, C.A.

2017-01-01

Prior to the arrival of the Dawn spacecraft at Ceres, the dwarf planet was anticipated to be ice-rich. Searches for morphological features related to ice have been ongoing during Dawn's mission at Ceres. Here we report the identification of pitted terrains associated with fresh Cerean impact craters. The Cerean pitted terrains exhibit strong morphological similarities to pitted materials previously identified on Mars (where ice is implicated in pit development) and Vesta (where the presence of ice is debated). We employ numerical models to investigate the formation of pitted materials on Ceres and discuss the relative importance of water ice and other volatiles in pit development there. We conclude that water ice likely plays an important role in pit development on Ceres. Similar pitted terrains may be common in the asteroid belt and may be of interest to future missions motivated by both astrobiology and in situ resource utilization.

Force-displacement measurements of earlywood bordered pits using a mesomechanical tester.

PubMed

Zelinka, Samuel L; Bourne, Keith J; Hermanson, John C; Glass, Samuel V; Costa, Adriana; Wiedenhoeft, Alex C

2015-10-01

The elastic properties of pit membranes are reported to have important implications in understanding air-seeding phenomena in gymnosperms, and pit aspiration plays a large role in wood technological applications such as wood drying and preservative treatment. Here we present force-displacement measurements for pit membranes of circular bordered pits, collected on a mesomechanical testing system. The system consists of a quartz microprobe attached to a microforce sensor that is positioned and advanced with a micromanipulator mounted on an inverted microscope. Membrane displacement is measured from digital image analysis. Unaspirated pits from earlywood of never-dried wood of Larix and Pinus and aspirated pits from earlywood of dried wood of Larix were tested to generate force-displacement curves up to the point of membrane failure. Two failure modes were observed: rupture or tearing of the pit membrane by the microprobe tip, and the stretching of the pit membrane until the torus was forced out of the pit chamber through the pit aperture without rupture, a condition we refer to as torus prolapse. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Online gas monitoring and sampling during drilling of the INFLUINS borehole EF-FB 1/12 into the Thuringian Syncline, Germany

NASA Astrophysics Data System (ADS)

Görlitz, Marco; Abratis, Michael; Wiersberg, Thomas

2014-05-01

Online monitoring and sampling of drill mud gas (OLGA) was conducted during standard rotary drilling and core drilling of the INFLUINS borehole EF-FB 1/12 to gain information on the composition of gases and their distribution at depth within the Thuringian Syncline (Germany). The method can help to identify areas of enhanced permeability and/or porosity, open fractures, and other strata associated with gases at depth. The gas-loaded drill mud was continuously degassed in a modified gas-water separator, which was installed in the mud ditch in close distance to the drill mud outlet. The extracted gas phase was pumped in a nearby field laboratory for continuous on-line analysis. First information on the gas composition (H2, He, N2, O2, CO2, CH4, Ar, Kr) was available only few minutes after gas extraction. More than 40 gas samples were taken from the gas line during drilling and pumping tests for further laboratory studies. Enhanced concentration of methane, helium, hydrogen and carbon dioxide were detected in drill mud when the drill hole encountered gas-rich strata. Down to a depth of 620 m, the drill mud contained maximum concentration of 55 ppmv He, 1400 ppmv of CH4, 400 ppmv of hydrogen and 1.1 vol-% of CO2. The drilling mud gas composition is linked with the drilled strata. Buntsandstein and Muschelkalk show different formation gas composition and are therefore hydraulically separated. Except for helium, the overall abundance of formation gases in drilling mud is relatively low. We therefore consider the INFLUINS borehole to be dry. The correlation between hydrogen and helium and the relatively high helium abundance rules out any artificial origin of hydrogen and suggest a radiolytic origin of hydrogen. Values CH4/(C2H6/C3H8)

The effect of mud pack therapy on serum YKL-40 and hsCRP levels in patients with knee osteoarthritis.

PubMed

Güngen, Gonca; Ardic, Fusun; Fındıkoğlu, Gülin; Rota, Simin

2012-05-01

The aim of this study was to evaluate the efficacy of treatment with mud pack in knee osteoarthritis (OA) and to determine whether mud pack effects serum levels of YKL-40 and high-sensitivity C-reactive protein (hsCRP) which are reported to be biological markers for articular damage or inflammation in patients with OA. Forty-four patients with the diagnosis of knee OA assigned into two groups were treated with local natural mineral-rich mud pack or hot pack. Treatments were applied for 6 days a week for 2 weeks as a total of 12 sessions. Patients were assessed at baseline, post-treatment, and 3 months after the treatment. VAS, range of motion, 15-m walking time, WOMAC index, Nottingham Health Profile, serum YKL-40, and hsCRP levels were the outcome measures. Pain intensity and joint stiffness decreased in both groups at all follow-ups. Physical activity status was found to persist for 3 months after treatment only in mud pack group. Serum mean YKL-40 and hsCRP levels of the patients were higher compared to healthy control group. Serum YKL-40 level increased significantly only in hot pack group 3 months after the treatment (P < 0.017). No significant change was observed in hsCRP levels in both groups during the whole follow-up periods (P > 0.05). Mud pack and hot pack therapy were both demonstrated to be effective in symptomatic treatment of knee OA until the end of the 2-week treatment period, whereas only mud pack therapy was shown to be effective in functional status over time. In the hot pack group, increased serum YKL-40 level 3 months after the treatment might indicate persistence of cartilage degradation. Maintenance of YKL-40 level in mud pack therapy seems to slow down the progression of knee OA.

Macrophage migration inhibitory factor (MIF) family in arthropods: Cloning and expression analysis of two MIF and one D-dopachrome tautomerase (DDT) homologues in mud crabs, Scylla paramamosain.

PubMed

Huang, Wen-Shu; Duan, Li-Peng; Huang, Bei; Wang, Ke-Jian; Zhang, Cai-Liang; Jia, Qin-Qin; Nie, Pin; Wang, Tiehui

2016-03-01

The macrophage migration inhibitory factor (MIF) family, consisting of MIF and D-dopachrome tautomerase (DDT) in vertebrates, is evolutionarily ancient and has been found across Kingdoms including vertebrates, invertebrates, plants and bacteria. The mammalian MIF family are chemokines at the top of the inflammatory cascade in combating infections. They also possess enzymatic activities, e.g. DDT catalysis results in the production of 5,6-dihydroxyindole (DHI), a precursor of eumelanin. MIF-like genes are widely distributed, but DDT-like genes have only been described in vertebrates and a nematode. In this report, we cloned a DDT-like gene, for the first time in arthropods, and a second MIF in mud crab. The mud crab MIF family have a three exon/two intron structure as seen in vertebrates. The identification of a DDT-like gene in mud crab and other arthropods suggests that the separation of MIF and DDT preceded the divergence of protostomes and deuterostomes. The MIF family is differentially expressed in tissues of adults and during embryonic development and early life. The high level expression of the MIF family in immune tissues, such as intestine and hepatopancreas, suggests an important role in mud crab innate immunity. Mud crab DDT is highly expressed in early embryos, in megalops and crablets and this coincides with the requirement for melanisation in egg chorion tanning and cuticular hardening in arthropods, suggesting a potential novel role of DDT in melanogenesis via its tautomerase activity to produce DHI in mud crab. The clarification of the presence of both MIF and DDT in this report paves the way for further investigation of their functional roles in immunity and in melanogenesis in mud crab and other arthropods. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evidence of episodic long-lived eruptions in the Yuma, Ginsburg, Jesús Baraza and Tasyo mud volcanoes, Gulf of Cádiz

NASA Astrophysics Data System (ADS)

Toyos, María H.; Medialdea, Teresa; León, Ricardo; Somoza, Luis; González, Francisco Javier; Meléndez, Nieves

2016-06-01

High-resolution single channel and multichannel seismic reflection profiles and multibeam bathymetric and backscatter data collected during several cruises over the period 1999 to 2007 have enabled characterising not only the seabed morphology but also the subsurface structural elements of the Yuma, Ginsburg, Jesús Baraza and Tasyo mud volcanoes (MVs) in the Gulf of Cádiz at 1,050-1,250 m water depth. These MVs vary strongly in morphology and size. The data reveal elongated cone-shaped edifices, rimmed depressions, and scarps interpreted as flank failures developed by collapse, faulting, compaction and gravitational processes. MV architecture is characterised by both extrusive and intrusive complexes, comprising stacked edifices (including seabed cones and up to four buried bicones) underlain by chaotic vertical zones and downward-tapering cones suggesting feeder systems. These intrusive structures represent the upper layer of the feeder system linking the fluid mud sources with the constructional edifices. The overall architecture is interpreted to be the result of successive events of mud extrusion and outbuilding alternating with periods of dormancy. Each mud extrusion phase is connected with the development of an edifice, represented by a seabed cone or a buried bicone. In all four MVs, the stacked edifices and the intrusive complexes penetrate Late Miocene-Quaternary units and are rooted in the Gulf of Cádiz wedge emplaced during the late Tortonian. Major phases of mud extrusion and outbuilding took place since the Late Pliocene, even though in the Yuma and Jesús Baraza MVs mud volcanism started in the Late Miocene shortly after the emplacement of the Gulf of Cádiz wedge. This study shows that fluid venting in the eastern sector of the Gulf of Cádiz promoted the outbuilding of large long-lived mud volcanoes active since the Late Miocene, and which have been reactivated repeatedly until recent times.

New mud gas monitoring system aboard D/V Chikyu

NASA Astrophysics Data System (ADS)

Kubo, Yusuke; Inagaki, Fumio; Eguchi, Nobuhisa; Igarashi, Chiaki

2013-04-01

Mud gas logging has been commonly used in oil industry and continental scientific drilling to detect mainly hydrocarbon gases from the reservoir formation. Quick analysis of the gas provides almost real-time information which is critical to evaluate the formation and, in particular, safety of drilling operation. Furthermore, mud gas monitoring complements the lack of core or fluid samples particularly in a deep hole, and strengthen interpretations of geophysical logs. In scientific ocean drilling, on the other hand, mud gas monitoring was unavailable in riserless drilling through the history of DSDP and ODP, until riser drilling was first carried out in 2009 by D/V Chikyu. In IODP Exp 319, GFZ installed the same system with that used in continental drilling aboard Chikyu. High methane concentrations are clearly correlated with increased wood content in the cuttings. The system installation was, however, temporary and gas separator was moved during the expedition for a technical reason. In 2011, new mud gas monitoring system was installed aboard Chikyu and was used for the first time in Exp 337. The gas separator was placed on a newly branched bypass mud flow line, and the gas sample was sent to analysis unit equipped with methane carbon isotope analyzer in addition to mass spectrometer and gas chromatograph. The data from the analytical instruments is converted to depth profiles by calculating the lag effects due to mud circulation. Exp 337 was carried out from July 26 to Sep 30, 2011, at offshore Shimokita peninsula, northeast Japan, targeting deep sub-seafloor biosphere in and around coal bed. Data from the hole C0020A, which was drilled to 2466 mbsf with riser drilling, provided insights into bio-geochemical process through the depth of the hole. In this presentation, we show the design of Chikyu's new mud gas monitoring system, with preliminary data from Exp 337.

Genesis of mud volcano fluids in the Gulf of Cadiz - A novel model approach

NASA Astrophysics Data System (ADS)

Schmidt, Christopher; Burwicz, Ewa; Hensen, Christian; Martínez-Loriente, Sara; Wallmann, Klaus; Gràcia, Eulàlia

2017-04-01

Mud volcanism and fluid seepage are common phenomena on the continental margin in the Gulf of Cadiz, North East Atlantic Ocean. Over the past 2 decades more than 50 mud volcanoes have been discovered and investigated interdisciplinarily. Mud volcano fluids emanating at these sites are sourced at great depths and migration is often mediated by strike slip faults in a seismically active region. The geochemical signals of the mud volcano fluids are affected by widespread various processes such as clay mineral dehydration, but also the recrystallization of ancient carbonate rocks and the alteration of oceanic crust have been suggested (Hensen et al., 2015). We developed a novel fully-coupled, basin-scale, reaction-transport model with an adaptive numerical mesh to simulate the fluid genesis in this region. An advantage of this model is the coupling of a realistic geophysical and geochemical approach, considering a growing sediment column over time together with instant compaction of sediments as well as diffusion and advection of dissolved pore water species and chemical reactions. In this proof of concept study, we looked at various scenarios to identify the processes of fluid genesis for 4 mud volcanoes, representing combinations in different subsurface settings. We can reproduce the fluid signatures (chloride, strontium, 87Sr/86Sr) of all mud volcanoes. Furthermore, we can give additional evidence that alteration of oceanic crust by fluid flow is a likely process affecting the fluid composition. Hensen, C., Scholz, F., Nuzzo, M., Valadares, V., Gràcia, E., Terrinha, P., Liebetrau, V., Kaul, N., Silva, S., Martínez-Loriente, S., Bartolome, R., Piñero, E., Magalhães, V. H., Schmidt, M., Weise, S. M., Cunha, M., Hilario, A., Perea, H., Rovelli, L., and Lackschewitz, K., 2015, Strike-slip faults mediate the rise of crustal-derived fluids and mud volcanism in the deep sea: Geology, v. 43, no. 4, p. 339-342.

