Sample records for assemblies combining sedimentation
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Preferential assembly of heteromeric kainate and AMPA receptor amino terminal domains
Lomash, Suvendu; Chittori, Sagar; Glasser, Carla
2017-01-01
Ion conductivity and the gating characteristics of tetrameric glutamate receptor ion channels are determined by their subunit composition. Competitive homo- and hetero-dimerization of their amino-terminal domains (ATDs) is a key step controlling assembly. Here we measured systematically the thermodynamic stabilities of homodimers and heterodimers of kainate and AMPA receptors using fluorescence-detected sedimentation velocity analytical ultracentrifugation. Measured affinities span many orders of magnitude, and complexes show large differences in kinetic stabilities. The association of kainate receptor ATD dimers is generally weaker than the association of AMPA receptor ATD dimers, but both show a general pattern of increased heterodimer stability as compared to the homodimers of their constituents, matching well physiologically observed receptor combinations. The free energy maps of AMPA and kainate receptor ATD dimers provide a framework for the interpretation of observed receptor subtype combinations and possible assembly pathways. PMID:29058671
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Preferential assembly of heteromeric kainate and AMPA receptor amino terminal domains.
Zhao, Huaying; Lomash, Suvendu; Chittori, Sagar; Glasser, Carla; Mayer, Mark L; Schuck, Peter
2017-10-23
Ion conductivity and the gating characteristics of tetrameric glutamate receptor ion channels are determined by their subunit composition. Competitive homo- and hetero-dimerization of their amino-terminal domains (ATDs) is a key step controlling assembly. Here we measured systematically the thermodynamic stabilities of homodimers and heterodimers of kainate and AMPA receptors using fluorescence-detected sedimentation velocity analytical ultracentrifugation. Measured affinities span many orders of magnitude, and complexes show large differences in kinetic stabilities. The association of kainate receptor ATD dimers is generally weaker than the association of AMPA receptor ATD dimers, but both show a general pattern of increased heterodimer stability as compared to the homodimers of their constituents, matching well physiologically observed receptor combinations. The free energy maps of AMPA and kainate receptor ATD dimers provide a framework for the interpretation of observed receptor subtype combinations and possible assembly pathways.
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Jochum, Lara M.; Chen, Xihan; Lever, Mark A.; Loy, Alexander; Jørgensen, Bo Barker; Schramm, Andreas
2017-01-01
ABSTRACT Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community. PMID:28939599
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Structure and assembly mechanism for heteromeric kainate receptors.
Kumar, Janesh; Schuck, Peter; Mayer, Mark L
2011-07-28
Native glutamate receptor ion channels are tetrameric assemblies containing two or more different subunits. NMDA receptors are obligate heteromers formed by coassembly of two or three divergent gene families. While some AMPA and kainate receptors can form functional homomeric ion channels, the KA1 and KA2 subunits are obligate heteromers which function only in combination with GluR5-7. The mechanisms controlling glutamate receptor assembly involve an initial step in which the amino terminal domains (ATD) assemble as dimers. Here, we establish by sedimentation velocity that the ATDs of GluR6 and KA2 coassemble as a heterodimer of K(d) 11 nM, 32,000-fold lower than the K(d) for homodimer formation by KA2; we solve crystal structures for the GluR6/KA2 ATD heterodimer and heterotetramer assemblies. Using these structures as a guide, we perform a mutant cycle analysis to probe the energetics of assembly and show that high-affinity ATD interactions are required for biosynthesis of functional heteromeric receptors. Copyright © 2011 Elsevier Inc. All rights reserved.
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Lu, Yanling; Longman, Emma; Davis, Kenneth G.; Ortega, Álvaro; Grossmann, J. Günter; Michaelsen, Terje E.; de la Torre, José García; Harding, Stephen E.
2006-01-01
Crystallohydrodynamics describes the domain orientation in solution of antibodies and other multidomain protein assemblies where the crystal structures may be known for the domains but not the intact structure. The approach removes the necessity for an ad hoc assumed value for protein hydration. Previous studies have involved only the sedimentation coefficient leading to considerable degeneracy or multiplicity of possible models for the conformation of a given protein assembly, all agreeing with the experimental data. This degeneracy can be considerably reduced by using additional solution parameters. Conformation charts are generated for the three universal (i.e., size-independent) shape parameters P (obtained from the sedimentation coefficient or translational diffusion coefficient), ν (from the intrinsic viscosity), and G (from the radius of gyration), and calculated for a wide range of plausible orientations of the domains (represented as bead-shell ellipsoidal models derived from their crystal structures) and after allowance for any linker or hinge regions. Matches are then sought with the set of functions P, ν, and G calculated from experimental data (allowing for experimental error). The number of solutions can be further reduced by the employment of the Dmax parameter (maximum particle dimension) from x-ray scattering data. Using this approach we are able to reduce the degeneracy of possible solution models for IgG3 to a possible representative structure in which the Fab domains are directed away from the plane of the Fc domain, a structure in accord with the recognition that IgG3 is the most efficient complement activator among human IgG subclasses. PMID:16766619
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Whole blood analysis rotor assembly having removable cellular sedimentation bowl
Burtis, C.A.; Johnson, W.F.
1975-08-26
A rotor assembly for performing photometric analyses using whole blood samples is described. Following static loading of a gross blood sample within a centrally located, removable, cell sedimentation bowl, the red blood cells in the gross sample are centrifugally separated from the plasma, the plasm displaced from the sedimentation bowl, and measured subvolumes of plasma distributed to respective sample analysis cuvettes positioned in an annular array about the rotor periphery. Means for adding reagents to the respective cuvettes are also described. (auth)
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A multi-sensor oceanographic measurement system for coastal environments
Martini, Marinna A.; Strahle, William J.
1993-01-01
An instrument system has been developed for long-term sediment transport studies that uses a modular design to combine off the shelf components into a complete and flexible package. A common data storage format is used in each instrument system so that the same hardware can be assembled in different ways to address specific scientific studies with minimal engineering support and modification. Three systems have been constructed and successfully deployed to date in two different coastal environments.
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Assembly of the epithelial Na+ channel evaluated using sucrose gradient sedimentation analysis.
Cheng, C; Prince, L S; Snyder, P M; Welsh, M J
1998-08-28
Three subunits, alpha, beta, and gamma, contribute to the formation of the epithelial Na+ channel. To investigate the oligomeric assembly of the channel complex, we used sucrose gradient sedimentation analysis to determine the sedimentation properties of individual subunits and heteromultimers comprised of multiple subunits. When the alpha subunit was expressed alone, it first formed an oligomeric complex with a sedimentation coefficient of 11 S, and then generated a higher order multimer of 25 S. In contrast, individual beta and gamma subunits predominately assembled into 11 S complexes. We obtained similar results with expression in cells and in vitro. When we co-expressed beta with alpha or with alpha plus gamma, the beta subunit assembled into a 25 S complex. Glycosylation of the alpha subunit was not required for assembly into a 25 S complex. We found that the alpha subunit formed intra-chain disulfide bonds. Although such bonds were not required to generate an oligomeric complex, under nonreducing conditions the alpha subunit formed a complex that migrated more homogeneously at 25 S. This suggests that intra-chain disulfide bonds may stabilize the complex. These data suggest that the epithelial Na+ channel subunits form high order oligomeric complexes and that the alpha subunit contains the information that facilitates such formation. Interestingly, the ability of the alpha, but not the beta or gamma, subunit to assemble into a 25 S homomeric complex correlates with the ability of these subunits to generate functional channels when expressed alone.
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Kuniyasu, Akihiko; Kaneko, Kazuyoshi; Kawahara, Kohichi; Nakayama, Hitoshi
2003-09-25
Cardiac ATP-sensitive K(+) (K(ATP)) channels are proposed to contribute to cardio-protection and ischemic preconditioning. Although mRNAs for all subunits of K(ATP) channels (Kir6.0 and sulfonylurea receptors SURs) were detected in hearts, subcellular localization of their proteins and the subunit combination are not well elucidated. We address these questions in rat hearts, using anti-peptide antibodies raised against each subunit. By immunoblot analysis, all of the subunits were detected in microsomal fractions including sarcolemmal membranes, while they were not detected in mitochondrial fractions at all. Immunoprecipitation and sucrose gradient sedimentation of the digitonin-solubilized microsomes indicated that Kir6.2 exclusively assembled with SUR2A. The molecular mass of the Kir6.2-SUR2A complex estimated by sucrose sedimentation was 1150 kDa, significantly larger than the calculated value for (Kir6.2)(4)-(SUR2A)(4), suggesting a potential formation of micellar complex with digitonin but no indication of hybrid channel formation under the conditions. These findings provide additional information on the structural and functional relationships of cardiac K(ATP) channel proteins involving subcellular localization and roles for cardioprotection and ischemic preconditioning.
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Chen, Yuanbo; Hu, Yongyou; Guo, Qian; Yan, Jia; Wu, Wenjin
2016-09-01
Cations had great influence on the self-assembly of rhamnolipid, which in turn affected the fate of triclosan. The migration of triclosan from sediment to water benefited its biodegradation but it could be transformed into more toxic compounds. To regulate the fate of triclosan and reduce environmental risks extremely, the effect of four common cations in surface water (Na(+)/K(+)/Ca(2+)/Mg(2+)) on the solubilization/deposition of triclosan in sediment-water-rhamnolipid system was investigated. The interaction among cations, triclosan and rhamnolipid was explored based on self-assembly of rhamnolipid and water solubility of triclosan in rhamnolipid solutions. Results showed that cations had little influence on the fate of triclosan in the absence of rhamnolipid. Cations, especially Ca(2+)/Mg(2+), reduced the critical micelle concentration, micellar size and zeta potential of rhamnolipid solutions. The changes in self-assembly of rhamnolipid with different cations led to the difference of residual rhamnolipid concentration in water, which was nearly invariant with 0.01 M Na(+)/K(+) while decreased significantly with 0.01 M Ca(2+)/Mg(2+). Consequently, water solubility of triclosan in rhamnolipid solutions increased with the addition of Na(+)/K(+) whereas decreased with Ca(2+)/Mg(2+). In sediment-water- rhamnolipid system, triclosan was slightly solubilized from sediment to water with Na(+)/K(+) while deposited in sediment with Ca(2+)/Mg(2+). These findings provided an alternative application of rhamnolipid for the remediation of triclosan-polluted sediment. Copyright © 2016. Published by Elsevier Ltd.