A seismic reflection velocity study of a Mississippian mud-mound in the Illinois basin

NASA Astrophysics Data System (ADS)

Ranaweera, Chamila Kumari

Two mud-mounds have been reported in the Ullin limestone near, but not in, the Aden oil field in Hamilton County, Illinois. One mud-mound is in the Broughton oil field of Hamilton County 25 miles to the south of Aden. The second mud-mound is in the Johnsonville oil field in Wayne County 20 miles to the north of Aden. Seismic reflection profiles were shot in 2012 adjacent to the Aden oil field to evaluate the oil prospects and to investigate the possibility of detecting Mississippian mud-mounds near the Aden field. A feature on one of the seismic profiles was interpreted to be a mud-mound or carbonate buildup. A well drilled at the location of this interpreted structure provided digital geophysical logs and geological logs used to refine the interpretation of the seismic profiles. Geological data from the new well at Aden, in the form of drill cuttings, have been used to essentially confirm the existence of a mud-mound in the Ullin limestone at a depth of 4300 feet. Geophysical well logs from the new well near Aden were used to create 1-D computer models and synthetic seismograms for comparison to the seismic data. The reflection seismic method is widely used to aid interpreting subsurface geology. Processing seismic data is an important step in the method as a properly processed seismic section can give a better image of the subsurface geology whereas a poorly processed section could mislead the interpretation. Seismic reflections will be more accurately depicted with careful determination of seismic velocities and by carefully choosing the processing steps and parameters. Various data processing steps have been applied and parameters refined to produce improved stacked seismic records. The resulting seismic records from the Aden field area indicate a seismic response similar to what is expected from a carbonate mud-mound. One-dimensional synthetic seismograms were created using the available sonic and density logs from the well drilled near the Aden seismic lines. The 1-D synthetics were used by Cory Cantrell of Royal Drilling and Producing Company to identify various reflections on the seismic records. Seismic data was compared with the modeled synthetic seismograms to identify what appears to be a carbonate mud-mound within the Aden study area. No mud-mounds have been previously found in the Aden oil field. Average and interval velocities obtained from the geophysical logs from the wells drilled in the Aden area was compared with the same type of well velocities from the Broughton known mud-mound area to observe the significance of velocity variation related to the un-known mud-mound in the Aden study area. The results of the velocity study shows a similar trends in the wells from both areas and are higher at the bottom of the wells. Another approach was used to observe the variation of root mean square velocities calculated from the sonic log from the well velocity from the Aden area and the stacking velocities obtained from the seismic data adjacent to the well.

Morphodynamic rotation of an embayed sandy beach in a mud-dominated setting

NASA Astrophysics Data System (ADS)

Brunier, Guillaume; Anthony, Edward; Gardel, Antoine; Millet, Bertrand; Fleury, Jules; Dussouillez, Philippe

2016-04-01

The morphodynamics of beaches between bedrock headlands along the muddy French Guiana coast in South America are controlled by rotation induced by the alongshore migration of mud banks from the mouths of the Amazon River. As they migrate alongshore, these mud banks generate changes in shore-incident wave angles, resulting in reversals in longshore drift. A poor appreciation of the problems caused by this process has resulted in the past in damages to the highly urbanized sea-fronts on these beaches, including erosion and flooding. This work enhances our understanding of this rather unusual type of mud-induced rotation based on surveys of the 4 km-long Montjoly beach near Cayenne, in French Guiana, in the course of an approaching mud bank between October 2013 and October 2014. Our method was based on innovative high-resolution topographic surveys from airborne Structure-from-Motion (SfM) photogrammetry over the beach in October 2013, March 2014 and October 2014. We produced digital surface models (DSM) with a resolution of 10 cm/pixel and an accuracy less than 10 cm from RTK-GPS measurements. We further measured incident wave heights from pressure sensors and conducted a bathymetric survey of the nearshore zone in October 2014. We also modelled high-tide wave propagation over the bathymetry using the REF/DIF v2.5 model. The results show the transfer of sand from the northern part of beach to the south between October 2013 and March 2014. The October 2013 DSM shows a reflective beach in the north indicative of erosion, with a narrow 50 m-wide upper beach. The southern sector was smoother and up to 90 m-wide. Between October 2013 and March 2014, the beach rotated under the influence of a mud bank, with a 30-m retreat of the berm in the north and an advance of 40 m in the south. We quantified a loss of ≈66,000 m³ of sand in the north and a gain of ≈22,000 m³ in the south over this six-month period. The October 2014 DSM shows minor morphological changes, thus indicating the end of the rotation around March 2014 and the beginning of a phase of nearshore mud-bounding of the beach as the mud bank migrated westward. The bathymetric survey showed a 2 m-high and 100 m-wide mud bar in the nearshore zone that dissipated wave energy. Hydrodynamic monitoring between March and October 2014 confirmed this low wave-energy regime (Hs < 0.5 m) compared to a more energetic regime in the neighbouring Montabo Bay beach (Hs up to 1.5 m) located downdrift of the mud bank. The REF/DIF model confirmed the strong wave energy dissipation over the mud bar. Our study highlights the rapidity and intensity of the morphodynamic changes these beaches can undergo in a muddy context, and the need for continuous and accurate monitoring in order to assess the erosion hazard caused by rotation. Keywords: Beach rotation; Mud banks; aerial SFM photogrammetry; bathymetric monitoring; hydrodynamic modelling; REF/DIF model.

Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation.

PubMed

Musharova, Olga; Klimuk, Evgeny; Datsenko, Kirill A; Metlitskaya, Anastasia; Logacheva, Maria; Semenova, Ekaterina; Severinov, Konstantin; Savitskaya, Ekaterina

2017-04-07

During primed CRISPR adaptation spacers are preferentially selected from DNA recognized by CRISPR interference machinery, which in the case of Type I CRISPR-Cas systems consists of CRISPR RNA (crRNA) bound effector Cascade complex that locates complementary targets, and Cas3 executor nuclease/helicase. A complex of Cas1 and Cas2 proteins is capable of inserting new spacers in the CRISPR array. Here, we show that in Escherichia coli cells undergoing primed adaptation, spacer-sized fragments of foreign DNA are associated with Cas1. Based on sensitivity to digestion with nucleases, the associated DNA is not in a standard double-stranded state. Spacer-sized fragments are cut from one strand of foreign DNA in Cas1- and Cas3-dependent manner. These fragments are generated from much longer S1-nuclease sensitive fragments of foreign DNA that require Cas3 for their production. We propose that in the course of CRISPR interference Cas3 generates fragments of foreign DNA that are recognized by the Cas1-Cas2 adaptation complex, which excises spacer-sized fragments and channels them for insertion into CRISPR array. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Transforming plant biology and breeding with CRISPR/Cas9, Cas12 and Cas13.

PubMed

Schindele, Patrick; Wolter, Felix; Puchta, Holger

2018-04-30

Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed. Cas9- and Cas12- mediated DNA binding is used to develop tools for many useful applications, such as transcriptional regulation or fluorescence-based imaging of specific chromosomal loci in plant genomes. Cas13 has recently been applied to degrade mRNAs and combat viral RNA replication. By the possibility to address multiple sequences with different guide RNAs and by the simultaneous use of different Cas proteins in a single cell, we should soon be able to achieve complex changes of plant metabolism in a controlled way. © 2018 Federation of European Biochemical Societies.

Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch.

PubMed

Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J C; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut; Saito, Hirohide

2017-07-27

The CRISPR-Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR-Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein.

PubMed

Yan, Winston X; Chong, Shaorong; Zhang, Huaibin; Makarova, Kira S; Koonin, Eugene V; Cheng, David R; Scott, David A

2018-04-19

Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c. Despite their small size, Cas13d orthologs from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) are active in both CRISPR RNA processing and targeting, as well as collateral RNA cleavage, with no target-flanking sequence requirements. The RspWYL1 protein stimulates RNA cleavage by both EsCas13d and RspCas13d, demonstrating a common regulatory mechanism for divergent Cas13d orthologs. The small size, minimal targeting constraints, and modular regulation of Cas13d effectors further expands the CRISPR toolkit for RNA manipulation and detection. Copyright © 2018 Elsevier Inc. All rights reserved.

Annotation and Classification of CRISPR-Cas Systems

PubMed Central

Makarova, Kira S.; Koonin, Eugene V.

2018-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods. PMID:25981466

Annotation and Classification of CRISPR-Cas Systems.

PubMed

Makarova, Kira S; Koonin, Eugene V

2015-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.

Genome Editing with CRISPR-Cas9: Can It Get Any Better?

PubMed

Haeussler, Maximilian; Concordet, Jean-Paul

2016-05-20

The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo. At the same time, the on-target activity of thousands of guides has been determined. These data have led to numerous online tools that facilitate the selection of guide RNAs in target sequences. It appears that for most basic research applications, cleavage activity can be maximized and off-targets minimized by carefully choosing guide RNAs based on computational predictions. Moreover, recent studies of Cas proteins have further improved the flexibility and precision of the CRISPR-Cas toolkit for genome editing. Inspired by the crystal structure of the complex of sgRNA-SpCas9 bound to target DNA, several variants of SpCas9 have recently been engineered, either with novel protospacer adjacent motifs (PAMs) or with drastically reduced off-targets. Novel Cas9 and Cas9-like proteins called Cpf1 have also been characterized from other bacteria and will benefit from the insights obtained from SpCas9. Genome editing with CRISPR-Cas9 may also progress with better understanding and control of cellular DNA repair pathways activated after Cas9-induced DNA cleavage. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Changes in ecdysteroid levels and expression patterns of ecdysteroid-responsive factors and neuropeptide hormones during the embryogenesis of the blue crab, Callinectes sapidus.

PubMed

Techa, Sirinart; Alvarez, Javier V; Sook Chung, J

2015-04-01

Embryogenesis requires the involvement and coordination of multiple networks of various genes, according to a timeline governing development. Crustacean embryogenesis usually includes the first molt, a process that is known to be positively controlled by ecdysteroids. We determined the amounts of ecdysteroids, as well as other related factors: the ecdysone receptor (CasEcR), the retinoid X receptor (CasRXR), the molt-inhibiting hormone (CasMIH), and crustacean hyperglycemic hormone (CasCHH) during the ovarian and embryonic developments of Callinectes sapidus. In summary, the ovaries at stages 1-4 have expression levels of maternal CasEcR and CasRXR 10-50 times higher than levels seen in embryos at the yolk stage. This large difference in the amount of the these factors in C. sapidus ovaries suggests that these maternal ecdysteroid-responsive factors may be utilized at the initiation of embryogenesis. During embryogenesis, the changes in total ecdysteroids and levels of CasEcR and CasRXR expression are similar to those observed in juvenile molts. The full-length cDNA sequence of the C. sapidus BTB domain protein (CasBTBDP) initially isolated from Y-organ cDNA, contains only Broad-Complex, Tramtrack, and Bric a brac (BTB) domains. The levels of CasBTBDP are kept constant throughout embryogenesis. The expression profiles of CasMIH and CasCHH are similar to the titers of ecdysteroids. However, the timing of their appearance is followed by increases in CasEcRs and CasRXRs, implying that the expressions of these neuropeptides may be influenced by ecdysteroids. Moreover, the ecdysteroid profile during embryogenesis may track directly with the timing of organogenesis of Y-organs and their activity. Our work reports, for first time, the observed expression and changes of ecdysteroid-responsive factors, along with CasCHH and CasMIH, during embryogenesis in the crustacean C. sapidus. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and Cas9 mRNA for Genome Editing in Zebrafish.

PubMed

Hu, Peinan; Zhao, Xueying; Zhang, Qinghua; Li, Weiming; Zu, Yao

2018-03-02

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has been proven to be an efficient and precise genome editing technology in various organisms. However, the gene editing efficiencies of Cas9 proteins with a nuclear localization signal (NLS) fused to different termini and Cas9 mRNA have not been systematically compared. Here, we compared the ability of Cas9 proteins with NLS fused to the N-, C-, or both the N- and C-termini and N-NLS-Cas9-NLS-C mRNA to target two sites in the tyr gene and two sites in the gol gene related to pigmentation in zebrafish. Phenotypic analysis revealed that all types of Cas9 led to hypopigmentation in similar proportions of injected embryos. Genome analysis by T7 Endonuclease I (T7E1) assays demonstrated that all types of Cas9 similarly induced mutagenesis in four target sites. Sequencing results further confirmed that a high frequency of indels occurred in the target sites ( tyr1 > 66%, tyr2 > 73%, gol1 > 50%, and gol2 > 35%), as well as various types (more than six) of indel mutations observed in all four types of Cas9-injected embryos. Furthermore, all types of Cas9 showed efficient targeted mutagenesis on multiplex genome editing, resulting in multiple phenotypes simultaneously. Collectively, we conclude that various NLS-fused Cas9 proteins and Cas9 mRNAs have similar genome editing efficiencies on targeting single or multiple genes, suggesting that the efficiency of CRISPR/Cas9 genome editing is highly dependent on guide RNAs (gRNAs) and gene loci. These findings may help to simplify the selection of Cas9 for gene editing using the CRISPR/Cas9 system. Copyright © 2018 Hu et al.

Least tern and piping plover nesting at sand pits in Nebraska

USGS Publications Warehouse

Sidle, John G.; Kirsch, E.M.

1993-01-01

Endangered Least Terns (Sterna antillarum) and threatened Piping Plovers (Charadrius melodus) nest at commercial sand and gravel mining operations (sand pits) along the Platte River system in Nebraska. Sandbar habitat has been disappearing since the early 1900's along the Platte River system, but numbers of sand pits have increased. We hypothesized that birds would more fully utilize sand pits where suitable sandbar habitat was limited. We inventoried sand pits and censused terns and plovers on both habitats along the Loup River, part of the North Loup River, and most of the Platte River during 1988-1991. Using aircraft, we also quantified features of suitable sand pits present on the central Platte in 1988 and lower Platte in 1990, and related features to abundance and presence of birds. We found 225 sand pits of which 78 were suitable and 187 were unsuitable for nesting. Along the central Platte, where sandbar habitat is severely degraded, birds nested at 81% of the suitable sand pits (N = 32) at least once during 1988-1991, and most birds (61-94%) nested on sand pits. Along the lower Platte, where both sandbar and sand pit habitat are plentiful, birds nested at 60% of the suitable sand pits (N = 35) at least once during 1988-1991, and most birds (60-86%) nested on sandbars. Numbers of terns and plovers were more weakly correlated with features of sand pits on the central Platte than on the lower Platte. Least Terns and Piping Plovers seem to use more of the suitable sand pit habitat on the central Platte than on the lower Platte. Sand pits probably have influenced the birds' distribution by providing alternative nesting habitat along rivers where suitable sandbars are rare or absent.

Efficacy of UV-Pit-light traps for discerning micro-habitat-specific beetle and ant species related with different oil palm age stands and tropical annual seasons for accurate ecology and diversity interpretations

NASA Astrophysics Data System (ADS)

Ahmad Bukhary, A. K.; Ruslan, M. Y.; Mohd. Fauzi, M. M.; Nicholas, S.; Muhamad Fahmi, M. H.; Izfa Riza, H.; Idris, A. B.

2015-09-01

A newly innovated and efficient UV-Pit-light Trap is described and the results of the experiments on its efficacy that were carried out within different oil palm age stands of the year 2013 were evaluated and compared with previous study year of 2010, with out the implementation of the UV-Pit-light Trap. In 2013 the UV-Pit-light Traps, the Malaise Traps, and the Pit-fall Traps were employed, while in 2010, the conventional canopy-height UV-Light Traps, Malaise Traps, and the Pit-fall Traps were employed. The UV-Pit-light traps caught more beetle and ant families, morpho-species, and individuals per species compared with the passive Pit-fall traps. The UV-Pit-light Trap targets different subsets of the oil palm beetles and ants' communities, specifying on epigaeic-related micro-habitats, with different oil palm age stands have different compositions of micro-habitats. The UV-Pit-light Traps have the dual quality for satisfying both the biological and statistical data requirements and evaluations. There were no significant difference between the UV-Pit-light Traps and the passive Pit-fall Traps, while the trapping difference with the Malaise traps for different seasons of the year 2013. The UV-Pit-light Traps and the Malaise Traps were complementary to each other, detecting the activities of beetles and ants around the epigaeic-related micro-habitats or having active flight activities respectively according to annual seasons. The UV-Pit-light Trap is an oil-palm specific type of passive trapping system, focusing on the insect species dwelling the upper-ground/epigaeic micro-habitats.

One dimensional Linescan x-ray detection of pits in fresh cherries

USDA-ARS?s Scientific Manuscript database

The presence of pits in processed cherries is a concern for both processors and consumers, in many cases causing injury and potential lawsuits. While machines used for pitting cherries are extremely efficient, if one or more plungers in a pitting head become misaligned, a large number of pits may p...

Large heterogeneities in comet 67P as revealed by active pits from sinkhole collapse.

PubMed

Vincent, Jean-Baptiste; Bodewits, Dennis; Besse, Sébastien; Sierks, Holger; Barbieri, Cesare; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst Uwe; Agarwal, Jessica; A'Hearn, Michael F; Auger, Anne-Thérèse; Barucci, M Antonella; Bertaux, Jean-Loup; Bertini, Ivano; Capanna, Claire; Cremonese, Gabriele; Da Deppo, Vania; Davidsson, Björn; Debei, Stefano; De Cecco, Mariolino; El-Maarry, Mohamed Ramy; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Gaskell, Robert; Giacomini, Lorenza; Groussin, Olivier; Guilbert-Lepoutre, Aurélie; Gutierrez-Marques, P; Gutiérrez, Pedro J; Güttler, Carsten; Hoekzema, Nick; Höfner, Sebastian; Hviid, Stubbe F; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kovacs, Gabor; Kramm, Rainer; Kührt, Ekkehard; Küppers, Michael; La Forgia, Fiorangela; Lara, Luisa M; Lazzarin, Monica; Lee, Vicky; Leyrat, Cédric; Lin, Zhong-Yi; Lopez Moreno, Josè J; Lowry, Stephen; Magrin, Sara; Maquet, Lucie; Marchi, Simone; Marzari, Francesco; Massironi, Matteo; Michalik, Harald; Moissl, Richard; Mottola, Stefano; Naletto, Giampiero; Oklay, Nilda; Pajola, Maurizio; Preusker, Frank; Scholten, Frank; Thomas, Nicolas; Toth, Imre; Tubiana, Cecilia

2015-07-02

Pits have been observed on many cometary nuclei mapped by spacecraft. It has been argued that cometary pits are a signature of endogenic activity, rather than impact craters such as those on planetary and asteroid surfaces. Impact experiments and models cannot reproduce the shapes of most of the observed cometary pits, and the predicted collision rates imply that few of the pits are related to impacts. Alternative mechanisms like explosive activity have been suggested, but the driving process remains unknown. Here we report that pits on comet 67P/Churyumov-Gerasimenko are active, and probably created by a sinkhole process, possibly accompanied by outbursts. We argue that after formation, pits expand slowly in diameter, owing to sublimation-driven retreat of the walls. Therefore, pits characterize how eroded the surface is: a fresh cometary surface will have a ragged structure with many pits, while an evolved surface will look smoother. The size and spatial distribution of pits imply that large heterogeneities exist in the physical, structural or compositional properties of the first few hundred metres below the current nucleus surface.

Study on shearing force and impact force of a volcanic mud flow on Mt. Sakurajima

Treesearch

Yoshinobu Taniguchi

1991-01-01

Two kinds of shearing stress meters (type A and type B) were set on the channel bottom in the Arimura River and the Mochiki River on Mt. Sakurajima. Volcanic mud flows take place there about 100 times a year. The results of the surveys demonstrated that the actual shearing force of a volcanic mud flow on Mt. Sakurajima was from 0.46 to 2.50 kgf/cm2...

A novel approach in red mud neutralization using cow dung.

PubMed

Patel, Sucharita; Pal, Bhatu Kumar; Patel, Raj Kishore

2018-05-01

In this study, cow dung was identified as a neutralizing agent for red mud (RM). Present research estimated a significant reduction in pH value of red mud (10 g) from 10.28 to 8.15 and reduction in alkalinity of ~148 mg/L from ~488 mg/L by adding 80 g of cow dung in 40 days of anaerobic condition. XRD results exhibit a high intensity of quartz and found new compound, the calcium carbide. The acid neutralizing capacity (ANC) of NRM reduces to ~0.87 from ~1.506 mol H + /kg. Based on the resultant research, present study proposes cow dung as an efficient neutralizing agent for reducing the pH and alkalinity in the red mud.

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

Valysaev, B.M.; Erokhin, V.E.; Grinchenko, Y.I.

A study has been made of the isotopic composition of the carbon in methane and carbon dioxide, as well as hydrogen in the methane, in the gases of mud volcanoes, for all main mud volcano areas in the USSR. The isotopic composition of carbon and hydrogen in methane shows that the gases resemble those of oil and gas deposits, while carbon dioxide of these volcanoes has a heavier isotopic composition with a greater presence of ''ultraheavy'' carbon dioxide. By the chemical and isotopic composition of gases, Azerbaidzhan and South Sakhalin types of mud volcano gases have been identified, as wellmore » as Bulganak subtypes and Akhtala and Kobystan varieties. Correlations are seen between the isotopic composition of gases and the geological build of mud volcano areas.« less

Effects of pore pressure and mud filtration on drilling rates in a permeable sandstone

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

Black, A.D.; DiBona, B.; Sandstrom, J.

1983-10-01

During laboratory drilling tests in a permeable sandstone, the effects of pore pressure and mud filtration on penetration rates were measured. Four water-base muds were used to drill four saturated sandstone samples. The drilling tests were conducted at constant borehole pressure with different back pressures maintained on the filtrate flowing from the bottom of the sandstone samples. Bit weight was also varied. Filtration rates were measured while drilling and with the bit off bottom and mud circulating. Penetration rates were found to be related to the difference between the filtration rates measured while drilling and circulating. There was no observedmore » correlation between standard API filtration measurements and penetration rate.« less

Effects of pore pressure and mud filtration on drilling rates in a permeable sandstone

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

Black, A.D.; Dearing, H.L.; DiBona, B.G.

1985-09-01

During laboratory drilling tests in a permeable sandstone, the effects of pore pressure and mud filtration on penetration rates were measured. Four water-based muds were used to drill four saturated sandstone samples. The drilling tests were conducted at constant borehole pressure while different backpressures were maintained on the filtrate flowing from the bottom of the sandstone samples. Bit weight was varied also. Filtration rates were measured while circulating mud during drilling and with the bit off bottom. Penetration rates were found to be related qualitatively to the difference between the filtration rates measured while drilling and circulating. There was nomore » observed correlation between standard API filtration measurements and penetration rate.« less

The CAS Classroom

ERIC Educational Resources Information Center

Garner, Sue

2004-01-01

The Victorian Curriculum and Assessment Authority (VCAA) Computer Algebra System (CAS)Pilot study (2001-2005) is monitoring the use of CAS in senior secondary mathematics. This article explores the author's experiences in the CAS classroom and delineates changes in teaching style, as a result of the introduction of CAS into the senior mathematics…

Complementary Information Derived from CRISPR Cas9 Mediated Gene Deletion and Suppression. | Office of Cancer Genomics

Cancer.gov

CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes.

Exploiting CRISPR/Cas systems for biotechnology

PubMed Central

Sampson, Timothy R.; Weiss, David S.

2015-01-01

The Cas9 endonuclease is the central component of the Type II CRISPR/Cas system, a prokaryotic adaptive restriction system against invading nucleic acids, such as those originating from bacteriophages and plasmids. Recently, this RNA-directed DNA endonuclease has been harnessed to target DNA sequences of interest. Here, we review the development of Cas9 as an important tool to not only edit the genomes of a number of different prokaryotic and eukaryotic species, but also as an efficient system for site-specific transcriptional repression or activation. Additionally, a specific Cas9 protein has been observed to target an RNA substrate, suggesting that Cas9 may have the ability to be programmed to target RNA as well. Cas proteins from other CRISPR/Cas subtypes may also be exploited in this regard. Thus, CRISPR/Cas systems represent an effective and versatile biotechnological tool, which will have significant impact on future advancements in genome engineering. PMID:24323919

Exploiting CRISPR/Cas systems for biotechnology.

PubMed

Sampson, Timothy R; Weiss, David S

2014-01-01

The Cas9 endonuclease is the central component of the Type II CRISPR/Cas system, a prokaryotic adaptive restriction system against invading nucleic acids, such as those originating from bacteriophages and plasmids. Recently, this RNA-directed DNA endonuclease has been harnessed to target DNA sequences of interest. Here, we review the development of Cas9 as an important tool to not only edit the genomes of a number of different prokaryotic and eukaryotic species, but also as an efficient system for site-specific transcriptional repression or activation. Additionally, a specific Cas9 protein has been observed to target an RNA substrate, suggesting that Cas9 may have the ability to be programmed to target RNA as well. Cas proteins from other CRISPR/Cas subtypes may also be exploited in this regard. Thus, CRISPR/Cas systems represent an effective and versatile biotechnological tool, which will have significant impact on future advancements in genome engineering. © 2014 WILEY Periodicals, Inc.

Evolution and classification of the CRISPR-Cas systems

PubMed Central

S. Makarova, Kira; H. Haft, Daniel; Barrangou, Rodolphe; J. J. Brouns, Stan; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; J. M. Mojica, Francisco; I. Wolf, Yuri; Yakunin, Alexander F.; van der Oost, John; V. Koonin, Eugene

2012-01-01

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a `polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci. PMID:21552286

Excision of Nucleopolyhedrovirus Form Transgenic Silkworm Using the CRISPR/Cas9 System.

PubMed

Dong, Zhanqi; Dong, Feifan; Yu, Xinbo; Huang, Liang; Jiang, Yaming; Hu, Zhigang; Chen, Peng; Lu, Cheng; Pan, Minhui

2018-01-01

The CRISPR/Cas9-mediated genome engineering has been shown to efficiently suppress infection by disrupting genes of the pathogen. We recently constructed transgenic lines expressing CRISPR/Cas9 and the double sgRNA target Bombyx mori nucleopolyhedrovirus (BmNPV) immediate early-1 ( ie-1 ) gene in the silkworm, respectively, and obtained four transgenic hybrid lines by G1 generation hybridization: Cas9(-)/sgRNA(-), Cas9(+)/sgRNA(-), Cas9(-)/sgRNA(+), and Cas9(+)/sgRNA(+). We demonstrated that the Cas9(+)/sgRNA(+) transgenic lines effectively edited the target site of the BmNPV genome, and large fragment deletion was observed after BmNPV infection. Further antiviral analysis of the Cas9(+)/sgRNA(+) transgenic lines shows that the median lethal dose (LD50) is 1,000-fold higher than the normal lines after inoculation with occlusion bodies. The analysis of economic characters and off-target efficiency of Cas9(+)/sgRNA(+) transgenic hybrid line showed no significant difference compared with the normal lines. Our findings indicate that CRISPR/Cas9-mediated genome engineering more effectively targets the BmNPV genomes and could be utilized as an insect antiviral treatment.

Functional Insights Revealed by the Kinetic Mechanism of CRISPR/Cas9.

PubMed

Raper, Austin T; Stephenson, Anthony A; Suo, Zucai

2018-02-28

The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined, and details of DNA cleavage are poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid. Moreover, an extremely slow release of DNA products essentially restricts Cas9 to be a single-turnover enzyme. By simultaneously measuring the contributions of the HNH and RuvC nuclease activities of Cas9 to DNA cleavage, we also uncovered the kinetic basis by which HNH conformationally regulates the RuvC cleavage activity. Together, our results provide crucial kinetic and functional details regarding Cas9 which will inform gene-editing experiments, guide future research to understand off-target DNA cleavage by Cas9, and aid in the continued development of Cas9 as a biotechnological tool.