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Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.
2018-01-01
The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012
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Design and initial evaluation of a portable in situ runoff and sediment monitoring device
NASA Astrophysics Data System (ADS)
Sun, Tao; Cruse, Richard M.; Chen, Qiang; Li, Hao; Song, Chunyu; Zhang, Xingyi
2014-11-01
An inexpensive portable runoff and sediment monitoring device (RSMD) requiring no external electric power was developed for measuring water runoff and associated sediment loss from field plots ranging from 0.005 to 0.1 ha. The device consists of runoff gauge, sediment mixing and sectional subsampling assemblies. The runoff hydrograph is determined using a calibrated tipping bucket. The sediment mixing assembly minimizes fluid splash while mixing the runoff water/sediment mixture prior to subsampling this material. Automatic flow-proportional sampling utilizes mechanical power supplied by the tipping bucket action, with power transmitted to the sample collection assembly via the tipping bucket pivot bar. Runoff is well-mixed and subdivided twice before subsamples are collected for analysis. The resolution of this device for a 100 m2 plot is 0.025 mm of runoff; the device is able to capture maximum flow rates up to 82 mm h-1 in a plot of the same dimension. Calibration results indicated the maximum error is 2.1% for estimating flow rate and less than 10% for sediment concentration in most of the flow range. The RSMD was assessed by measuring field runoff and soil loss from different tillage and slope treatments for a single natural rainfall event. Results were in close agreement with those in published literature, giving additional evidence that this device is performing acceptably well. The RSMD is uniquely adapted for a wide range of field sites, especially for those without electric power, making it a useful tool for studying soil management strategies.
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Microbial community assembly and evolution in subseafloor sediment.
Starnawski, Piotr; Bataillon, Thomas; Ettema, Thijs J G; Jochum, Lara M; Schreiber, Lars; Chen, Xihan; Lever, Mark A; Polz, Martin F; Jørgensen, Bo B; Schramm, Andreas; Kjeldsen, Kasper U
2017-03-14
Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.
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NASA Astrophysics Data System (ADS)
Hernsdorf, A. W.; Amano, Y.; Suzuki, Y.; Ise, K.; Thomas, B. C.; Banfield, J. F.
2015-12-01
Terrestrial sediments are an important global reservoir for methane. Microorganisms in the deep subsurface play a critical role in the methane cycle, yet much remains to be learned about their diversity and metabolisms. To provide more comprehensive insight into the microbiology of the methane cycle in the deep subsurface, we conducted a genome-resolved study of samples collected from the Horonobe Underground Research Laboratory (HURL), Japan. Groundwater samples were obtained from three boreholes from a depth range of between 140 m and 250 m in two consecutive years. Groundwater was filtered and metagenomic DNA extracted and sequenced, and the sequence data assembled. Based on the sequences of phylogenetically informative genes on the assembled fragments, we detected a high degree of overlap in community composition across a vertical transect within one borehole at the two sampling times. However, there was comparatively little similarity observed among communities across boreholes. Spatial and temporal abundance patterns were used in combination with tetranucleotide signatures of assembled genome fragments to bin the data and reconstruct over 200 unique draft genomes, of which 137 are considered to be of high quality (>90% complete). The deepest samples from one borehole were highly dominated by an archaeon identified as ANME-2D; this organism was also present at lower abundance in all other samples from that borehole. Also abundant in these microbial communities were novel members of the Gammaproteobacteria, Saccharibacteria (TM7) and Tenericute phyla. Notably, a ~2 Mbp draft genome for the ANME-2D archaeon was reconstructed. As expected, the genome encodes all of the genes predicted to be involved in the reverse methanogenesis pathway. In contrast with the previously reported ANME2-D genome, the HURL ANME-2D genome lacks the capacity to reduce nitrate. However, we identified many multiheme cytochromes with closest similarity to those of the known Fe-reducing/oxidizing archaeon Ferroglobus placidus. Thus, we suggest that ANME2-D may couple methane oxidation to reduction of ferric iron minerals in the sediment and may be generally important as a link between the iron and methane cycles in deep subsurface environments. Such information has important implications for modeling the global carbon cycle.
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The geomorphic legacy of water and sediment control structures in a semiarid rangeland watershed
USDA-ARS?s Scientific Manuscript database
An inventory of water and sediment control structures remnant of historic cattle ranching was assembled for the Buenos Aires National Wildlife Refuge (BANWR) in southern Arizona, USA. An assessment of structural condition based on aerial imagery identified headcut initiation and channel incision as...
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Sensing Shallow Seafloor and Sediment Properties, Recent History
2008-09-01
instances, larger samplers, i.e. box corers, can be further subsampled with small push-in tubes , yielding relatively undisturbed specimens. Corers...sediment within the sampling tube 3 during retrieval. Generally, common gravity corers can retrieve up to 5m (in softer sediments) of soil, whereas... tube that can be generated. Vibro-corers are similar to the gravity corers but have a motorized unit added to the top of the assembly, generating an
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MYBPH inhibits NM IIA assembly via direct interaction with NMHC IIA and reduces cell motility
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hosono, Yasuyuki; Usukura, Jiro; Yamaguchi, Tomoya
2012-11-09
Highlights: Black-Right-Pointing-Pointer MYBPH inhibits NMHC IIA assembly and cell motility. Black-Right-Pointing-Pointer MYBPH interacts to assembly-competent NM IIA. Black-Right-Pointing-Pointer MYBPH inhibits RLC and NMHC IIA, independent components of NM IIA. -- Abstract: Actomyosin filament assembly is a critical step in tumor cell migration. We previously found that myosin binding protein H (MYBPH) is directly transactivated by the TTF-1 lineage-survival oncogene in lung adenocarcinomas and inhibits phosphorylation of the myosin regulatory light chain (RLC) of non-muscle myosin IIA (NM IIA) via direct interaction with Rho kinase 1 (ROCK1). Here, we report that MYBPH also directly interacts with an additional molecule, non-muscle myosinmore » heavy chain IIA (NMHC IIA), which was found to occur between MYBPH and the rod portion of NMHC IIA. MYBPH inhibited NMHC IIA assembly and reduced cell motility. Conversely, siMYBPH-induced increased motility was partially, yet significantly, suppressed by blebbistatin, a non-muscle myosin II inhibitor, while more profound effects were attained by combined treatment with siROCK1 and blebbistatin. Electron microscopy observations showed well-ordered paracrystals of NMHC IIA reflecting an assembled state, which were significantly less frequently observed in the presence of MYBPH. Furthermore, an in vitro sedimentation assay showed that a greater amount of NMHC IIA was in an unassembled state in the presence of MYBPH. Interestingly, treatment with a ROCK inhibitor that impairs transition of NM IIA from an assembly-incompetent to assembly-competent state reduced the interaction between MYBPH and NMHC IIA, suggesting that MYBPH has higher affinity to assembly-competent NM IIA. These results suggest that MYBPH inhibits RLC and NMHC IIA, independent components of NM IIA, and negatively regulates actomyosin organization at 2 distinct steps, resulting in firm inhibition of NM IIA assembly.« less
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Zhang, Y.-S.; Collins, A.L.; Horowitz, A.J.
2012-01-01
Reliable information on catchment scale suspended sediment sources is required to inform the design of management strategies for helping abate the numerous environmental issues associated with enhanced sediment mobilization and off-site loadings. Since sediment fingerprinting techniques avoid many of the logistical constraints associated with using more traditional indirect measurement methods at catchment scale, such approaches have been increasingly reported in the international literature and typically use data sets collected specifically for sediment source apportionment purposes. There remains scope for investigating the potential for using geochemical data sets assembled by routine monitoring programmes to fingerprint sediment provenance. In the United States, routine water quality samples are collected as part of the US Geological Survey's revised National Stream Quality Accounting Network programme. Accordingly, the geochemistry data generated from these samples over a 10-year period (1996-2006) were used as the basis for a fingerprinting exercise to assess the key tributary sub-catchment spatial sources of contemporary suspended sediment transported by the Ohio River. Uncertainty associated with the spatial source estimates was quantified using a Monte Carlo approach in conjunction with mass balance modelling. Relative frequency weighted means were used as an alternative way of summarizing the spatial source contributions, thereby avoiding the need to use confidence limits. The results should be interpreted in the context of the routine, but infrequent nature, of the suspended sediment samples used to assemble geochemistry as a basis for the sourcing exercise. Nonetheless, the study demonstrates how routine monitoring samples can be used to provide some preliminary information on sediment provenance in large drainage basins. ?? 2011 John Wiley & Sons, Ltd.
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Laboratory measurements of grain-bedrock interactions using inertial sensors.