Excision of Nucleopolyhedrovirus Form Transgenic Silkworm Using the CRISPR/Cas9 System

PubMed Central

Dong, Zhanqi; Dong, Feifan; Yu, Xinbo; Huang, Liang; Jiang, Yaming; Hu, Zhigang; Chen, Peng; Lu, Cheng; Pan, Minhui

2018-01-01

The CRISPR/Cas9-mediated genome engineering has been shown to efficiently suppress infection by disrupting genes of the pathogen. We recently constructed transgenic lines expressing CRISPR/Cas9 and the double sgRNA target Bombyx mori nucleopolyhedrovirus (BmNPV) immediate early-1 (ie-1) gene in the silkworm, respectively, and obtained four transgenic hybrid lines by G1 generation hybridization: Cas9(-)/sgRNA(-), Cas9(+)/sgRNA(-), Cas9(-)/sgRNA(+), and Cas9(+)/sgRNA(+). We demonstrated that the Cas9(+)/sgRNA(+) transgenic lines effectively edited the target site of the BmNPV genome, and large fragment deletion was observed after BmNPV infection. Further antiviral analysis of the Cas9(+)/sgRNA(+) transgenic lines shows that the median lethal dose (LD50) is 1,000-fold higher than the normal lines after inoculation with occlusion bodies. The analysis of economic characters and off-target efficiency of Cas9(+)/sgRNA(+) transgenic hybrid line showed no significant difference compared with the normal lines. Our findings indicate that CRISPR/Cas9-mediated genome engineering more effectively targets the BmNPV genomes and could be utilized as an insect antiviral treatment. PMID:29503634

Disabling Cas9 by an anti-CRISPR DNA mimic.

PubMed

Shin, Jiyung; Jiang, Fuguo; Liu, Jun-Jie; Bray, Nicolas L; Rauch, Benjamin J; Baik, Seung Hyun; Nogales, Eva; Bondy-Denomy, Joseph; Corn, Jacob E; Doudna, Jennifer A

2017-07-01

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established. We show that the anti-CRISPR protein AcrIIA4 binds only to assembled Cas9-single-guide RNA (sgRNA) complexes and not to Cas9 protein alone. A 3.9 Å resolution cryo-electron microscopy structure of the Cas9-sgRNA-AcrIIA4 complex revealed that the surface of AcrIIA4 is highly acidic and binds with a 1:1 stoichiometry to a region of Cas9 that normally engages the DNA protospacer adjacent motif. Consistent with this binding mode, order-of-addition experiments showed that AcrIIA4 interferes with DNA recognition but has no effect on preformed Cas9-sgRNA-DNA complexes. Timed delivery of AcrIIA4 into human cells as either protein or expression plasmid allows on-target Cas9-mediated gene editing while reducing off-target edits. These results provide a mechanistic understanding of AcrIIA4 function and demonstrate that inhibitors can modulate the extent and outcomes of Cas9-mediated gene editing.

Light scattering from laser induced pit ensembles on high power laser optics

DOE PAGES

Feigenbaum, Eyal; Elhadj, Selim; Matthews, Manyalibo J.

2015-01-01

Far-field light scattering characteristics from randomly arranged shallow Gaussian-like shaped laser induced pits, found on optics exposed to high energy laser pulses, is studied. Closed-form expressions for the far-field intensity distribution and scattered power are derived for individual pits and validated using numerical calculations of both Fourier optics and FDTD solutions to Maxwell’s equations. It is found that the scattered power is proportional to the square of the pit width and approximately also to the square of the pit depth, with the proportionality factor scaling with pit depth. As a result, the power scattered from shallow pitted optics is expectedmore » to be substantially lower than assuming complete scattering from the total visible footprint of the pits.« less

A Statistical Study on the Effect of Hydrostatic Pressure on Metastable Pitting Corrosion of X70 Pipeline Steel.

PubMed

Yang, Zixuan; Kan, Bo; Li, Jinxu; Qiao, Lijie; Volinsky, Alex A; Su, Yanjing

2017-11-14

Hydrostatic pressure effects on pitting initiation and propagation in X70 steel are investigated by evaluating metastable pitting probability using electrochemical methods and immersion corrosion tests in containing chlorine ion solution. Potentiodynamic tests indicated that hydrostatic pressure can decrease the breakdown potential and lead to a reduced transpassivity region. Metastable test results revealed that hydrostatic pressure can increase metastable pitting formation frequency and promote stabilization of metastable pitting growth. Electrochemical impedance spectroscopy (EIS) results indicate that Hydrostatic pressure decreases the charge transfer resistance and increases the dissolution rate within the cavities. Corrosion test results also indicated that pitting initiation and propagation are accelerated by hydrostatic pressure. Result validity was verified by evaluating metastable pitting to predict pitting corrosion resistance.

A Statistical Study on the Effect of Hydrostatic Pressure on Metastable Pitting Corrosion of X70 Pipeline Steel

PubMed Central

Yang, Zixuan; Kan, Bo; Li, Jinxu; Su, Yanjing; Qiao, Lijie; Volinsky, Alex A.

2017-01-01

Hydrostatic pressure effects on pitting initiation and propagation in X70 steel are investigated by evaluating metastable pitting probability using electrochemical methods and immersion corrosion tests in containing chlorine ion solution. Potentiodynamic tests indicated that hydrostatic pressure can decrease the breakdown potential and lead to a reduced transpassivity region. Metastable test results revealed that hydrostatic pressure can increase metastable pitting formation frequency and promote stabilization of metastable pitting growth. Electrochemical impedance spectroscopy (EIS) results indicate that Hydrostatic pressure decreases the charge transfer resistance and increases the dissolution rate within the cavities. Corrosion test results also indicated that pitting initiation and propagation are accelerated by hydrostatic pressure. Result validity was verified by evaluating metastable pitting to predict pitting corrosion resistance. PMID:29135912

The Effects of Hot Corrosion Pits on the Fatigue Resistance of a Disk Superalloy

NASA Technical Reports Server (NTRS)

Gabb, Timothy P.; Telesman, Jack; Hazel, Brian; Mourer, David P.

2009-01-01

The effects of hot corrosion pits on low cycle fatigue life and failure modes of the disk superalloy ME3 were investigated. Low cycle fatigue specimens were subjected to hot corrosion exposures producing pits, then tested at low and high temperatures. Fatigue lives and failure initiation points were compared to those of specimens without corrosion pits. Several tests were interrupted to estimate the fraction of fatigue life that fatigue cracks initiated at pits. Corrosion pits significantly reduced fatigue life by 60 to 98 percent. Fatigue cracks initiated at a very small fraction of life for high temperature tests, but initiated at higher fractions in tests at low temperature. Critical pit sizes required to promote fatigue cracking were estimated, based on measurements of pits initiating cracks on fracture surfaces.

[Stoma use in the general surgery service of CHU Gabriel Touré].

PubMed

Traore, A; Diakite, I; Togo, A; Dembele, B T; Kante, L; Coulibaly, Y; Keita, M; Diango, D M; Diallo, A; Diallo, G

2010-01-01

Were to determine the frequency, to describe the clinical and therapeutic aspects digestive stoma. It was about six months an exploratory study from January 1st to June 30th, 2008 in the department of surgery general of the CHU Gabriel Touré. Were included in this study all the patients carrying a enter stoma or a colostomy, old of more than 15 ans. The digestive dents, the other types of stoma and the patients old of less than 15 years, were excluded. The results were analyzed by the software Epi information version 6.4 Fr, the tests of Khi 2 and Student with a threshold of significance for P < 0.05. We college 32 patients are 7.4% of all digestive surgical operations, 13.3% of the abdominal urgencies; composed of 26 men (81.25%) and 6 women (18.75%). The sex ratio at summer of 4.3. The average age was 44, 8 years with a standard deviation 8, 13 and the extremes varying between 16-80 years. Twenty and one (65.6%) sick were operated in urgency. We carried out 29 cases (90.6%) of final stoma, 3 cas (9.4%) side, 21 cas (65.6%) of colostomy, 9 cas (28.1%) of ileostomies. They were temporary in 25 cas (78.1%) and final 7 cas (21.9%). The volvulus of the sigmoid colonist with necroses 10 cas (31.3%), the peritonitis by typhus perforation ilea 9 cas (28.1%), occlusions on tumor of the left colonist 8 cas (25%), the traumatic perforations ileales 2 cas (6.3%), the digestive dents post appendicectomies 2 cas (6.3%) and the congenital megacolon 1 cas (3%) was the indications of the stoma. the operational continuations were simple in 21 cas (65.6%). The principal found complications were: coetaneous irritation 7 cas (21.8%), the prolapsed stomiale 4 cas (12.5%), the suppuration peristomial 3 cas (9.4%), the releasing of Stoma 3 cas (9.4%), the retraction of the stoma 3 cas (9.4%),the psychological disorders 3 cases (9.4%), the hemorrhage 2 cas (6.3), necroses peristomial 2 cas (3.1%), septic shock 2 cas (6.3%), and 1 cas (3.1%) of evisceration, obstruction of the bowels, shock hypovolemic. The intermediate duration of hospitalization was of 37,5 jours with a standard deviation = 13.58 and extremes varying between 02-73 days. Death rate was of 9.4%. The assumption of responsibility of the stomies is difficult in the absence of stomatherapeutes, and of the high cost of the parenteral nutrition in our context .

Pit-1/growth hormone factor 1 splice variant expression in the rhesus monkey pituitary gland and the rhesus and human placenta.

PubMed

Schanke, J T; Conwell, C M; Durning, M; Fisher, J M; Golos, T G

1997-03-01

We have examined the expression of Pit-1 messenger RNA (mRNA) splice variants in the nonhuman primate pituitary and in rhesus and human placenta. Full-length complementary DNAs (cDNAs) representing Pit-1 and the Pit-1 beta splice variants were cloned from a rhesus monkey pituitary cDNA library and were readily detectable by RT-PCR with rhesus pituitary gland RNA. The Pit-1T variant previously reported in mouse pituitary tumor cell lines was not detectable in normal rhesus pituitary tissue, although two novel splice variants were detected. A cDNA approximating the rat Pit-1 delta 4 variant was cloned but coded for a truncated and presumably nonfunctional protein. Only by using a nested RT-PCR approach were Pit-1 and Pit-1 beta variants consistently detectable in both human and rhesus placental tissue. The Pit-1 beta variant mRNA was not detectable in JEG-3 choriocarcinoma cells unless the cells were stimulated with 8-Br-cAMP. Immunoblot studies with nuclear extracts from primary rhesus syncytiotrophoblast cultures or JEG-3 choriocarcinoma cells indicated that although mRNA levels were very low, Pit-1 protein was detectable in differentiated cytotrophoblasts, and levels increased after treatment with 8-Br-cAMP. Two major species of Pit-1 protein were detected that corresponded to the two major bands in rat pituitary GH3 cell nuclear extracts. Low levels of slightly larger bands also were seen, which may represent Pit-1 beta protein or phosphorylated species. We conclude that Pit-1 splice variants expressed in the primate pituitary gland differ from those in the rodent gland and that the Pit-1 and Pit-1 beta mRNAs expressed in the placenta give rise to a pattern of protein expression similar to that seen in pituitary cells, which is inducible by treatment with 8-Br-cAMP.

Advantages and limitations for users of double pit pour-flush latrines: a qualitative study in rural Bangladesh.

PubMed

Hussain, Faruqe; Clasen, Thomas; Akter, Shahinoor; Bawel, Victoria; Luby, Stephen P; Leontsini, Elli; Unicomb, Leanne; Barua, Milan Kanti; Thomas, Brittany; Winch, Peter J

2017-05-25

In rural Bangladesh, India and elsewhere, pour-flush pit latrines are the most common sanitation system. When a single pit latrine becomes full, users must empty it themselves and risk exposure to fresh feces, pay an emptying service to remove pit contents or build a new latrine. Double pit pour-flush latrines may serve as a long-term sanitation option including high water table areas because the pits do not need to be emptied immediately and the excreta decomposes into reusable soil. Double pit pour-flush latrines were implemented in rural Bangladesh for 'hardcore poor' households by a national NGO, BRAC. We conducted interviews, focus groups, and spot checks in two low-income, rural areas of Bangladesh to explore the advantages and limitations of using double pit latrines compared to single pit latrines. The rural households accepted the double pit pour-flush latrine model and considered it feasible to use and maintain. This latrine design increased accessibility of a sanitation facility for these low-income residents and provided privacy, convenience and comfort, compared to open defecation. Although a double pit latrine is more costly and requires more space than a single pit latrine the households perceived this sanitation system to save resources, because households did not need to hire service workers to empty pits or remove decomposed contents themselves. In addition, the excreta decomposition process produced a reusable soil product that some households used in homestead gardening. The durability of the latrine superstructures was a problem, as most of the bamboo-pole superstructure broke after 6-18 months of use. Double pit pour-flush latrines are a long-term improved sanitation option that offers users several important advantages over single pit pour-flush latrines like in rural Bangladesh which can also be used in areas with high water table. Further research can provide an understanding of the comparative health impacts and effectiveness of the model in preventing human excreta from entering the environment.

Involvement of the pituitary-specific transcription factor pit-1 in somatolactotrope cell growth and death: an approach using dominant-negative pit-1 mutants.

PubMed

Pellegrini, Isabelle; Roche, Cathy; Quentien, Marie-Helene; Ferrand, Mireille; Gunz, Ginette; Thirion, Sylvie; Bagnis, Claude; Enjalbert, Alain; Franc, Jean-Louis

2006-12-01

The anterior pituitary-specific transcription factor Pit-1 was initially identified and cloned as a transactivator of the prolactin (PRL) and GH genes and later as a regulator of the TSHb gene. It was found to be a major developmental regulator, because natural Pit-1 gene mutations cause a dwarf phenotype in mice and cause combined pituitary hormone deficiency associated with pituitary hypoplasia in humans. To further investigate the growth-promoting effects of Pit-1, we used a strategy based on the use of dominant-negative Pit-1 mutants as an alternative means of inactivating endogenous Pit-1 functions. R271W, a Pit-1 mutant identified in one allele in patients with severe combined pituitary hormone deficiency, and Pit-1Delta1-123, a deletion mutant in which only the DNA binding domain of Pit-1 is conserved, were generated, and their ability to abolish the effects of the endogenous native Pit-1 in the differentiated proliferating somatolactotrope GH4C1 cell line was investigated. Enforced expression of the dominant-negative mutants in GH4C1 cells using recombinant lentiviral vectors decreased the levels of expression of known Pit-1 target genes such as PRL and GH, abolished the hormone release, and reduced cell viability by decreasing the growth rate and inducing apoptosis via a caspase-independent pathway. These results show for the first time that the growth-promoting effects of Pit-1 are at least partly due to the fact that this transcription factor prevents apoptotic cell death.

CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome.

PubMed

Tajkarimi, Mehrdad; Wexler, Hannah M

2017-01-01

Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis ( n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains from a variety of sources. There are four apparent CRISPR-Cas systems in B. fragilis -three systems have adjacent cas genes. Understanding CRISPR/Cas function in B. fragilis will elucidate their role in gene expression, DNA repair and ability to survive exposure to antibiotics. Also, based on their unique CRISPR-Cas arrays, their phylogenetic clustering and their virulence potential, we are proposing that blood isolates of B. fragilis be viewed a separate subgroup.

Cas9-nickase-mediated genome editing corrects hereditary tyrosinemia in rats.

PubMed

Shao, Yanjiao; Wang, Liren; Guo, Nana; Wang, Shengfei; Yang, Lei; Li, Yajing; Wang, Mingsong; Yin, Shuming; Han, Honghui; Zeng, Li; Zhang, Ludi; Hui, Lijian; Ding, Qiurong; Zhang, Jiqin; Geng, Hongquan; Liu, Mingyao; Li, Dali

2018-05-04

Hereditary tyrosinemia type I (HTI) is a metabolic genetic disorder caused by mutation of fumarylacetoacetate hydrolase (FAH). Because of the accumulation of toxic metabolites, HTI causes severe liver cirrhosis, liver failure, and even hepatocellular carcinoma. HTI is an ideal model for gene therapy, and several strategies have been shown to ameliorate HTI symptoms in animal models. Although CRISPR/Cas9-mediated genome editing is able to correct the Fah mutation in mouse models, WT Cas9 induces numerous undesired mutations that have raised safety concerns for clinical applications. To develop a new method for gene correction with high fidelity, we generated a Fah mutant rat model to investigate whether Cas9 nickase (Cas9n)-mediated genome editing can efficiently correct the Fah First, we confirmed that Cas9n rarely induces indels in both on-target and off-target sites in cell lines. Using WT Cas9 as a positive control, we delivered Cas9n and the repair donor template/single guide (sg)RNA through adenoviral vectors into HTI rats. Analyses of the initial genome editing efficiency indicated that only WT Cas9 but not Cas9n causes indels at the on-target site in the liver tissue. After receiving either Cas9n or WT Cas9-mediated gene correction therapy, HTI rats gained weight steadily and survived. Fah-expressing hepatocytes occupied over 95% of the liver tissue 9 months after the treatment. Moreover, CRISPR/Cas9-mediated gene therapy prevented the progression of liver cirrhosis, a phenotype that could not be recapitulated in the HTI mouse model. These results strongly suggest that Cas9n-mediated genome editing is a valuable and safe gene therapy strategy for this genetic disease. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and functional insights into the interaction between the Cas family scaffolding protein p130Cas and the focal adhesion-associated protein paxillin

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

Zhang, Chi; Miller, Darcie J.; Guibao, Cristina D.

The Cas family scaffolding protein p130Cas is a Src substrate localized in focal adhesions (FAs) and functions in integrin signaling to promote cell motility, invasion, proliferation, and survival. p130Cas targeting to FAs is essential for its tyrosine phosphorylation and downstream signaling. Although the N-terminal SH3 domain is important for p130Cas localization, it has also been reported that the C-terminal region is involved in p130Cas FA targeting. The C-terminal region of p130Cas or Cas family homology domain (CCHD) has been reported to adopt a structure similar to that of the focal adhesion kinase C-terminal focal adhesion-targeting domain. The mechanism by whichmore » the CCHD promotes FA targeting of p130Cas, however, remains unclear. In this study, using a calorimetry approach, we identified the first LD motif (LD1) of the FA-associated protein paxillin as the binding partner of the p130Cas CCHD (in a 1:1 stoichiometry with a Kd ~4.2 μM) and elucidated the structure of the p130Cas CCHD in complex with the paxillin LD1 motif by X-ray crystallography. Of note, a comparison of the CCHD/LD1 complex with a previously solved structure of CCHD in complex with the SH2-containing protein NSP3 revealed that LD1 had almost identical positioning of key hydrophobic and acidic residues relative to NSP3. Because paxillin is one of the key scaffold molecules in FAs, we propose that the interaction between the p130Cas CCHD and the LD1 motif of paxillin plays an important role in p130Cas FA targeting.« less

Influence of organic waste and residue mud additions on chemical, physical and microbial properties of bauxite residue sand.

PubMed

Jones, Benjamin E H; Haynes, Richard J; Phillips, Ian R

2011-02-01

In an alumina refinery, bauxite ore is treated with sodium hydroxide at high temperatures and pressures and for every tone of alumina produced, about 2 tones of alkaline, saline bauxite processing waste is also produced. At Alcoa, a dry stacking system of disposal is used, and it is the sand fraction of the processing waste that is rehabilitated. There is little information available regarding the most appropriate amendments to add to the processing sand to aid in revegetation. The purpose of this study was to investigate how the addition of organic wastes (biosolids and poultry manure), in the presence or absence of added residue mud, would affect the properties of the residue sand and its suitability for revegetation. Samples of freshly deposited residue sand were collected from Alcoa's Kwinana refinery. Samples were treated with phosphogypsum (2% v/v), incubated, and leached. A laboratory experiment was then set up in which the two organic wastes were applied at 0 or the equivalent to 60 tones ha(-1) in combination with residue mud added at rates of 0%, 10% and 20% v/v. Samples were incubated for 8 weeks, after which, key chemical, physical and microbial properties of the residue sand were measured along with seed germination. Additions of residue mud increased exchangeable Na(+), ESP and the pH, and HCO (3) (-) and Na(+) concentrations in saturation paste extracts. Additions of biosolids and poultry manure increased concentrations of extractable P, NH (4) (+) , K, Mg, Cu, Zn, Mn and Fe. Addition of residue mud, in combination with organic wastes, caused a marked decrease in macroporosity and a concomitant increase in mesoporosity, available water holding capacity and the quantity of water held at field capacity. With increasing residue mud additions, the percentage of sample present as sand particles (<1 mm diameter) decreased, and the percentage present in aggregated form (>2 mm diameter) increased; greatest aggregation occurred where a combination of residue mud and poultry manure were added. Stability of aggregates, as measured by wet sieving, was greatest where poultry manure was applied. Although total organic C and soluble organic C were greater in biosolids than poultry manure treatments, the reverse was the case for microbial biomass C and basal respiration. In the biosolids and poultry manure treatments, increasing residue mud additions tended to increase soluble C, microbial biomass C and basal respiration. Germination index of watercress was highest in control samples and reduced by additions of biosolids and poultry manure which was attributed to the high EC and possibly high extractable P and NH (4) (+) . The concurrent addition of residue mud and organic wastes can improve chemical, microbial and particularly physical properties of residue sand. Future research should include neutralisation of the mud (e.g. with gypsum) and subsequent leaching to remove salts originating from both the mud and organic wastes.

Force-displacement measurements of earlywood bordered pits using a mesomechanical tester

Treesearch

Samuel L. Zelinka; Keith J. Bourne; John C. Hermanson; Samuel V. Glass; Adriana Costa; Alex C. Wiedenhoeft

2015-01-01

The elastic properties of pit membranes are reported to have important implications in understanding air-seeding phenomena in gymnosperms, and pit aspiration plays a large role in wood technological applications such as wood drying and preservative treatment. Here we present force–displacement measurements for pit membranes of circular bordered pits, collected on a...

Fusion of SpCas9 to E. coli Rec A protein enhances CRISPR-Cas9 mediated gene knockout in mammalian cells.

PubMed

Lin, Lin; Petersen, Trine Skov; Jensen, Kristopher Torp; Bolund, Lars; Kühn, Ralf; Luo, Yonglun

2017-04-10

Mammalian cells repair double-strand DNA breaks (DSB) by a range of different pathways following DSB induction by the engineered clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein Cas9. While CRISPR-Cas9 thus enables predesigned modifications of the genome, applications of CRISPR-Cas9-mediated genome-editing are frequently hampered by the unpredictable and varying pathways for DSB repair in mammalian cells. Here we present a strategy of fusing Cas9 to recombinant proteins for fine-tuning of the DSB repair preferences in mammalian cells. By fusing Streptococcus Pyogenes Cas9 (SpCas9) to the recombinant protein A (Rec A, NP_417179.1) from Escherichia coli, we create a recombinant Cas9 protein (rSpCas9) which enhances the generation of indel mutations at DSB sites in mammalian cells, increases the frequency of DSB repair by homology-directed single-strand annealing (SSA), and represses homology-directed gene conversion by approximately 33%. Our study thus proves for the first time that fusing SpCas9 to recombinant proteins can influence the balance between DSB repair pathways in mammalian cells. This approach may form the basis for further investigations of the applications of recombinant Cas9 proteins to fine-tuning DSB repair pathways in eukaryotic cells. Copyright © 2017 Elsevier B.V. All rights reserved.

A study of inter-particle bonds in dry bauxite waste resulting in atmospheric aerosols

NASA Astrophysics Data System (ADS)

Wagh, Arun S.; Thompson, Bentley

1988-02-01

Bauxite and Alumina production are one of the main activities of several third world countries such as Jamaica, Brazil, India, Guinea, eastern European countries such as Hungary and Rumania and advanced countries such as Australia, West Germany, Japan and the United States. The mining operations lead to dust pollution, but the refining of bauxite to alumina yield large amounts of highly caustic sludge waste, called "Red Mud". Millions of tons of the waste produced in every country are stored in containment dams or natural valleys. This leads to ground water pollution, destruction of plant and bird life and is hazardous to human settlement in earthquake prone regions like Jamaica. As a result several companies have been looking into dry mud stacking which involves thickening the mud in the refining plants and sprying it on the slopes to sun dry it. Typically it involves a drying field of about two hundred acres, which could act as a potential source of caustic dust. In Jamaica one company has started disposing of the mud in this way. The aerosol formation from such areas depends mainly on the integrity of the top dry layers. Presently this is done by studying the approximate parameters such as the friability of the mud. However, following the recent advances in powder technology it has been possible for us to develop an instrument to study the average interparticle forces between the red mud particles. The instrument is based on the principle of a tensometer and a split cell is used to load specimens. A load cell is used to measure the force and a chart recorder is used for plotting separation and the force. The present study reports elemental composition of the dust and its health hazards. It also reports the physical measurement of the average interparticle force as a function of their separation in the Jamaican mud. The effect of ultraviolet radiation on the strength of the material is studied to see the effect of sun-drying of the waste. The five-fold increase in tensile strength indicates that laterisation process is responsible for this phenomenon in Jamaican red mud. The study is crucial to the development of dust free mud stacking by the proper modifications in the process technology. Finally, such a case study is general enough in the characterisation of other sources of aerosols.

Manipulation of nanoscale V-pits to optimize internal quantum efficiency of InGaN multiple quantum wells

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

Chang, Chiao-Yun; Li, Heng; Shih, Yang-Ta

2015-03-02

We systematically investigated the influence of nanoscale V-pits on the internal quantum efficiency (IQE) of InGaN multiple quantum wells (MQWs) by adjusting the underlying superlattices (SLS). The analysis indicated that high barrier energy of sidewall MQWs on V-pits and long diffusion distance between the threading dislocation (TD) center and V-pit boundary were crucial to effectively passivate the non-radiative centers of TDs. For a larger V-pit, the thicker sidewall MQW on V-pit would decrease the barrier energy. On the contrary, a shorter distance between the TD center and V-pit boundary would be observed in a smaller V-pit, which could increase themore » carrier capturing capability of TDs. An optimized V-pit size of approximately 200–250 nm in our experiment could be concluded for MQWs with 15 pairs SLS, which exhibited an IQE value of 70%.« less

Assisting Students' Cognitive Strategies with the Use of CAS

ERIC Educational Resources Information Center

Sarvari, Csaba; Lavicza, Zsolt; Klincsik, Mihaly

2010-01-01

This paper examines various cognitive strategies applied while CAS (Computer Algebra System) are used in undergraduate-level engineering mathematics teaching and learning. We posed some questions in relation to such CAS use: What kind of tools can CAS offer to enhance different cognitive strategies of students? How can the use of CAS widen the…

Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes

PubMed Central

Ma, Enbo; Harrington, Lucas B.; O’Connell, Mitchell R.; Zhou, Kaihong; Doudna, Jennifer A.