NASA Astrophysics Data System (ADS)
Maniatis, Georgios; Hoey, Trevor; Hodge, Rebecca; Valyrakis, Manousos; Drysdale, Tim
2016-04-01
Sediment transport in steep mountain streams is characterized by the movement of coarse particles (diameter c.100 mm) over beds that are not fully sediment-covered. Under such conditions, individual grain dynamics become important for the prediction of sediment movement and subsequently for understanding grain-bedrock interaction. Technological advances in micro-mechanical-electrical systems now provide opportunities to measure individual grain dynamics and impact forces from inside the sediments (grain inertial frame of reference) instead of trying to infer them indirectly from water flow dynamics. We previously presented a new prototype sensor specifically developed for monitoring sediment transport [Maniatis et al. EGU 2014], and have shown how the definition of the physics of the grain using the inertial frame and subsequent derived measurements which have the potential to enhance the prediction of sediment entrainment [Maniatis et al. 2015]. Here we present the latest version of this sensor and we focus on beginning of the cessation of grain motion: the initial interaction with the bed after the translation phase. The sensor is housed in a spherical case, diameter 80mm, and is constructed using solid aluminum (density = 2.7 kg.m-3) after detailed 3D-CAD modelling. A complete Inertial Measurement Unit (a combination of micro- accelerometer, gyroscope and compass) was placed at the center of the mass of the assembly, with measurement ranges of 400g for acceleration, and 1200 rads/sec for angular velocity. In a 0.9m wide laboratory flume, bed slope = 0.02, the entrainment threshold of the sensor was measured, and the water flow was then set to this value. The sensor was then rolled freely from a static cylindrical bar positioned exactly on the surface of the flowing water. As the sensor enters the flow we record a very short period of transport (1-1.5 sec) followed by the impact on the channel bed. The measured Total Kinetic Energy (Joules) includes the translational energy component of transport (defined as a function of 3-dimensional translational velocity) as well as the rotational component (a function of the 3-axis angular velocity measurements from the gyroscope) which is neglected in the majority of contemporary saltation models. The results suggest that, for this grain scale, the magnitude of the impact of mobile grains on the bed is primarily controlled by their inertia. References Maniatis et al. 2014 EGU General assembly http://meetingorganizer.copernicus.org/EGU2014/EGU2014-12829.pdf Maniatis et. al 2015: "CALCULATION OF EXPLICIT PROBABILITY OF ENTRAINMENT BASED ON INERTIAL ACCELERATION MEASUREMENTS" J. Hydraulic Engineering, Under review.
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NASA Astrophysics Data System (ADS)
Fu, Yanan; Xie, Honglan; Deng, Biao; Du, Guohao; Xiao, Tiqiao
2017-06-01
The floatage self-assembly method was introduced with mixed solvent as the medium of polystyrene sphere suspension to fabricate the colloidal crystal. The three dimensional (3D) void system of the colloidal crystal was noninvasively characterized by synchrotron radiation phase-contrast computed tomography, and the quantitative image analysis was implemented aiming to the polystyrene sphere colloidal crystal. Comparing with gravity sedimentation method, the three samples fabricated from floatage self-assembly with mixed solvents have the lowest porosity, and when ethylene glycol and water were mixed with ratio of 1:1, the lowest porosity of 27.49% could be achieved, that has been very close to the minimum porosity of ordered 3D monodisperse sphere array (26%). In single slices, the porosities and fractal dimension for the voids were calculated. The results showed that two factors would significantly influence the porosity of the whole colloidal crystal: the first deposited sphere layer's orderliness and the sedimentation speed of the spheres. The floatage self-assembly could induce a stable close-packing process, resulted from the powerful nucleation force-lateral capillary force coupled with the mixed solvent to regulate the floating upward speed for purpose of matching the assembly rate.
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Growing And Assembling Cells Into Tissues
NASA Technical Reports Server (NTRS)
Wolf, David A.; Schwarz, Ray P.; Lewis, Marian L.; Cross, John H.; Huls, M. Helen
1990-01-01
Laboratory process for growth and assembly of mammalian cells into tissue-like masses demonstrated with hamster and rat cells. New process better able to provide culture environment with reduced fluid shear stress, freedom for three-dimensional spatial orientation of particles suspended in culture medium, and localization of particles of different or similar sedimentation properties in similar spatial region.
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7 CFR 58.634 - Assembling and combining mix ingredients.
Code of Federal Regulations, 2014 CFR
2014-01-01
... 7 Agriculture 3 2014-01-01 2014-01-01 false Assembling and combining mix ingredients. 58.634... Service 1 Operations and Operating Procedures § 58.634 Assembling and combining mix ingredients. The assembling and combining of mix ingredients for processing shall be in accordance with clean and sanitary...
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7 CFR 58.634 - Assembling and combining mix ingredients.
Code of Federal Regulations, 2012 CFR
2012-01-01
... 7 Agriculture 3 2012-01-01 2012-01-01 false Assembling and combining mix ingredients. 58.634... Service 1 Operations and Operating Procedures § 58.634 Assembling and combining mix ingredients. The assembling and combining of mix ingredients for processing shall be in accordance with clean and sanitary...
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7 CFR 58.634 - Assembling and combining mix ingredients.
Code of Federal Regulations, 2013 CFR
2013-01-01
... 7 Agriculture 3 2013-01-01 2013-01-01 false Assembling and combining mix ingredients. 58.634... Service 1 Operations and Operating Procedures § 58.634 Assembling and combining mix ingredients. The assembling and combining of mix ingredients for processing shall be in accordance with clean and sanitary...
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Assembly of the Herpes Simplex Virus Capsid: Preformed Triplexes Bind to the Nascent Capsid
Spencer, Juliet V.; Newcomb, William W.; Thomsen, Darrell R.; Homa, Fred L.; Brown, Jay C.
1998-01-01
The herpes simplex virus type 1 (HSV-1) capsid is a T=16 icosahedral shell that forms in the nuclei of infected cells. Capsid assembly also occurs in vitro in reaction mixtures created from insect cell extracts containing recombinant baculovirus-expressed HSV-1 capsid proteins. During capsid formation, the major capsid protein, VP5, and the scaffolding protein, pre-VP22a, condense to form structures that are extended into procapsids by addition of the triplex proteins, VP19C and VP23. We investigated whether triplex proteins bind to the major capsid-scaffold protein complexes as separate polypeptides or as preformed triplexes. Assembly products from reactions lacking one triplex protein were immunoprecipitated and examined for the presence of the other. The results showed that neither triplex protein bound unless both were present, suggesting that interaction between VP19C and VP23 is required before either protein can participate in the assembly process. Sucrose density gradient analysis was employed to determine the sedimentation coefficients of VP19C, VP23, and VP19C-VP23 complexes. The results showed that the two proteins formed a complex with a sedimentation coefficient of 7.2S, a value that is consistent with formation of a VP19C-VP232 heterotrimer. Furthermore, VP23 was observed to have a sedimentation coefficient of 4.9S, suggesting that this protein exists as a dimer in solution. Deletion analysis of VP19C revealed two domains that may be required for attachment of the triplex to major capsid-scaffold protein complexes; none of the deletions disrupted interaction of VP19C with VP23. We propose that preformed triplexes (VP19C-VP232 heterotrimers) interact with major capsid-scaffold protein complexes during assembly of the HSV-1 capsid. PMID:9557680
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Different erosion characteristics of sediment deposits in combined and storm sewers.
Xu, Zuxin; Wu, Jun; Li, Huaizheng; Liu, Zhenghua; Chen, Keli; Chen, Hao; Xiong, Lijun
2017-04-01
To investigate the different erosion patterns of sediments in combined and storm sewers, sediments from three separate sewer systems and two combined sewer systems in urban Shanghai were collected for the flushing experiments. These experiments were conducted with different consolidation periods and shear velocities. As the consolidation period increases, dissolved oxygen exhibits a positive effect on the microbial transformations of organic substrates. Potential structural changes and separations of the surface and bottom layers of sediments are observed. The results also reveal that the organic matter, particle size and moisture have different effects on the erosion resistance of sediments. Furthermore, illicit connections behaved as an important factor affecting the viscosity and static friction force of particles, which directly alter the erosion resistance of sewer sediments.
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Zhao, Huaying; Fu, Yan; Glasser, Carla; Andrade Alba, Eric J; Mayer, Mark L; Patterson, George; Schuck, Peter
2016-01-01
The dynamic assembly of multi-protein complexes underlies fundamental processes in cell biology. A mechanistic understanding of assemblies requires accurate measurement of their stoichiometry, affinity and cooperativity, and frequently consideration of multiple co-existing complexes. Sedimentation velocity analytical ultracentrifugation equipped with fluorescence detection (FDS-SV) allows the characterization of protein complexes free in solution with high size resolution, at concentrations in the nanomolar and picomolar range. Here, we extend the capabilities of FDS-SV with a single excitation wavelength from single-component to multi-component detection using photoswitchable fluorescent proteins (psFPs). We exploit their characteristic quantum yield of photo-switching to imprint spatio-temporal modulations onto the sedimentation signal that reveal different psFP-tagged protein components in the mixture. This novel approach facilitates studies of heterogeneous multi-protein complexes at orders of magnitude lower concentrations and for higher-affinity systems than previously possible. Using this technique we studied high-affinity interactions between the amino-terminal domains of GluA2 and GluA3 AMPA receptors. DOI: http://dx.doi.org/10.7554/eLife.17812.001 PMID:27436096
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Denadai, Angelo M L; De Sousa, Frederico B; Passos, Joel J; Guatimosim, Fernando C; Barbosa, Kirla D; Burgos, Ana E; de Oliveira, Fernando Castro; da Silva, Jeann C; Neves, Bernardo R A; Mohallem, Nelcy D S; Sinisterra, Rubén D
2012-01-01
Organic-inorganic magnetic hybrid materials (MHMs) combine a nonmagnetic and a magnetic component by means of electrostatic interactions or covalent bonds, and notable features can be achieved. Herein, we describe an application of a self-assembled material based on ferrite associated with β-cyclodextrin (Fe-Ni/Zn/βCD) at the nanoscale level. This MHM and pure ferrite (Fe-Ni/Zn) were used as an adsorbent system for Cr(3+) and Cr(2)O(7) (2-) ions in aqueous solutions. Prior to the adsorption studies, both ferrites were characterized in order to determine the particle size distribution, morphology and available binding sites on the surface of the materials. Microscopy analysis demonstrated that both ferrites present two different size domains, at the micro- and nanoscale level, with the latter being able to self-assemble into larger particles. Fe-Ni/Zn/βCD presented smaller particles and a more homogeneous particle size distribution. Higher porosity for this MHM compared to Fe-Ni/Zn was observed by Brunauer-Emmett-Teller isotherms and positron-annihilation-lifetime spectroscopy. Based on the pKa values, potentiometric titrations demonstrated the presence of βCD in the inorganic matrix, indicating that the lamellar structures verified by transmission electronic microscopy can be associated with βCD assembled structures. Colloidal stability was inferred as a function of time at different pH values, indicating the sedimentation rate as a function of pH. Zeta potential measurements identified an amphoteric behavior for the Fe-Ni/Zn/βCD, suggesting its better capability to remove ions (cations and anions) from aqueous solutions compared to that of Fe-Ni/Zn.