2015-01-01

Summary Double-stranded DNA (dsDNA) cleavage by Cas9 is a hallmark of type II CRISPR-Cas immune systems. Cas9–guide RNA complexes recognize 20-base-pair sequences in DNA and generate a site-specific double-strand break, a robust activity harnessed for genome editing. DNA recognition by all studied Cas9 enzymes requires a protospacer adjacent motif (PAM) next to the target site. We show that Cas9 enzymes from evolutionarily divergent bacteria can recognize and cleave single-stranded DNA (ssDNA) by an RNA-guided, PAM-independent recognition mechanism. Comparative analysis shows that in contrast to the type II-A S. pyogenes Cas9 that is widely used for genome engineering, the smaller type II-C Cas9 proteins have limited dsDNA binding and unwinding activity and promiscuous guide-RNA specificity. These results indicate that inefficiency of type II-C Cas9 enzymes for genome editing results from a limited ability to cleave dsDNA, and suggest that ssDNA cleavage was an ancestral function of the Cas9 enzyme family. PMID:26545076

OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE - A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING

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

Gordon Tibbitts; Arnis Judzis

2002-04-01

This document details the progress to date on the OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE--A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING contract for the quarter starting January 2002 through March 2002. Accomplishments include the following: In accordance to Task 7.0 (D. No.2 Technical Publications) TerraTek, NETL, and the Industry Contributors successfully presented a paper detailing Phase 1 testing results at the February 2002 IADC/SPE Drilling Conference, a prestigious venue for presenting DOE and private sector drilling technology advances. The full reference is as follows: (1) IADC/SPE 74540 ''World's First Benchmarking of Drilling Mud Hammer Performance atmore » Depth Conditions'' authored by Gordon A. Tibbitts, TerraTek; Roy C. Long, US Department of Energy, Brian E. Miller, BP America, Inc.; Arnis Judzis, TerraTek; and Alan D. Black, TerraTek. Gordon Tibbitts, TerraTek, will presented the well-attended paper in February of 2002. The full text of the Mud Hammer paper was included in the last quarterly report. (2) The Phase 2 project planning meeting (Task 6) was held at ExxonMobil's Houston Greenspoint offices on February 22, 2002. In attendance were representatives from TerraTek, DOE, BP, ExxonMobil, PDVSA, Novatek, and SDS Digger Tools. (3) PDVSA has joined the advisory board to this DOE mud hammer project. PDVSA's commitment of cash and in-kind contributions were reported during the last quarter. (4) Strong Industry support remains for the DOE project. Both Andergauge and Smith Tools have expressed an interest in participating in the ''optimization'' phase of the program. The potential for increased testing with additional Industry cash support was discussed at the planning meeting in February 2002.« less

Quantitative X-ray Diffraction (QXRD) analysis for revealing thermal transformations of red mud.

PubMed

Liao, Chang-Zhong; Zeng, Lingmin; Shih, Kaimin

2015-07-01

Red mud is a worldwide environmental problem, and many authorities are trying to find an economic solution for its beneficial application or/and safe disposal. Ceramic production is one of the potential waste-to-resource strategies for using red mud as a raw material. Before implementing such a strategy, an unambiguous understanding of the reaction behavior of red mud under thermal conditions is essential. In this study, the phase compositions and transformation processes were revealed for the Pingguo red mud (PRM) heat-treated at different sintering temperatures. Hematite, perovskite, andradite, cancrinite, kaolinite, diaspore, gibbsite and calcite phases were observed in the samples. However, unlike those red mud samples from the other regions, no TiO2 (rutile or anatase) or quartz were observed. Titanium was found to exist mainly in perovskite and andradite while the iron mainly existed in hematite and andradite. A new silico-ferrite of calcium and aluminum (SFCA) phase was found in samples treated at temperatures above 1100°C, and two possible formation pathways for SFCA were suggested. This is the first SFCA phase to be reported in thermally treated red mud, and this finding may turn PRM waste into a material resource for the iron-making industry. Titanium was found to be enriched in the perovskite phase after 1200°C thermal treatment, and this observation indicated a potential strategy for the recovery of titanium from PRM. In addition to noting these various resource recovery opportunities, this is also the first study to quantitatively summarize the reaction details of PRM phase transformations at various temperatures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mechanism of red mud combined with Fenton's reagent in sewage sludge conditioning.

PubMed

Zhang, Hao; Yang, Jiakuan; Yu, Wenbo; Luo, Sen; Peng, Li; Shen, Xingxing; Shi, Yafei; Zhang, Shinan; Song, Jian; Ye, Nan; Li, Ye; Yang, Changzhu; Liang, Sha

2014-08-01

Red mud was evaluated as an alternative skeleton builder combined with Fenton's reagent in sewage sludge conditioning. The results show that red mud combined with Fenton's reagent showed good conditioning capability with the pH of the filtrate close to neutrality, indicating that red mud acted as a neutralizer as well as a skeleton builder when jointly used with Fenton's reagent. Through response surface methodology (RSM), the optimal dosages of Fe(2+), H2O2 and red mud were proposed as 31.9, 33.7 and 275.1 mg/g DS (dry solids), respectively. The mechanism of the composite conditioner could be illuminated as follows: (1) extracellular polymeric substances (EPS), including loosely bound EPS and tightly bound EPS, were degraded into dissolved organics, e.g., proteins and polysaccharides; (2) bound water was released and converted into free water due to the degradation of EPS; and (3) morphology of the conditioned sludge exhibited a porous structure in contrast with the compact structure of raw sludge, and the addition of red mud formed new mineral phases and a rigid lattice structure in sludge, allowing the outflow of free water. Thus, sludge dewatering performance was effectively improved. The economic assessment for a wastewater treatment plant of 370,000 equivalent inhabitants confirms that using red mud conditioning, combined with Fenton's reagent, leads to a saving of approximately 411,000 USD/y or 50.8 USD/t DS comparing with using lime and ordinary Portland cement combined with Fenton's reagent, and approximately 612,000 USD/y or 75.5 USD/t DS comparing with the traditional treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Purification, cloning, expression and immunological analysis of Scylla serrata arginine kinase, the crab allergen.

PubMed

Shen, Yuan; Cao, Min-Jie; Cai, Qiu-Feng; Su, Wen-Jin; Yu, Hui-Lin; Ruan, Wei-Wei; Liu, Guang-Ming

2011-05-01

Although crustaceans have been reported to be one of the most common causes of IgE-mediated allergic reactions, there are no reports about the characterization and identification of arginine kinase (AK) from the mud crab (Scylla serrata) as allergen. In the present study, the purification, molecular cloning, expression and immunological analyses of the IgE allergen AK from the mud crab were investigated. The results showed that cloned DNA fragments of AK from the mud crab had open reading frames of 1021 bp, predicted to encode proteins with 356 amino acid residues. Sequence alignment revealed that mud crab AK shares high homology with other crustacean species. Mud crab AK gene was further recombined with the vector of pGEX-4T-3 and expressed in Escherichia coli BL 21. 2-D electrophoresis suggested that native AK (nAK) and recombinant AK (rAK) shared the same molecular weight of 40 kDa, and the pI is 6.5 and 6.3, respectively. The nAK and rAK were further confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Immunoblotting analysis and colloidal gold immunochromatographic assay (GICA) using sera from subjects with crustacean allergy confirmed that the nAK and rAK reacted positively with these sera, indicating AK is a specific allergen of mud crab. Both of purified nAK and rAK reacted positively with sera from subjects with crustacean allergy in immunoblotting and GICA analysis, indicating AK is a common allergen of mud crab. In vitro expressed AK is proposed as a source of the protein for immunological or clinical studies. Copyright © 2011 Society of Chemical Industry.

Early Carboniferous (Tournasian-early Visean) global paleogeography, Paleostorm tracts, and the distribution of Waulsortian and Waulsortian-like carbonate mud mounds

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

King, D.T. Jr.

1990-05-01

Tournasian-early Visean mud mounds (i.e., Waulsortian and Waulsortian-like mounds) are unlike other carbonate buildups in the stratigraphic record because they lack an identifiable frame-building organism. Waulsortian mounds are comprised mainly of carbonate mud; Waulsortian-like mounds are mud-rich and contain a significant percent of skeletal grains, especially crinoids and bryozoa. This study has revealed that all of the reported Waulsortian and Waulsortian-like mounds developed in low paleolatitudes either on the southern shelf margin of the Laurussian paleocontinent or in the Laurussian interior seaway. Waulsortian and Waulsortian-like mounds are specifically not present in low-latitude regions of other paleocontinents. As Tournasian-early Visean carbonatemore » deposition was widespread in the range of 30{degree}N to 10{degree}S, the very restricted paleogeographic distribution of Waulsortian and Waulsortian-like mound locations suggests a mechanism or set of conditions that effectively limited the distribution of mud mounds. Considering the Tournasian-early Visean distribution of paleocontinents and the principles that govern the movement of modern hurricanes, tropical storms, and winter storms, the tracts of hurricanes, tropical storms, and winter storms probably crossed all main submerged paleocontinental areas except the southern Laurussian shelf margin and the Laurussian interior seaway, the two areas where mud mounds developed. The lack of storm energy in these two large areas of Laurussia provided long-term stability and thus enhanced the growth prospects of the frame-deficient Waulsortian and Waulsortian-like mud mounds. Lack of extensive periodic wave reworking and other storm-induced devastation helps to account for enigmatic features such as general mound symmetry, great size, high depositional relief (as much as 220 m), and side steepness (as steep as 50{degree}).« less

Experimental Study of Sand Production and Mud Erosion Phenomena for Sand Mud Alternate Layer

NASA Astrophysics Data System (ADS)

Oyama, H.; Sato, T.

2014-12-01

Methane hydrates are crystalline, ice-like compounds under specific thermodynamic conditions. The existence of methane hydrates is confirmed in the Nankai Trough, an offshore area of Japan. Japan's Methane Hydrate Research and Development Program (MH21) has been under way at this area. In the early 2013, the world's first intentional gas production attempt from marine gas hydrate deposits was tried and accomplished in the Daini Atumi Knoll area of the Eastern Nankai Trough. For gas production, depressurization method has been considered as a promising gas production technique from methane hydrate reservoirs. However, considering of continuous gas production over a long period, there is still something to clarify. The methane hydrate crystals are very small and existed in the intergranular pores of sandy layer of turbidite sediments. When the intergranular methane hydrates will be dissociated, it is considered that dissociated gas and water flow will cause sand production and mud erosion phenomena of turbidite sediments. The production of framework sands into a well is one of the problems plaguing the gas because of its adverse effects on well productivity and equipment. If the eroded mud is accumulated in the pore space of sand, skin is generated and permeability becomes lower. In addition, mud erosion has a negative effect for the well stability. This research presents an experimental study to understand sand production and mud erosion phenomena for sand mud alternate layer. The aims of this study are to understand these phenomena and clarify driving forces. In our experiments, we used an artificial sedimentary core and performed experiments under various conditions. As the results, the driving forces of these phenomena are not dissociation gas flow but water flow through pore.

Predation and control efficacies of Misgurnus mizolepis (Cypriniformes: Cobitidae) toward Culex pipiens molestus (Diptera: Culicidae) and fish toxicity of temephos in laboratory and septic tank conditions.

PubMed

Chae, Seong Chun; Kwon, Young Hyun; Min, Kyung Il; Kim, Hyung Soo; Kim, Nam-Jin; Kim, Jun-Ran; Son, Bong Gi; Ahn, Young-Joon

2014-07-01

Culex pipiens molestus Forskal (Diptera: Culicidae) is the dominant mosquito species in septic tanks in South Korea. An assessment was made of the biological control potential of mud loaches, Misgurnus mizolepis Günther (Cypriniformes: Cobitidae), toward Cx. p. molestus larvae in laboratory and septic tanks. Results were compared with those of temephos 20% emulsifiable concentrate. In laboratory tests, all mud loaches survived on sedimentation chamber- and effluent chamber-collected water of aerobic septic tanks (ASTs), whereas all mud loaches died within 3-12 h after introduction into sedimentation chamber- and effluent chamber-collected water of anaerobic septic tanks, Gill hyperplasia and hemorrhages at the bases of pectoral fins were detected in all dead mud loaches. These appeared to have been caused by bacterial disease, rather than the physical and chemical characteristics of the septic tank water. A mud loach consumed an average range of 1,072-1,058 larvae of Cx. p. molestus in the AST water at 24 h. At the manufacturer's recommended rate (10 ml/ton) in the AST water, the temephos formulation did not cause fish mortality. In the AST experiment, predation of mosquito larvae by mud loaches at a release rate of one fish per 900 mosquito larvae resulted in complete mosquito control from the third day after treatment throughout the 18-wk survey period, compared with temephos 20% emulsifiable concentrate-treated AST water (reduction rate, 40% at 28 days after treatment). Reasonable mosquito control in aerobic septic tanks can be achieved by mosquito breeding season stocking of a rate of one mud loach per 900 mosquito larvae.

Comparison of health service use among veterans with methamphetamine versus alcohol use disorders.

PubMed

Morasco, Benjamin J; OʼNeil, Maya E; Duckart, Jonathan P; Ganzini, Linda

2014-01-01

Methamphetamine use disorders (MUD) are associated with severe health effects and psychiatric comorbidities, but little is known about the health care utilization of patients with MUD. The goal of this study was to describe health service use among veterans with MUD relative to a group of veterans with an alcohol use disorder (AUD). Using Veterans Affairs (VA) administrative data, we identified 718 patients who were diagnosed with MUD and had confirmatory drug testing. Data were compared with those of 744 patients who had diagnoses of an AUD also with confirmatory testing. We examined diagnoses and medical utilization for 5 years after their index date. Patients with MUD and laboratory-confirmed recent use were younger and more likely to be diagnosed with a mood disorder, posttraumatic stress disorder, and a psychotic-spectrum disorder (all P values < 0.05). After statistical controls, patients with MUD were more likely to have an inpatient hospitalization (80% vs 70%, odds ratio [OR] = 1.8; 95% confidence interval [CI] = 1.4-2.3), discharge from an inpatient admission against medical advice (23.4% vs 8.3%, OR = 2.6, 95% CI = 1.9-3.7), receive care at 3 or more VA medical centers (13.1% vs 5.4%, OR = 2.3, 95% CI = 1.5-3.5), have a behavioral flag in the medical record (5.6% vs 1.1%, OR = 4.6, 95% CI = 2.1-10.6), and have more total missed appointments in the 5-year study period (M = 33.1 vs M = 23.5, P < 0.001). Among veterans with substance use disorders, those with MUD and laboratory-confirmed recent use have additional behavioral, health care utilization, and psychiatric characteristics that need to be considered in developing programs of care.