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NASA Astrophysics Data System (ADS)
Costa, A.; Stutenbecker, L.; Anghileri, D.; Bakker, M.; Lane, S. N.; Molnar, P.; Schlunegger, F.
2017-12-01
In Alpine basins, sediment production and transfer is increasingly affected by climate change and human activities, specifically hydropower exploitation. Changes in sediment sources and pathways significantly influence basin management, biodiversity and landscape evolution. We explore the dynamics of sediment sources in a partially glaciated and highly regulated Alpine basin, the Borgne basin, by combining geochemical fingerprinting with the modelling of erosion and sediment transfer. The Borgne basin in southwest Switzerland is composed of three main litho-tectonic units, which we characterised following a tributary-sampling approach from lithologically characteristic sub-basins. We analysed bulk geochemistry using lithium borate fusion coupled with ICP-ES, and we used it to discriminate the three lithologic sources using statistical methods. Finally, we applied a mixing model to estimate the relative contributions of the three sources to the sediment sampled at the outlet. We combine results of the sediment fingerprinting with simulations of a spatially distributed conceptual model for erosion and transport of fine sediment. The model expresses sediment erosion by differentiating the contributions of erosional processes driven by erosive rainfall, snowmelt, and icemelt. Soil erodibility is accounted for as function of land-use and sediment fluxes are linearly convoluted to the outlet by sediment transfer rates for hillslope and river cells, which are a function of sediment connectivity. Sediment connectivity is estimated on the basis of topographic-hydraulic connectivity, flow duration associated with hydropower flow abstraction and permanent storage in hydropower reservoirs. Sediment fingerprinting at the outlet of the Borgne shows a consistent dominance (68-89%) of material derived from the uppermost, highly glaciated reaches, while contributions of the lower part (10-25%) and middle part (1-16%), where rainfall erosion is predominant, are minor. This result is confirmed by the model simulation which shows that, despite the large flow abstraction (about 90%), the upstream reaches contribute the most of the sediments. This study shows how combining geochemical techniques and sediment erosion models provides insight in the dynamics of sediment sources.
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Nucleolar proteins Bfr2 and Enp2 interact with DEAD-box RNA helicase Dbp4 in two different complexes
Soltanieh, Sahar; Lapensée, Martin; Dragon, François
2014-01-01
Different pre-ribosomal complexes are formed during ribosome biogenesis, and the composition of these complexes is highly dynamic. Dbp4, a conserved DEAD-box RNA helicase implicated in ribosome biogenesis, interacts with nucleolar proteins Bfr2 and Enp2. We show that, like Dbp4, Bfr2 and Enp2 are required for the early processing steps leading to the production of 18S ribosomal RNA. We also found that Bfr2 and Enp2 associate with the U3 small nucleolar RNA (snoRNA), the U3-specific protein Mpp10 and various pre-18S ribosomal RNA species. Thus, we propose that Bfr2, Dbp4 and Enp2 are components of the small subunit (SSU) processome, a large complex of ∼80S. Sucrose gradient sedimentation analyses indicated that Dbp4, Bfr2 and Enp2 sediment in a peak of ∼50S and in a peak of ∼80S. Bfr2, Dbp4 and Enp2 associate together in the 50S complex, which does not include the U3 snoRNA; however, they associate with U3 snoRNA in the 80S complex (SSU processome). Immunoprecipitation experiments revealed that U14 snoRNA associates with Dbp4 in the 50S complex, but not with Bfr2 or Enp2. The assembly factor Tsr1 is not part of the ‘50S’ complex, indicating this complex is not a pre-40S ribosome. A combination of experiments leads us to propose that Bfr2, Enp2 and Dbp4 are recruited at late steps during assembly of the SSU processome. PMID:24357410
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In-situ Adsorption-Biological Combined Technology Treating Sediment Phosphorus in all Fractions
NASA Astrophysics Data System (ADS)
Zhang, Y.; Wang, C.; He, F.; Liu, B.; Xu, D.; Xia, S.; Zhou, Q.; Wu, Z.
2016-07-01
The removal efficiency of sediment phosphorus (P) in all fractions with in-situ adsorption-biological combined technology was studied in West Lake, Hangzhou, China. The removal amounts of sediment Ca-P, Fe/Al-P, IP, OP and TP by the combined effect of PCFM (Porous ceramic filter media) and V. spiralis was 61 mg/kg, 249 mg/kg, 318 mg/kg, 85 mg/kg and 416 mg/kg, respectively, and the corresponding removing rate reached 10.5%, 44.6%, 27.5%, 30.6% and 29.2%. This study suggested that the combination of PCFM and V. spiralis could achieve a synergetic sediment P removal because the removal rates of the combinations were higher than the sum of that of PCFM and macrophytes used separately. From analysis of sediment microbial community and predicted function, we found that the combined PCFM and V. spiralis enhanced the function of P metabolism by increasing specific genus that belong to phylum Firmicutes and Nitrospirae. Thus it can be seen the in-situ adsorption-biological combined technology could be further applied to treat internal P loading in eutrophic waters.
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In-situ Adsorption-Biological Combined Technology Treating Sediment Phosphorus in all Fractions
Zhang, Y.; Wang, C.; He, F.; Liu, B.; Xu, D.; Xia, S.; Zhou, Q.; Wu, Z.
2016-01-01
The removal efficiency of sediment phosphorus (P) in all fractions with in-situ adsorption-biological combined technology was studied in West Lake, Hangzhou, China. The removal amounts of sediment Ca-P, Fe/Al-P, IP, OP and TP by the combined effect of PCFM (Porous ceramic filter media) and V. spiralis was 61 mg/kg, 249 mg/kg, 318 mg/kg, 85 mg/kg and 416 mg/kg, respectively, and the corresponding removing rate reached 10.5%, 44.6%, 27.5%, 30.6% and 29.2%. This study suggested that the combination of PCFM and V. spiralis could achieve a synergetic sediment P removal because the removal rates of the combinations were higher than the sum of that of PCFM and macrophytes used separately. From analysis of sediment microbial community and predicted function, we found that the combined PCFM and V. spiralis enhanced the function of P metabolism by increasing specific genus that belong to phylum Firmicutes and Nitrospirae. Thus it can be seen the in-situ adsorption-biological combined technology could be further applied to treat internal P loading in eutrophic waters. PMID:27418242
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Enhancing the bioremediation by harvesting electricity from the heavily contaminated sediments.
Yang, Yonggang; Lu, Zijiang; Lin, Xunke; Xia, Chunyu; Sun, Guoping; Lian, Yingli; Xu, Meiying
2015-03-01
To test the long-term applicability of scaled-up sediment microbial fuel cells (SMFCs) in simultaneous bioremediation of toxic-contaminated sediments and power-supply for electronic devices, a 100 L SMFC inoculate with heavily contaminated sediments has been assembled and operated for over 2 years without external electron donor addition. The total organic chemical (TOC) degradation efficiency was 22.1% in the electricity generating SMFCs, which is significantly higher than that in the open-circuited SMFC (3.8%). The organic matters including contaminants in the contaminated sediments were sufficient for the electricity generation of SMFCs, even up to 8.5 years by the present SMFC theoretically. By using a power management system (PMS), the SMFC electricity could be harvested into batteries and used by commercial electronic devices. The results indicated that the SMFC-PMS system could be applied as a long-term and effective tool to simultaneously stimulate the bioremediation of the contaminated sediments and supply power for commercial devices. Copyright © 2014 Elsevier Ltd. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Berland, Brian Spencer; Lanning, Bruce Roy; Stowell, Jr., Michael Wayne
This disclosure describes system and methods for creating an autonomous electrochromic assembly, and systems and methods for use of the autonomous electrochromic assembly in combination with a window. Embodiments described herein include an electrochromic assembly that has an electrochromic device, an energy storage device, an energy collection device, and an electrochromic controller device. These devices may be combined into a unitary electrochromic insert assembly. The electrochromic assembly may have the capability of generating power sufficient to operate and control an electrochromic device. This control may occur through the application of a voltage to an electrochromic device to change its opacitymore » state. The electrochromic assembly may be used in combination with a window.« less
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Rogge, Ryan A; Hansen, Jeffrey C
2015-01-01
Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volume, and shape of macromolecules in solution affect their sedimentation rates as reflected in the sedimentation coefficient. The sedimentation coefficient is obtained by measuring the solute concentration as a function of radial distance during centrifugation. Monitoring the concentration can be accomplished using interference optics, absorbance optics, or the fluorescence detection system, each with inherent advantages. The interference optical system captures data much faster than these other optical systems, allowing for sedimentation velocity analysis of extremely large macromolecular complexes that sediment rapidly at very low rotor speeds. Supramolecular oligomeric complexes produced by self-association of 12-mer chromatin fibers are used to illustrate the advantages of the interference optics. Using interference optics, we show that chromatin fibers self-associate at physiological divalent salt concentrations to form structures that sediment between 10,000 and 350,000S. The method for characterizing chromatin oligomers described in this chapter will be generally useful for characterization of any biological structures that are too large to be studied by the absorbance optical system. © 2015 Elsevier Inc. All rights reserved.