Pre-eruptive ground deformation of Azerbaijan mud volcanoes detected through satellite radar interferometry (DInSAR)

NASA Astrophysics Data System (ADS)

Antonielli, Benedetta; Monserrat, Oriol; Bonini, Marco; Righini, Gaia; Sani, Federico; Luzi, Guido; Feyzullayev, Akper A.; Aliyev, Chingiz S.

2014-12-01

Mud volcanism is a process that leads to the extrusion of subsurface mud, fragments of country rocks, saline waters and gases. This mechanism is typically linked to hydrocarbon traps, and the extrusion of this material builds up a variety of conical edifices with a similar morphology to those of magmatic volcanoes, though smaller in size. The Differential Interferometry Synthetic Aperture Radar (DInSAR) technique has been used to investigate the ground deformation related to the activity of the mud volcanoes of Azerbaijan. The analysis of a set of wrapped and unwrapped interferograms, selected according to their coherence, allowed the detection of significant superficial deformation related to the activity of four mud volcanoes. The ground displacement patterns observed during the period spanning from October 2003 to November 2005 are dominated by uplift, which reach a cumulative value of up to 20 and 10 cm at the Ayaz-Akhtarma and Khara-Zira Island mud volcanoes, respectively. However, some sectors of the mud volcano edifices are affected by subsidence, which might correspond to deflation zones that coexist with the inflation zones characterized by the dominant uplift. Important deformation events, caused by fluid pressure and volume variations, have been observed both (1) in connection with main eruptive events in the form of pre-eruptive uplift, and (2) in the form of short-lived deformation pulses that interrupt a period of quiescence. Both deformation patterns show important similarities to those identified in some magmatic systems. The pre-eruptive uplift has been observed in many magmatic volcanoes as a consequence of magma intrusion or hydrothermal fluid injection. Moreover, discrete short-duration pulses of deformation are also experienced by magmatic volcanoes and are repeated over time as multiple inflation and deflation events.

Corrective Action Investigation Plan for Corrective Action Unit 486: Double Tracks RADSAFE Ares, Nellis Air Force Range, Nevada, Rev. 0; DOE/NV--523 UPDATED WITH ROTC No.1 and 2

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

ITLV

This CAIP presents a plan to investigate the DTRSA where unregulated disposal of radioactive and possibly hazardous waste occurred during decontamination activities for the Double Tracks test. The purpose of the corrective action investigation described in this CAIP is to: Identify and verify the locations of the decontamination facility and animal burial pit within the DTRSA; Identify the presence and nature of COPCs; Determine the vertical and lateral extent of COPCs; and Provide sufficient information and data to develop and evaluate appropriate corrective actions for the CAS. This CAIP was developed using the U.S. Environmental Protection Agency (EPA) Data Qualitymore » Objectives (DQOs) (EPA, 1994d) process to clearly define the goals for collecting environmental data, to determine data uses, and to design a data collection program that will satisfy these uses. A DQO scoping meeting was held prior to preparation of this plan; a brief summary of the DQOs is presented in Section 3.4. A more detailed summary of the DQO process and results is included in Appendix A.« less

Methods for decoding Cas9 protospacer adjacent motif (PAM) sequences: A brief overview.

PubMed

Karvelis, Tautvydas; Gasiunas, Giedrius; Siksnys, Virginijus

2017-05-15

Recently the Cas9, an RNA guided DNA endonuclease, emerged as a powerful tool for targeted genome manipulations. Cas9 protein can be reprogrammed to cleave, bind or nick any DNA target by simply changing crRNA sequence, however a short nucleotide sequence, termed PAM, is required to initiate crRNA hybridization to the DNA target. PAM sequence is recognized by Cas9 protein and must be determined experimentally for each Cas9 variant. Exploration of Cas9 orthologs could offer a diversity of PAM sequences and novel biochemical properties that may be beneficial for genome editing applications. Here we briefly review and compare Cas9 PAM identification assays that can be adopted for other PAM-dependent CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Distribution, formation mechanisms, and significance of lunar pits

NASA Astrophysics Data System (ADS)

Wagner, Robert V.; Robinson, Mark S.

2014-07-01

Lunar Reconnaissance Orbiter Camera images reveal the presence of steep-walled pits in mare basalt (n = 8), impact melt deposits (n = 221), and highland terrain (n = 2). Pits represent evidence of subsurface voids of unknown extents. By analogy with terrestrial counterparts, the voids associated with mare pits may extend for hundreds of meters to kilometers in length, thereby providing extensive potential habitats and access to subsurface geology. Because of their small sizes relative to the local equilibrium crater diameters, the mare pits are likely to be post-flow features rather than volcanic skylights. The impact melt pits are indirect evidence both of extensive subsurface movement of impact melt and of exploitable sublunarean voids. Due to the small sizes of pits (mare, highland, and impact melt) and the absolute ages of their host materials, it is likely that most pits formed as secondary features.

Pit Latrine Fecal Sludge Resistance Using a Dynamic Cone Penetrometer in Low Income Areas in Mzuzu City, Malawi

PubMed Central

Chirwa, Charles F. C.; Hall, Ralph P.; Krometis, Leigh-Anne H.; Vance, Eric A.; Edwards, Adam; Guan, Ting; Holm, Rochelle H.

2017-01-01

Pit latrines can provide improved household sanitation, but without effective and inexpensive emptying options, they are often abandoned once full and may pose a public health threat. Emptying techniques can be difficult, as the sludge contents of each pit latrine are different. The design of effective emptying techniques (e.g., pumps) is limited by a lack of data characterizing typical in situ latrine sludge resistance. This investigation aimed to better understand the community education and technical engineering needs necessary to improve pit latrine management. In low income areas within Mzuzu city, Malawi, 300 pit latrines from three distinct areas were assessed using a dynamic cone penetrometer to quantify fecal sludge strength, and household members were surveyed to determine their knowledge of desludging procedures and practices likely to impact fecal sludge characteristics. The results demonstrate that there is a significant difference in sludge strength between lined and unlined pits within a defined area, though sludge hardened with depth, regardless of the pit type or region. There was only limited association between cone penetration depth and household survey data. To promote the adoption of pit emptying, it is recommended that households be provided with information that supports pit emptying, such as latrine construction designs, local pit emptying options, and cost. This study indicates that the use of a penetrometer test in the field prior to pit latrine emptying may facilitate the selection of appropriate pit emptying technology. PMID:28165378

The efficiencies of cast blasting in wide pits

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

Martin, R.L.; King, M.G.

Blasting activities in all four pits at Thunder Basin Coal`s Black Thunder Mine are focused on cast blasting. With widths varying from 190 feet to 265 feet and bench heights varying from 90 feet to 175 feet, casting efficiencies vary with different geometry`s. For example, the percent cast to final in the 200 foot pit is on the average higher than the 270 foot pit. The powder factors are somewhat higher in the narrower pits, thus increasing the cost of blasting. This leads to a very detailed look at the actual benefit of cast blasting and the associated cost ofmore » these benefits. The simple solution would be to reduce the width of the pits, thereby increasing the percent cast to final. However, the lower rehandle and low coal loss associated with wide pits would be fortified. Upon further review it becomes obvious that the wider pits could not be compared to the narrow pits with the cast to final percent indices. The focus should be shifted to cubic yards cast to final per lineal foot of pit. This will allow for more accurate measures of the casting efficiency of the shot. When comparing the pits with these indices their performances were much closer than the percent cast to final indices. The powder factors being higher in the narrow pits drove up the cost per cubic yard cast to final. Therefore, even though the percent cast to final was higher, the cost per cubic yard was also higher.« less

The presence of an insulin-like androgenic gland factor (IAG) and insulin-like peptide binding protein (ILPBP) in the ovary of the blue crab, Callinectes sapidus and their roles in ovarian development.

PubMed

Huang, Xiaoshuai; Ye, Haihui; Chung, J Sook

2017-08-01

Insulin-like androgenic gland factor (IAG) that is produced by the male androgenic gland (AG), plays a role in sexual differentiation and maintenance of male secondary sex characteristics in decapod crustaceans. With an earlier finding of IAG expression in a female Callinectes sapidus ovary, we aimed to examine a putative role of IAG during the ovarian development of this species. To this end, the full-length cDNA sequence of the ovarian CasIAG (termed CasIAG-ova) has been isolated. The predicted mature peptide sequence of CasIAG-ova is identical to that of the IAG from the AG, except in their signal peptide regions. The CasIAG-ova contains an alternative initiation codon (UUG) as the start codon, which suggests that the translational regulation of CasIAG-ova may differ from that of the IAG from AG. To define the function of CasIAG-ova, the expressions of CasIAG-ova as well as its putative binding protein, insulin-like peptide binding protein (ILPBP), are measured in the ovaries at various developmental stages obtained from different seasons. Season affects both CasIAG and ILPBP expression in the ovary. Overall, summer females at earlier ovarian stages contain high levels of CasIAG and ILPBP than spring or fall females. These findings indicate that CasIAG-ova and CasILPBP may be involved in the ovarian development. When comparing the levels of CasIAG and CasILPBP in the ovary, the latter are much higher (∼10-10000 fold) than the former. Expression patterns of CasILPBP differ from those of CasIAG-ova during ovarian development and by season, suggesting that ILPBP may have an additional role in ovarian development rather than a function of a putative binding protein of IAG. Copyright © 2017 Elsevier Inc. All rights reserved.

Low Pressure Tires in Mud

DTIC Science & Technology

1944-03-01

Scope 1 II AUTHORITY 1 2. Directives 1 III PREVIOUS INVESTIGATION 1 3 . Summary 1 IV PRES {T INVESTIGATION 2 4. Purpose of Tests 2 5. Tests Conducted... 3 V DISCUSSION 3 6. Importanc-? of Tosts 3 7. The Low Pressure Tire 3 8. Mud Conditions 4 9. Factors Influencing laud Porformanco 4 10. Reasons for...data on general service durability, which is * deemed satisfactory, are included in the report. 3 . The report concludes that mud performance of those

Testing of Compounds for Efficacy against Schistosomiasis.

DTIC Science & Technology

1986-07-22

4); 2) a petri dish containing a centrally placed mud mound, blue-green aglae ( Nostoc muscorum) and water Is used for rearing young snails and...maintaining both pre-exposed and exposed snails (5); 3) a petri dish containing small amounts of blue-green algae ( Nostoc muscoru), mud and water is used...25-27 C. 4. Food. Blue-green algae ( Nostoc muscorum) grown in petri dishes with mud (5) is used exclusively as the food source. C. Breedin A

Estimation of bioavailability of metals from drilling mud barite.

PubMed

Neff, Jerry M

2008-04-01

Drilling mud and associated drill cuttings are the largest volume wastes associated with drilling of oil and gas wells and often are discharged to the ocean from offshore drilling platforms. Barite (BaSO4) often is added as a weighting agent to drilling muds to counteract pressure in the geologic formations being drilled, preventing a blowout. Some commercial drilling mud barites contain elevated (compared to marine sediments) concentrations of several metals. The metals, if bioavailable, may harm the local marine ecosystem. The bioavailable fraction of metals is the fraction that dissolves from the nearly insoluble, solid barite into seawater or sediment porewater. Barite-seawater and barite-porewater distribution coefficients (Kd) were calculated for determining the predicted environmental concentration (PEC; the bioavailable fraction) of metals from drilling mud barite in the water column and sediments, respectively. Values for Kdbarite-seawater and Kdbarite-porewater were calculated for barium, cadmium, chromium, copper, mercury, lead, and zinc in different grades of barite. Log Kdbarite-seawater values were higher (solubility was lower) for metals in the produced water plume than log Kdbarite-porewater values for metals in sediments. The most soluble metals were cadmium and zinc and the least soluble were mercury and copper. Log Kd values can be used with data on concentrations of metals in barite and of barite in the drilling mud-cuttings plume and in bottom sediments to calculate PECseawater and PECsediment.

Composites based on PET and red mud residues as catalyst for organic removal from water.

PubMed

Bento, Natálya I; Santos, Patrícia S C; de Souza, Talita E; Oliveira, Luiz C A; Castro, Cínthia S

2016-08-15

In this study, we obtained a composite based on carbon/iron oxide from red mud and PET (poly(ethylene terephthalate)) wastes by mechanical mixture (10, 15 and 20wt.% of PET powder/red mud) followed by a controlled thermal treatment at 400°C under air. XRD analyses revealed that the α-Fe2O3 is the main phase formed from red mud. TPR analyses showed that the iron oxide present in the composites undergoes reduction at lower temperature to form Fe(2+) species present in Fe3O4, indicating that the iron oxide in the composite can exhibit greater reactivity in the catalytic processes compared to the original red mud. In fact, catalytic tests showed that the composites presented higher capacity to remove methylene blue dye (MB), presenting about 90% of removal after 24h of reaction. The MB removal was also monitored by mass spectrometer with ionization via electrospray (ESI-MS), which demonstrated the occurrence of the oxidation process, showing the formation of MB oxidation products. The stability of the composites was confirmed after four reuse cycles. The results seem to indicate that PET carbon deposited over the iron oxide from red mud promotes adsorption of the contaminant allowing its contact with the iron atoms and their consequent reaction. Copyright © 2016 Elsevier B.V. All rights reserved.

Oil Palm Empty Fruit Bunch (OPEFB) Fiber as Lost Circulation Material (LCM) in Water Based Mud (WBM)

NASA Astrophysics Data System (ADS)

Ghazali, N. A.; Sauki, A.; Abu Bakar, N. F.; Mohamed, S.

2018-05-01

Lost Circulation Material (LCM) is an additive used to prevent lost of mud to the formation as a results from natural or induced fractured during drilling operation. Losses of mud could give great impact to the oil industry as it increases mud cost and rig time. The objective of this research was to investigate the effect of size and concentration of Oil Palm Empty Fruit Bunch (OPEFB) as LCM in water based mud (WBM). Several important properties of WBM rheology after adding the OPEFB namely plastic viscosity, apparent viscosity, yield point and gel strength were characterized. The sizes of OPEFB added into the WBM were 150μm, 250μm, 500μm and 1000μm while the concentration of OPEFB used were 5g, 10g, 15g and 20g in 350 mL of WBM. Results indicated that the plastic viscosity and apparent viscosity increased with increasing of the OPEFB concentrations. On the other hand, the plastic viscosity and apparent viscosity decreased with increasing sizes of OPEFB. Yield point increased as the concentration and size of OPEFB increases. This study indicated that OPEFB was effective to be used as LCM for size of 150μm and concentration of 15g whereby it produced least amount of filtrate volume as well as good control in mud rheology.

The effect of amino acid lysine and methionine addition on feed toward the growth and retention on mud crab (Scylla serrata)

NASA Astrophysics Data System (ADS)

Alissianto, Y. R.; Sandriani, Z. A.; Rahardja, B. S.; Agustono; Rozi

2018-04-01

High market demand of mud crab (Scylla serrata) encourages farmers to increase the production of mud crab. However, mud crab can not synthesize essential amino acids, so it is necessary to supply essential amino acids such as lysine and methionine in the diet. This study aims to determine the effect of lysine and methionine on feeds to increase growth and retention of mud crabs (Scylla serrata). In this study the amount of lysine amino acid and methionine added to the trash fish diet were: P0 (0: 0%); P1 (0.75: 0.75%); P2 (1: 1%); P3 (1.25: 1.25%); P4 (1.5: 1.5%) with the ratio of lysine and methionine 1: 1. The parameters observed in this study were Survival Rate (SR), Specific Growth Rate (SGR), Feed Conversion Ratio (FCR), Efficiency Feed (EF), protein retention and energy retention. The results of the 35-day maintenance study showed significant differences (P <0.05) against Specific Growth Rate (SGR), Feed Conversion Ratio (FCR), Efficiency Feed (EF), protein retention and no significant effect (P> 0.05) on energy retention and Survival Rate (SR) on mud crab. The best results in this study were found in P4 treatment with addition of lysine amino acids and methionine (1.5: 1.5%).

Clinical and anti-aging effect of mud-bathing therapy for patients with fibromyalgia.

PubMed

Maeda, Toyoki; Kudo, Yoshihiro; Horiuchi, Takahiko; Makino, Naoki

2017-12-06

Spa bathing is known as a medical treatment for certain diseases causing chronic pains. Spa water contains mineral components which lower the specific heat of the water, resulting in a higher efficiency to warm body-core temperature. This phenomenon yields pain-relieving effect for rheumatoid arthritis, low back pain, sciatic neuralgia, fibromyalgia, etc. Here we introduce medical and biological effects of mud-spa-bathing therapy for fibromyalgia other than pain relief, the changes of blood examination data, and the telomere length of circulating leukocytes. The enrolled 7 patients with fibromyalgia syndrome were hospitalized and were subject to daily mud bathing at 40 °C for 10 min for about a month. Then, their subjective pain was reduced to about a quarter in average. They also showed lowered serum triglyceride and C-reactive protein level, maintaining the levels of aspartate transaminase and creatine phosphokinase, and increases of the red blood cell count, the serum albumin level, and the serum LDL-cholesterol level in comparison with cases without mud-bathing therapy, suggesting that mud bathing prevents inflammation and muscle atrophy and improves nutritional condition in fibromyalgia. In addition, the analysis of telomere length of peripheral leukocytes revealed a trend of negative correlation between telomere shortening and laboratory data change of hemoglobin and serum albumin. These telomeric changes can be explained hypothetically by an effect of mud bathing extending life-span of circulating leukocytes.

Real time drilling mud gas response to small-moderate earthquakes in Wenchuan earthquake Scientific Drilling Hole-1 in SW China

NASA Astrophysics Data System (ADS)

Gong, Zheng; Li, Haibing; Tang, Lijun; Lao, Changling; Zhang, Lei; Li, Li

2017-05-01

We investigated the real time drilling mud gas of the Wenchuan earthquake Fault Scientific Drilling Hole-1 and their responses to 3918 small-moderate aftershocks happened in the Longmenshan fault zone. Gas profiles for Ar, CH4, He, 222Rn, CO2, H2, N2, O2 are obtained. Seismic wave amplitude, energy density and static strain are calculated to evaluate their power of influence to the drilling site. Mud gases two hours before and after each earthquake are carefully analyzed. In total, 25 aftershocks have major mud gas response, the mud gas concentrations vary dramatically immediately or minutes after the earthquakes. Different gas species respond to earthquakes in different manners according to local lithology encountered during the drill. The gas variations are likely controlled by dynamic stress changes, rather than static stress changes. They have the seismic energy density between 10-5 and 1.0 J/m3 whereas the static strain are mostly less than 10-8. We suggest that the limitation of the gas sources and the high hydraulic diffusivity of the newly ruptured fault zone could have inhibited the drilling mud gas behaviors, they are only able to respond to a small portion of the aftershocks. This work is important for the understanding of earthquake related hydrological changes.

Limitations of microbial hydrocarbon degradation at the Amon mud volcano (Nile deep-sea fan)

NASA Astrophysics Data System (ADS)

Felden, J.; Lichtschlag, A.; Wenzhöfer, F.; de Beer, D.; Feseker, T.; Pop Ristova, P.; de Lange, G.; Boetius, A.

2013-05-01

The Amon mud volcano (MV), located at 1250 m water depth on the Nile deep-sea fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulfate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition, and microbial activities over 3 yr, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulfide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. The low microbial activity in the hydrocarbon-vented areas of Amon MV is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer MV area is limited by hydrocarbon transport.

OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE - A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING

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

Arnis Judzis

2003-01-01

This document details the progress to date on the ''OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE -- A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING'' contract for the quarter starting October 2002 through December 2002. Even though we are awaiting the optimization portion of the testing program, accomplishments included the following: (1) Smith International participated in the DOE Mud Hammer program through full scale benchmarking testing during the week of 4 November 2003. (2) TerraTek acknowledges Smith International, BP America, PDVSA, and ConocoPhillips for cost-sharing the Smith benchmarking tests allowing extension of the contract to add to themore » benchmarking testing program. (3) Following the benchmark testing of the Smith International hammer, representatives from DOE/NETL, TerraTek, Smith International and PDVSA met at TerraTek in Salt Lake City to review observations, performance and views on the optimization step for 2003. (4) The December 2002 issue of Journal of Petroleum Technology (Society of Petroleum Engineers) highlighted the DOE fluid hammer testing program and reviewed last years paper on the benchmark performance of the SDS Digger and Novatek hammers. (5) TerraTek's Sid Green presented a technical review for DOE/NETL personnel in Morgantown on ''Impact Rock Breakage'' and its importance on improving fluid hammer performance. Much discussion has taken place on the issues surrounding mud hammer performance at depth conditions.« less

[CRISPR/CAS9, the King of Genome Editing Tools].

PubMed

Bannikov, A V; Lavrov, A V

2017-01-01

The discovery of CRISPR/Cas9 brought a hope for having an efficient, reliable, and readily available tool for genome editing. CRISPR/Cas9 is certainly easy to use, while its efficiency and reliability remain the focus of studies. The review describes the general principles of the organization and function of Cas nucleases and a number of important issues to be considered while planning genome editing experiments with CRISPR/Cas9. The issues include evaluation of the efficiency and specificity for Cas9, sgRNA selection, Cas9 variants designed artificially, and use of homologous recombination and nonhomologous end joining in DNA editing.

A novel association between p130Cas and resistance to the chemotherapeutic drug adriamycin in human breast cancer cells.

PubMed

Ta, Huy Q; Thomas, Keena S; Schrecengost, Randy S; Bouton, Amy H

2008-11-01

Resistance to chemotherapy remains a major obstacle for the treatment of breast cancer. Understanding the molecular mechanism(s) of resistance is crucial for the development of new effective therapies to treat this disease. This study examines the putative role of p130(Cas) (Cas) in resistance to the cytotoxic agent Adriamycin. High expression of Cas in primary breast tumors is associated with the failure to respond to the antiestrogen tamoxifen and poor prognosis, highlighting the potential clinical importance of this molecule. Here, we show a novel association between Cas and resistance to Adriamycin. We show that Cas overexpression renders MCF-7 breast cancer cells less sensitive to the growth inhibitory and proapoptotic effects of Adriamycin. The catalytic activity of the nonreceptor tyrosine kinase c-Src, but not the epidermal growth factor receptor, is critical for Cas-mediated protection from Adriamycin-induced death. The phosphorylation of Akt and extracellular signal-regulated kinase 1/2 (ERK1/2) is elevated in Cas-overexpressing cells treated with Adriamycin, whereas expression of the proapoptotic protein Bak is decreased. Conversely, Cas depletion in the more resistant T47D and MDA-MB-231 cell lines increases sensitivity to Adriamycin. Based on these data, we propose that Cas activates growth and survival pathways regulated by c-Src, Akt, and ERK1/2 that lead to the inhibition of mitochondrial-mediated apoptosis in the presence of Adriamycin. Because Cas is frequently expressed at high levels in breast cancers, these findings raise the possibility of resensitizing Cas-overexpressing tumors to chemotherapy through perturbation of Cas signaling pathways.

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

Phelps, J.; Hoopingarner, J.

Effective techniques have been developed from work on dozens of North Sea Wells to minimize the amount of oil-based mud discharged to the sea while maintaining acceptable levels of solids. Pressure to reduce pollution during the course of drilling prompted the development of these techniques. They involve personnel and optimization of mud system and procedures. Case histories demonstrate that regulations may be met with economical techniques using existing technology. The benefits of low solids content are widely known, and are a key part of any successful mud program. Good solids control should result in lower mud costs and better drillingmore » performance. Operators have specified high-performance shakers to accomplish this and have revised their mud programs with lower and lower allowable drilled solids percentages. This will pay off in certain areas. But with the U.K. Department of Energy regulations requiring cuttings oil discharge content (CODC) to be less than 150 g of oil/kg of dry solids discharge that went into effect Jan. 1, 1989, oil-loss control has a higher profile in the U.K. sector of the North Sea.« less

The use of mud as an alternative source for bioelectricity using microbial fuel cells

NASA Astrophysics Data System (ADS)

Darmawan, Raden; Widjaja, Arief; Juliastuti, Sri Rachmania; Hendrianie, Nuniek; Hidaya, Chanifah; Sari, Dessy Rosita; Suwito, Morimura, Shigeru; Tominaga, Masato

2017-05-01

Alternative energy sources to substitute fossil-based energy is expected, as the fossil energy reserves decreasing every day. Mud is considered to be economical as the material sources for generating the electricity where it could be found easily and abundantly in Indonesia. The existence of a lot of mud that contains organic material has great potential as a source of electrical energy using microbial fuel cells (MFCs). It provides a promising technology by degrading organic compounds to yield the sustainable energy. The different sampling sites were determined to find out the electricity production, i.e. mud from soil water, brackish water and sea water using an anode immersed of 10 cm2. The results suggest that the electricity generation of the three areas are 0.331, 0.327 and 0.398 V (in terms of voltage); 0.221, 0.050 and 0.325 mA (in terms of electric current), respectively. It is investigated that the mud obtained the sea water exhibits the highest power potential compared to that obtained from the brackish and soil water.

A double-regulated oncolytic adenovirus with improved safety for adenocarcinoma therapy

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

Wei, Na; Fan, Jun Kai; Gu, Jin Fa

2009-10-16

Safety and efficiency are equally important to be considered in developing oncolytic adenovirus. Previously, we have reported that ZD55, an oncolytic adenovirus with the deletion of E1B-55K gene, exhibited potent antitumor activity. In this study, to improve the safety of ZD55, we utilized MUC1 promoter to replace the native promoter of E1A on the basis of ZD55, and generated a double-regulated adenovirus, named MUD55. Our data demonstrated that the expression of early and late genes of MUD55 was both reduced in MUC1-negative cells, resulting in its stricter glandular-tumor selective progeny production. The cytopathic effect of MUD55 was about 10-fold lowermore » than mono-regulated adenovirus ZD55 or Ad.MUC1 in normal cells and not obviously attenuated in glandular tumor cells. Moreover, MUD55 showed the least liver toxicity when administrated by intravenous injection in nude mice. These results indicate that MUD55 could be a promising candidate for the treatment of adenocarcinoma.« less

Study of change of hydrophysical properties of bore mud in process of its utilization into man-induced soil

NASA Astrophysics Data System (ADS)

Gaevaya, E. V.; Bogaychuk, Y. E.; Tarasova, S. S.; Skipin, L. N.; Zaharova, E. V.

2017-10-01

The article considers the results of studies of the chemical and granulometric content and the factor of bore mud filtration in the process of its utilization. When the phosphogypsum is added, hydrophysical properties of the bore mud improve. At the same time, gradation of soil from the water-proof to weakly permeable takes place. This phenomenon is connected with recovery of filterability at the expense of ion-exchange reaction and a decrease of the silt fraction content in the bore mud. During the adding of phosphogypsum in the bore mud, pH decreased and made up 7.6-7.8 U. The decrease of the concentration of chloride-ions and sulphate-ions took place at the expense of replacement of Na+ by cations of Ca2+ that contributed to the formation of the water-stable structure with good filterability. The content of total forms of heavy metals in man-induced soil was lower than MAC (APC) for the loams. Man-induced soil has a V class of danger for the surrounding environment.