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Denadai, Ângelo M L; De Sousa, Frederico B; Passos, Joel J; Guatimosim, Fernando C; Barbosa, Kirla D; Burgos, Ana E; de Oliveira, Fernando Castro; da Silva, Jeann C; Neves, Bernardo R A; Mohallem, Nelcy D S
2012-01-01
Summary Organic–inorganic magnetic hybrid materials (MHMs) combine a nonmagnetic and a magnetic component by means of electrostatic interactions or covalent bonds, and notable features can be achieved. Herein, we describe an application of a self-assembled material based on ferrite associated with β-cyclodextrin (Fe-Ni/Zn/βCD) at the nanoscale level. This MHM and pure ferrite (Fe-Ni/Zn) were used as an adsorbent system for Cr3+ and Cr2O7 2− ions in aqueous solutions. Prior to the adsorption studies, both ferrites were characterized in order to determine the particle size distribution, morphology and available binding sites on the surface of the materials. Microscopy analysis demonstrated that both ferrites present two different size domains, at the micro- and nanoscale level, with the latter being able to self-assemble into larger particles. Fe-Ni/Zn/βCD presented smaller particles and a more homogeneous particle size distribution. Higher porosity for this MHM compared to Fe-Ni/Zn was observed by Brunauer–Emmett–Teller isotherms and positron-annihilation-lifetime spectroscopy. Based on the pKa values, potentiometric titrations demonstrated the presence of βCD in the inorganic matrix, indicating that the lamellar structures verified by transmission electronic microscopy can be associated with βCD assembled structures. Colloidal stability was inferred as a function of time at different pH values, indicating the sedimentation rate as a function of pH. Zeta potential measurements identified an amphoteric behavior for the Fe-Ni/Zn/βCD, suggesting its better capability to remove ions (cations and anions) from aqueous solutions compared to that of Fe-Ni/Zn. PMID:23209524
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Global ecological pattern of ammonia-oxidizing archaea.
Cao, Huiluo; Auguet, Jean-Christophe; Gu, Ji-Dong
2013-01-01
The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats. Based on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.
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High-Frequency Sound Interaction in Ocean Sediments
2003-09-30
results, combined with measured sediment properties, to test the validity of sediment acoustic models , and in particular the poroelastic (Biot...understanding of the dominant scatterers versus frequency near the sediment surface, the potential need for poroelastic sediment models , the...work are described under a separate ONR project titled “ Acoustic propagation and scattering within sand sediments: Laboratory experiments, modeling
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Remote sensing of suspended sediment water research: principles, methods, and progress
NASA Astrophysics Data System (ADS)
Shen, Ping; Zhang, Jing
2011-12-01
In this paper, we reviewed the principle, data, methods and steps in suspended sediment research by using remote sensing, summed up some representative models and methods, and analyzes the deficiencies of existing methods. Combined with the recent progress of remote sensing theory and application in water suspended sediment research, we introduced in some data processing methods such as atmospheric correction method, adjacent effect correction, and some intelligence algorithms such as neural networks, genetic algorithms, support vector machines into the suspended sediment inversion research, combined with other geographic information, based on Bayesian theory, we improved the suspended sediment inversion precision, and aim to give references to the related researchers.
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Identifying sediment sources in the sediment TMDL process
Gellis, Allen C.; Fitzpatrick, Faith A.; Schubauer-Berigan, Joseph P.; Landy, R.B.; Gorman Sanisaca, Lillian E.
2015-01-01
Sediment is an important pollutant contributing to aquatic-habitat degradation in many waterways of the United States. This paper discusses the application of sediment budgets in conjunction with sediment fingerprinting as tools to determine the sources of sediment in impaired waterways. These approaches complement monitoring, assessment, and modeling of sediment erosion, transport, and storage in watersheds. Combining the sediment fingerprinting and sediment budget approaches can help determine specific adaptive management plans and techniques applied to targeting hot spots or areas of high erosion.
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NASA Astrophysics Data System (ADS)
Pondell, C.; Kuehl, S. A.; Canuel, E. A.
2016-12-01
There are several methodologies used to determine chronologies for sediments deposited within the past 100 years, including 210Pb and 137Cs radioisotopes and organic and inorganic contaminants. These techniques are quite effective in fine sediments, which generally have a high affinity for metals and organic compounds. However, the application of these chronological tools becomes limited in systems where coarse sediments accumulate. Englebright Lake is an impoundment in northern California where sediment accumulation is characterized by a combination of fine and coarse sediments. This combination of sediment grain size complicated chronological analysis using the more traditional 137Cs chronological approach. This study established a chronology of these sediments using 239+240Pu isotopes. While most of the 249+240Pu activity was measured in the fine grain size fraction (<63 microns), up to 25% of the plutonium activity was detected in the coarse size fractions of sediments from Englebright Lake. Profiles of 239+240Pu were similar to available 137Cs profiles, verifying the application of plutonium isotopes for determining sediment chronologies and expanding the established geochronology for Englebright Lake sediments. This study of sediment accumulation in Englebright Lake demonstrates the application of plutonium isotopes in establishing chronologies in coarse sediments and highlights the potential for plutonium to offer new insights into patterns of coarse sediment accumulation.
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Plante, Craig J; Fleer, Virginia; Jones, Martin L
2016-10-01
Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa-abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches, BMA α-diversity will decrease, and (ii) As migration decreases, BMA community dissimilarity (β-diversity) will increase. Co-occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa-abundances fit those predicted from NCMs reasonably well (R 2 of 0.68-0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co-occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics. BMA at low tide (lowest migration) exhibited reduced α-diversity as compared to periods of immersion at both mudflat and sand bar sites. β-diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between-site metacommunity comparisons, low- and high-resuspension sites exhibited distinct community compositions while the low-energy mudflats contained higher microalgal biomass and greater α-diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring local BMA community assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats. © 2016 Phycological Society of America.
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Microbes of deep marine sediments as viewed by metagenomics
NASA Astrophysics Data System (ADS)
Biddle, J.
2015-12-01
Ten years after the first deep marine sediment metagenome was produced, questions still exist about the nucleic acid sequences we have retrieved. Current data sets, including the Peru Margin, Costa Rica Margin and Iberian Margin show that consistently, data forms larger assemblies at depth due to the reduced complexity of the microbial community. But are these organisms active or preserved? At SMTZs, a change in the assembly statistics is noted, as well as an increase in cell counts, suggesting that cells are truly active. As depth increases, genome sizes are consistently large, suggesting that much like soil microbes, sedimentary microbes may maintain a larger reportorie of genomic potential. Functional changes are seen with depth, but at many sites are not correlated to specific geochemistries. Individual genomes show changes with depth, which raises interesting questions on how the subsurface is settled and maintained. The subsurface does have a distinct genomic signature, including unusual microbial groups, which we are now able to analyze for total genomic content.
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Identification of in-sewer sources of organic solids contributing to combined sewer overflows.
Ahyerre, M; Chebbo, G
2002-09-01
Previous research has shown that combined sewer systems are the main source of particle and organic pollution during rainfall events contributing to combined sewer overflow. The aim of this article is to identify in an urban catchment area called "Le Marais", in the center of Paris, the types of sediments that are eroded and contribute to the pollution of combined sewer overflow. Three sediment types are considered: granular material found in the inverts of pipes, organic biofilms and organic sediment at the water bed interface, identified as an immobile layer in the "Le Marais" catchment area. The method used consist, firstly, of sampling and assessing the organic pollutant loads and metallic loads of the particles in each type of sediment. Then, the mass of each type of sediment is assessed. The mass and the characteristics of each type of sediment is finally compared to the mass and characteristics of the particles eroded in the catchment area, estimated by mass balances, in order to find the source of eroded particles. The only identified type of deposit that can contribute to combined sewer overflows is the organic layer. Indeed, the solids of this layer have mean and metallic loads that are of the same order of magnitude as the eroded particles. Moreover, the mass of the organic layer considered over different time scales is of the same order of magnitude as the eroded masses during rainfall events and an erosion experiment showed that the organic layer is actually eroded.
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Sediment Toxicity Identification Evaluation
Approach combining chemical manipulations and aquatic toxicity testing, generally with whole organisms, to systematically characterize, identify and confirm toxic substances causing toxicity in whole sediments and sediment interstitial waters. The approach is divided into thre...
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Takesue, Renee K.; Conn, Kathleen E.; Dinicola, Richard S.
2017-09-29
Large rivers carry terrestrial sediment, contaminants, and other materials to the coastal zone where they can affect marine biogeochemical cycles and ecosystems. This U.S. Geological Survey study combined river and marine sediment geochemistry and organic contaminant analyses to identify riverborne sediment and associated contaminants at shoreline sites in Commencement Bay, Puget Sound, Washington, that could be used by adult forage fish and other marine organisms. Geochemical signatures distinguished the fine fraction (<0.063 millimeter, mm) of Puyallup River sediment—which originates from Mount Rainier, a Cascade volcano—from glacial fine sediment in lowland bluffs that supply sediment to beaches. In combination with activities of beryllium-7 (7Be), a short-lived radionuclide, geochemical signatures showed that winter 2013–14 sediment runoff from the Puyallup River was transported to and deposited along the north shore of Commencement Bay, then mixed downward into the sediment column. The three Commencement Bay sites at which organic contaminants were measured in surface sediment did not have measurable 7Be activities in that layer, so their contaminant assemblages were attributed to sources from previous years. Concentrations of organic contaminants (the most common of which were polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and fecal sterols) were higher in the <0.063-mm fraction compared to the <2-mm fraction, in winter compared to summer, in river suspended sediment compared to river bar and bank sediment, and in marine sediment compared to river sediment. The geochemical property barium/aluminum (Ba/Al) showed that the median percentage of Puyallup River derived fine surface sediment along the shoreline of Commencement Bay was 77 percent. This finding, in combination with higher concentrations of organic contaminants in marine rather than river sediment, indicates that riverborne sediment-bound contaminants are retained in shallow marine habitats of Commencement Bay. The retention of earlier inputs complicates efforts to identify recent inputs and sources. Understanding modern sources and fates of riverborne sediment and contaminants and their potential ecological impacts will therefore require a suite of targeted geochemical studies in such marine depositional environments.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.
Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less
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Effects of detergents on ribosomal precursor subunits of Bacillus megaterium.
Body, A; Brownstein, B H
1978-01-01
Cell extracts prepared by osmotic lysis of protoplasts were analyzed by sucrose gradient sedimentation. In the absence of detergents, ribosomal precursor particles were found in a gradient fraction which sedimented faster than mature 50S subunits and in two other fractions coincident with mature 50S and 30S ribosomal subunits. Phospholipid, an indicator of membrane, was shown to be associated with only the fastest-sedimenting ribosomal precursor particle fraction. After the extracts were treated with detergents, all phospholipid was found at the top of the gradients. Brij 58, Triton X-100, and Nonidet P-40 did not cause a change in the sedimentation values of precursors; however, the detergents deoxycholate or LOC (Amway Corp.) disrupted the fastest-sedimenting precursor and converted the ribosomal precursor subunits which sedimented at the 50S and 30S positions to five different classes of more slowly sedimenting particles. Earlier reports on the in vivo assembly of ribosomal subunits have shown that several stages of ribosomal precursor subunits exist, and, in the presence of the detergents deoxycholate and LOC, which had been used to prepare cell extracts, the precursors sedimented more slowly. Our data are consistent with the hypothesis that those detergents selectively modify the structure of ribosomal precursors and lend further support to the hypothesis that the in vivo ribosomal precursor subunits have 50S and 30S sedimentation values. In addition, these data support the idea that the ribosomal precursor particles found in the fast-sedimenting fraction may constitute a unique precursor fraction.
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Effects of Detergents on Ribosomal Precursor Subunits of Bacillus megaterium
Body, Barbara A.; Brownstein, Bernard H.
1978-01-01
Cell extracts prepared by osmotic lysis of protoplasts were analyzed by sucrose gradient sedimentation. In the absence of detergents, ribosomal precursor particles were found in a gradient fraction which sedimented faster than mature 50S subunits and in two other fractions coincident with mature 50S and 30S ribosomal subunits. Phospholipid, an indicator of membrane, was shown to be associated with only the fastest-sedimenting ribosomal precursor particle fraction. After the extracts were treated with detergents, all phospholipid was found at the top of the gradients. Brij 58, Triton X-100, and Nonidet P-40 did not cause a change in the sedimentation values of precursors; however, the detergents deoxycholate or LOC (Amway Corp.) disrupted the fastest-sedimenting precursor and converted the ribosomal precursor subunits which sedimented at the 50S and 30S positions to five different classes of more slowly sedimenting particles. Earlier reports on the in vivo assembly of ribosomal subunits have shown that several stages of ribosomal precursor subunits exist, and, in the presence of the detergents deoxycholate and LOC, which had been used to prepare cell extracts, the precursors sedimented more slowly. Our data are consistent with the hypothesis that those detergents selectively modify the structure of ribosomal precursors and lend further support to the hypothesis that the in vivo ribosomal precursor subunits have 50S and 30S sedimentation values. In addition, these data support the idea that the ribosomal precursor particles found in the fast-sedimenting fraction may constitute a unique precursor fraction. PMID:412833
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Xander: employing a novel method for efficient gene-targeted metagenomic assembly
Wang, Qiong; Fish, Jordan A.; Gilman, Mariah; ...
2015-08-05
Here, metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility ofmore » this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. In conclusion, xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines.« less
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NASA Astrophysics Data System (ADS)
Jenkins, Jessica Shawn
Advanced composite materials could be revolutionized by the development of methods to incorporate living cells into functional materials and devices. This could be accomplished by continuously and rapidly depositing thin ordered arrays of adhesive colloidal latex particles and live cells that maintain stability and preserve microbial reactivity. Convective assembly is one method of rapidly assembling colloidal particles into thin (<10 microm thick), ordered films with engineered compositions, thicknesses, and particle packing that offer several advantages over thicker randomly ordered composites, including enhanced cell stability and increased reactivity through minimized diffusion resistance to nutrients and reduced light scattering. This method can be used to precisely deposit live bacteria, cyanobacteria, yeast, and algae into biocomposite coatings, forming reactive biosensors, photoabsorbers, or advanced biocatalysts. This dissertation developed new continuous deposition and coating characterization methods for fabricating and characterizing <10 microm thick colloid coatings---monodispersed latex particle or cell suspensions, bimodal blends of latex particles or live cells and microspheres, and trimodal formulations of biomodal latex and live cells on substrates such as aluminum foil, glass, porous Kraft paper, polyester, and polypropylene. Continuous convective-sedimentation assembly (CSA) is introduced to enable fabrication of larger surface area and long coatings by constantly feeding coating suspension to the meniscus, thus expanding the utility of convective assembly to deposit monolayer or very thin films or multi-layer coatings composed of thin layers on a large scale. Results show thin, tunable coatings can be fabricated from diverse coating suspensions and critical coating parameters that control thickness and structure. Particle size ratio and charge influence deposition, convective mixing or demixing and relative particle locations. Substrate wettability and suspension composition influence coating microstructure by controlling suspension delivery and spreading across the substrate. Microbes behave like colloidal particles during CSA, allowing for deposition of very thin stable biocomposite coatings of latex-live cell blends. CSA of particle-cell blends result in open-packed structures (15-45% mean void space), instead of tightly packed coatings attainable with single component systems, confirming the existence of significant polymer particle-cell interactions and formation of particle aggregates that disrupt coating microstructure during deposition. Tunable process parameters, such as particle concentration, fluid sonication, and fluid density, influence coating homogeneity when the meniscus is continuously supplied. Fluid density modification and fluid sonication affect particle sedimentation and distribution in the coating growth front whereas the suspended particle concentration strongly affects coating thickness, but has almost no effect on void space. Changing the suspension delivery mode (topside versus underside CCSA) yields disparate meniscus volumes and uneven particle delivery to the drying front, which enables control of the coating microstructure by varying the total number of particles available for deposition. The judicious combination of all these parameters will enable deposition of uniform, thin, latex-cell monolayers over areas on the order of tens of square centimeters or larger. To demonstrate the utility of biocomposite coatings, this dissertation investigated photoreactive coatings (artificial leaves) from suspensions of latex particles and nitrogen-limited Rps. palustris CGA009 or sulfur-limited C. reinhardtii CC-124. These coatings demonstrated stable, sustained (>90 hours) photohydrogen production under anoxygenic conditions. Nutrient reduction slows cell division, minimizing coating outgrowth, and promotes photohydrogen generation, improving coating reactivity. Scanning electron microscopy of microstructure revealed how coating reactivity can be controlled by the size and distribution of the nanopores in the biocomposite layers. Variations in colloid microsphere size and suspension composition do not affect coating reactivity, but both parameters alter coating microstructure. Porous paper coated with thin coatings of colloidal particles and cells to enable coatings to be used in a gas-phase without dehydration may offer higher volumetric productivity for hydrogen production. Future work should focus on optimization of cell density, light intensity, media cycling, and acetate concentration.
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Chen, Juan; Wang, Pei-Fang; Wang, Chao; Wang, Xun; Gao, Han
2018-03-01
While nitrogen (N) fixation and ammonia oxidation by microorganisms are two important N cycling processes, little is known about how the microbes that drive these two processes respond when sediments are contaminated with persistent organic pollutants. In this study, we carried out a laboratory microcosm experiment to examine the effects of decabromodiphenyl ether (BDE-209), either on its own or combined with a common mangrove species, Avicennia marina, on the abundance, diversity, and community composition of N-fixing bacteria (NFB) and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in mangrove sediments. The sediments were very N-limited after one year. The rates of N fixation and NFB abundance were significantly higher in the sediments that contaminated by BDE-209, especially in the planted sediment, indicating that both BDE-209 and planting stimulated N fixation in N-limited mangrove sediments. In contrast, the potential nitrification rate and abundance of AOA and AOB decreased significantly under BDE-209 and planting, and the inhibitory effects were stronger in the sediment with both planting and BDE-209 than in the sediments with either BDE-209 or planting. The results from pyrosequencing showed that the richness and diversity of NFB increased, while those of AOA and AOB decreased, in the sediments treated with BDE-209 only and with BDE-209 combined with planting. The community compositions of NFB, AOA, and AOB in the sediments shifted significantly because of BDE-209, either alone or particularly when combined with planting, as shown by the increases in some NFB from the Proteobacteria phylum and decreases in AOA in the Nitrosopumilus genus and AOB in the Nitrosospira genus, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.
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Xu, Ran; Obbard, Jeffrey P
2003-01-01
Nutrient amendment to oil-contaminated beach sediments is a critical factor for the enhancement of indigenous microbial activity and biodegradation of petroleum hydrocarbons in the intertidal marine environment. In this study, we investigated the stimulatory effect of the slow-release fertilizers Osmocote (Os; Scotts, Marysville, OH) and Inipol EAP-22 (Ip; ATOFINA Chemicals, Philadelphia, PA) combined with inorganic nutrients on the bioremediation of oil-spiked beach sediments using an open irrigation system with artificial seawater over a 45-d period. Osmocote is comprised of a semipermeable membrane surrounding water-soluble inorganic N, P, and K. Inipol, which contains organic N and P, has been used for oil cleanup on beach substrate. Nutrient concentrations and microbial activity in sediments were monitored by analyzing sediment leachates and metabolic dehydrogenase activity of the microbial biomass, respectively. Loss of aliphatics (n-C12 to n-C33, pristane, and phytane) was significantly greater (total loss between 95 and 97%) in oil-spiked sediments treated with Os alone or in combination with other nutrient amendments, compared with an unamended oil-spiked control (26% loss) or sediments treated with the other nutrient amendments (28-65% loss). A combination of Os and soluble nutrients (SN) was favorable for the rapid metabolic stimulation of the indigenous microbial biomass, the sustained release of nutrients, and the enhanced biodegradation of petroleum hydrocarbons in leached, oil-contaminated sediments.
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Kissoon, La Toya T; Jacob, Donna L; Hanson, Mark A; Herwig, Brian R; Bowe, Shane E; Otte, Marinus L
2015-06-01
We measured concentrations of multiple elements, including rare earth elements, in waters and sediments of 38 shallow lakes of varying turbidity and macrophyte cover in the Prairie Parkland (PP) and Laurentian Mixed Forest (LMF) provinces of Minnesota. PP shallow lakes had higher element concentrations in waters and sediments compared to LMF sites. Redundancy analysis indicated that a combination of site- and watershed-scale features explained a large proportion of among-lake variability in element concentrations in lake water and sediments. Percent woodland cover in watersheds, turbidity, open water area, and macrophyte cover collectively explained 65.2 % of variation in element concentrations in lake waters. Sediment fraction smaller than 63 µm, percent woodland in watersheds, open water area, and sediment organic matter collectively explained 64.2 % of variation in element concentrations in lake sediments. In contrast to earlier work on shallow lakes, our results showed the extent to which multiple elements in shallow lake waters and sediments were influenced by a combination of variables including sediment characteristics, lake morphology, and percent land cover in watersheds. These results are informative because they help illustrate the extent of functional connectivity between shallow lakes and adjacent lands within these lake watersheds.
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Jacob, Donna L.; Hanson, Mark A.; Herwig, Brian R.; Bowe, Shane E.; Otte, Marinus L.
2015-01-01
We measured concentrations of multiple elements, including rare earth elements, in waters and sediments of 38 shallow lakes of varying turbidity and macrophyte cover in the Prairie Parkland (PP) and Laurentian Mixed Forest (LMF) provinces of Minnesota. PP shallow lakes had higher element concentrations in waters and sediments compared to LMF sites. Redundancy analysis indicated that a combination of site- and watershed-scale features explained a large proportion of among-lake variability in element concentrations in lake water and sediments. Percent woodland cover in watersheds, turbidity, open water area, and macrophyte cover collectively explained 65.2 % of variation in element concentrations in lake waters. Sediment fraction smaller than 63 µm, percent woodland in watersheds, open water area, and sediment organic matter collectively explained 64.2 % of variation in element concentrations in lake sediments. In contrast to earlier work on shallow lakes, our results showed the extent to which multiple elements in shallow lake waters and sediments were influenced by a combination of variables including sediment characteristics, lake morphology, and percent land cover in watersheds. These results are informative because they help illustrate the extent of functional connectivity between shallow lakes and adjacent lands within these lake watersheds. PMID:26074657
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Xander: employing a novel method for efficient gene-targeted metagenomic assembly.
Wang, Qiong; Fish, Jordan A; Gilman, Mariah; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R
2015-01-01
Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.
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Synthesis and assembly of retrovirus Gag precursors into immature capsids in vitro.
Sakalian, M; Parker, S D; Weldon, R A; Hunter, E
1996-01-01
The assembly of retroviral particles is mediated by the product of the gag gene; no other retroviral gene products are necessary for this process. While most retroviruses assemble their capsids at the plasma membrane, viruses of the type D class preassemble immature capsids within the cytoplasm of infected cells. This has allowed us to determine whether immature capsids of the prototypical type D retrovirus, Mason-Pfizer monkey virus (M-PMV), can assemble in a cell-free protein synthesis system. We report here that assembly of M-PMV Gag precursor proteins can occur in this in vitro system. Synthesized particles sediment in isopycnic gradients to the appropriate density and in thin-section electron micrographs have a size and appearance consistent with those of immature retrovirus capsids. The in vitro system described in this report appears to faithfully mimic the process of assembly which occurs in the host cell cytoplasm, since M-PMV gag mutants defective in in vivo assembly also fail to assemble in vitro. Likewise, the Gag precursor proteins of retroviruses that undergo type C morphogenesis, Rous sarcoma virus and human immunodeficiency virus, which do not preassemble capsids in vivo, fail to assemble particles in this system. Additionally, we demonstrate, with the use of anti-Gag antibodies, that this cell-free system can be utilized for analysis in vitro of potential inhibitors of retrovirus assembly. PMID:8648705
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Borehole geophysical logs at Naval Weapons Industrial Reserve Plant, Dallas, Texas
Braun, Christopher L.; Anaya, Roberto; Kuniansky, Eve L.
2000-01-01
A shallow alluvial aquifer at the Naval Weapons Industrial Reserve Plant near Dallas, Texas, has been contaminated by organic solvents used in the fabrication and assembly of aircraft and aircraft parts. Natural gamma-ray and electromagnetic-induction borehole geophysical logs were obtained from 162 poly vinyl-chloride-cased wells at the plant and were integrated with existing lithologic data to improve site characterization of the subsurface alluvium. Software was developed for filtering and classifying the log data and for processing, analyzing, and creating graphical output of the digital data. The alluvium consists of mostly fine-grained low-permeability sediments; however for this study, the alluvium was classified into low, intermediate, and high clay-content sediments on the basis of the gamma-ray logs. The low clay-content sediments were interpreted as being relatively permeable, whereas the high clay-content sediments were interpreted as being relatively impermeable. Simple statistics were used to identify zones of potentially contaminated sediments on the basis of the gamma-ray log classifications and the electromagnetic-induction log conductivity data.
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Forwardly-placed firearm fire control assembly
Frickey, Steven J.
2001-12-22
A firearm fire control assembly for disposition in a forwardly placed support-hand operative relationship within a firearm having a combination of a firing pin and a firearm hammer adapted to engage and fire a cartridge, a sear assembly to alternately engage and disengage the combination of the firearm hammer and firing pin, and a trigger assembly including a movable trigger mechanism that is operable to engage the sear assembly to cause the firearm hammer firing pin combination to fire the firearm, a fire control assembly including a fire control depression member and a fire control rod operably connected to the depression member, and being positioned in a forward disposition disposed within a forestock of the firearm, and the depression member adapted to be operably engaged and depressed by the user's conventional forwardly placed support hand to maneuver the fire control rod to provide firing control of the firing of the firearm.
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Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.
Davidson, Nadia M; Oshlack, Alicia
2018-05-01
RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking. Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing. Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods.
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NASA Astrophysics Data System (ADS)
Xu, Feng; Rao, Qiuhua; Ma, Wenbo
2018-03-01
The sinkage of a moving tracked mining vehicle is greatly affected by the combined compression-shear rheological properties of soft deep-sea sediments. For test purposes, the best sediment simulant is prepared based on soft deep-sea sediment from a C-C poly-metallic nodule mining area in the Pacific Ocean. Compressive creep tests and shear creep tests are combined to obtain compressive and shear rheological parameters to establish a combined compressive-shear rheological constitutive model and a compression-sinkage rheological constitutive model. The combined compression-shear rheological sinkage of the tracked mining vehicle at different speeds is calculated using the RecurDyn software with a selfprogrammed subroutine to implement the combined compression-shear rheological constitutive model. The model results are compared with shear rheological sinkage and ordinary sinkage (without consideration of rheological properties). These results show that the combined compression-shear rheological constitutive model must be taken into account when calculating the sinkage of a tracked mining vehicle. The combined compression-shear rheological sinkage decrease with vehicle speed and is the largest among the three types of sinkage. The developed subroutine in the RecurDyn software can be used to study the performance and structural optimization of moving tracked mining vehicles.
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NASA Astrophysics Data System (ADS)
Kirby, David J.
This dissertation explores the fundamental interparticle and particle-substrate forces that contribute to nanowire assembly. Nanowires have a large aspect ratio which has made them favorable materials for applications in energy and sensing technologies. However, this anisotropy means that nanowires must be positioned and oriented during an assembly process. Within this work, the roles of gravity, van der Waals (VDW) attractions, and electrostatic repulsions are explored when different nanowire assemblies are created. Particles were synthesized by the template electrodeposition process so that stripes of different materials and therefore different VDW interactions could be patterned along the particle length. Electrostatic repulsions were provided by a small molecule coating or a porous silica shell to prevent aggregation during the assembly process. Chapters 2, 3, 5, 6, and 8 all used particles whose asymmetry was further adjusted by removal of a sacrificial segment to leave a partially etched nanowire (PEN), a rigid silica shell partially filled with a metal core. For these particles, the role of gravity was amplified due to the drastic density differences between the two segments. Topographic and high VDW surface interactions were patterned onto assembly substrates using photolithographic processing. These forces served as a passive template to direct nanowire assembly. The segment anisotropy of PENs allowed gravity to drive their sedimentation with the long axis perpendicular to the surface. The density difference between the two ends allowed them to convert between the horizontal and vertical orientation as they diffused on the substrate. Vertical arrays formed as particle concentrations increased while VDW attractions from neighboring PENs or the physical barrier of a microwell wall supported this structure. While vertical arrays were typically PENs, microwell walls were also able to enforce a vertical orientation on solid Au nanowires. These particles typically formed horizontal arrays on planar surfaces, but careful design of the microwell and nanowire dimensions enabled these particles to take on the vertical orientation. Solid nanowires and PENs with greater segment symmetry aligned parallel to the surface as gravity did not allow a conversion to the vertical orientation. When concentrated, these particles formed smectic row arrangements which were previously shown to originate from a balance of VDW attractions and electrostatic repulsions. Within rows of segmented particles, a preference was observed for like orientation of nearest neighbor particles (Chapter 6). With the aid of Monte Carlo simulations, it was determined that this observation was the result of small differences in VDW attractions between the two nanowire ends. Differences in VDW attraction were also applied to patterned surfaces (Chapter 7). Stripes of high VDW material (Au) were placed on a silica surface (a low VDW material). When relatively low surface concentrations were used, the high VDW regions collected Au nanowires and organized them into rows that were reminiscent of those observed on un-patterned surfaces at high particle concentrations. VDW and the gravitational force were explored as they combined to influence array orientation in binary PEN mixtures. Depending on the geometries of the particles combined, the contributions of gravity and interparticle interactions exhibited different balance in creating the final array. VDW and gravitational forces could also act as a force for reconfigurable nanowire assembly. In chapter 8, fluid flow was used to concentrate PENs and force them into horizontal arrangements. When fluid flow was stopped, van der Waals forces and gravity were responsible for a reorientation of the assembled particles into a standing array. These studies represent early steps into the future of nanowire assembly methods. I conclude this dissertation by discussing the implications of my work and providing perspective on their importance to the scientific community. I also offer suggestions for future work in nanowire assembly. These areas focus on the development of assembled nanowire devices, mixed nanowire assembly techniques, and potential stimuli responsive reconfigurable assemblies.
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Juracek, Kyle E.
2015-01-01
Biological indicators in the bottom sediment provided evidence for an improving, or at least not worsening, lake trophic condition. The occurrence of multiple diatom species, none of which were overwhelmingly dominant, was indicative of a minimally contaminated lake ecosystem. The combined evidence of several diatom species in the recent sediment indicated that the lake had not become more productive in recent decades. The combined evidence provided by akinetes for three cyanobacterial genera in the recent and predevelopment sediment indicated similar nutrient conditions in the lake during the past 40 years and possibly back to at least the mid-1800s.
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Hydrocarbon pollution fixed to combined sewer sediment: a case study in Paris.
Rocher, Vincent; Garnaud, Stéphane; Moilleron, Régis; Chebbo, Ghassan
2004-02-01
Over a period of two years (2000-2001), sediment samples were extracted from 40 silt traps (STs) spread through the combined sewer system of Paris. All sediment samples were analysed for physico-chemical parameters (pH, organic matter content, grain size distribution), with total hydrocarbons (THs) and 16 polycyclic aromatic hydrocarbons (PAHs) selected from the priority list of the US-EPA. The two main objectives of the study were (1) to determine the hydrocarbon contamination levels in the sediments of the Paris combined sewer system and (2) to investigate the PAH fingerprints in order to assess their spatial variability and to elucidate the PAH origins. The results show that there is some important inter-site and intra-site variations in hydrocarbon contents. Despite this variability, TH and PAH contamination levels (50th percentile) in the Parisian sewer sediment are estimated at 530 and 18 microg g(-1), respectively. The investigation of the aromatic compound distributions in all of the 40 STs has underlined that there is, at the Paris sewer system scale, a homogeneous PAH background pollution. Moreover, the study of the PAH fingerprints, using specific ratios, suggests the predominance of a pyrolytic origin for those PAHs fixed to the sewer sediment.
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Roosa, Stéphanie; Prygiel, Emilie; Lesven, Ludovic; Wattiez, Ruddy; Gillan, David; Ferrari, Benoît J D; Criquet, Justine; Billon, Gabriel
2016-06-01
The bioavailability of metals was estimated in three river sediments (Sensée, Scarpe, and Deûle Rivers) impacted by different levels of Cu, Cd, Pb, and Zn (Northern France). For that, a combination of geochemistry and biological responses (bacteria and chironomids) was used. The results obtained illustrate the complexity of the notion of "bioavailability." Indeed, geochemical indexes suggested a low toxicity, even in surface sediments with high concentrations of total metals and a predicted severe effect levels for the organisms. This was also suggested by the abundance of total bacteria as determined by DAPI counts, with high bacterial cell numbers even in contaminated areas. However, a fraction of metals may be bioavailable as it was shown for chironomid larvae which were able to accumulate an important quantity of metals in surface sediments within just a few days.We concluded that (1) the best approach to estimate bioavailability in the selected sediments is a combination of geochemical and biological approaches and that (2) the sediments in the Deûle and Scarpe Rivers are highly contaminated and may impact bacterial populations but also benthic invertebrates.
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Metal concentrations in urban riparian sediments along an urbanization gradient
Daniel J. Bain; Ian D. Yesilonis; Richard V. Pouyat
2012-01-01
Urbanization impacts fluvial systems via a combination of changes in sediment chemistry and basin hydrology. While chemical changes in urban soils have been well characterized, similar surveys of riparian sediments in urbanized areas are rare. Metal concentrations were measured in sediments collected from riparian areas across the urbanization gradient in Baltimore, MD...
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2012-12-01
mineral and organic materials situated beneath an aqueous layer. PEDs assembled, installed, and retrieved following these procedures will be suitable...at a minimum, wearing adequate protective equipment, flotation devices, and making use of lifelines. 8.0 References Massachusetts Institute of
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Mobility of maerl-siliciclastic mixtures: Impact of waves, currents and storm events
NASA Astrophysics Data System (ADS)
Joshi, Siddhi; Duffy, Garret Patrick; Brown, Colin
2017-04-01
Maerl beds are free-living, non-geniculate coralline algae habitats which form biogenic reefs with high micro-scale complexity supporting a diversity and abundance of rare epifauna and epiflora. These habitats are highly mobile in shallow marine environments where substantial maerl beds co-exist with siliciclastic sediment, exemplified by our study site of Galway Bay. Coupled hydrodynamic-wave-sediment transport models have been used to explore the transport patterns of maerl-siliciclastic sediment during calm summer conditions and severe winter storms. The sediment distribution is strongly influenced by storm waves even in water depths greater than 100 m. Maerl is present at the periphery of wave-induced residual current gyres during storm conditions. A combined wave-current Sediment Mobility Index during storm conditions shows correlation with multibeam backscatter and surficial sediment distribution. A combined wave-current Mobilization Frequency Index during storm conditions acts as a physical surrogate for the presence of maerl-siliciclastic mixtures in Galway Bay. Both indices can provide useful integrated oceanographic and sediment information to complement coupled numerical hydrodynamic, sediment transport and erosion-deposition models.
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The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes.
Vincent, Nicholas G; Charette, J Michael; Baserga, Susan J
2018-01-01
Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the preribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined. Here, we have used a semi-high-throughput yeast two-hybrid (Y2H) assay and coimmunoprecipitation validation method to produce a high-confidence interactome of SSU processome assembly factors (SPAFs), providing essential insight into SSU assembly and ribosome biogenesis. Further, we used glycerol density-gradient sedimentation to reveal the presence of protein subcomplexes that have not previously been observed. Our work not only provides essential insight into SSU assembly and ribosome biogenesis, but also serves as an important resource for future investigations into how defects in biogenesis and assembly cause congenital disorders of ribosomes known as ribosomopathies. © 2018 Vincent et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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[Transport and sources of runoff pollution from urban area with combined sewer system].
Li, Li-Qing; Yin, Cheng-Qing
2009-02-15
Sampling and monitoring of runoff and sewage water in Wuhan urban area with combined sewer system were carried out during the period from 2003 to 2006, to study the transport and sources of runoff pollution at the catchment scale coupled with environmental geochemistry method. The results showed a change in quality between the runoff entering the sewer network and the combined storm water flow at the sewer's outlet. A significant increase was observed in the concentrations of total suspended solids (TSS), volatile suspended solids (VSS), COD, TN, and TP, and in the proportion of COD linked to particles. During the runoff production and transport, the concentrations of TSS and COD increased from 18.7 mg/L and 37.0 mg/L in roof runoff, to 225.3 mg/L and 176.5 mg/L in street runoff, and to 449.7 mg/L and 359.9 mg/L in combined storm water flow, respectively. The proportion of COD linked to particles was increased by 18%. In addition, the total phosphorus (P) and iron (Fe) contents in urban ground dust, storm drain sediment, sewage sewer sediment and combined sewer sediment were measured to identify the potential sources of suspended solids in the combined flow. The urban ground dust andstorm drain sediment wererich in Fe, whereas the sewage sewer sediment was rich in P. The P/Fe ratios in these groups were significantly distinct and able to differentiate them. A calculation of the two storm events based on the P/Fe rations showed that 56% +/- 26% of suspended solids in combined flow came from urban ground and storm drain. The rest wer e originated from the sewage sewer sediments which deposited in combined sewer on the dry weather days and were eroded on the wet weather days. The combined sewer network not only acts as a transport system, but also constitutes a physicochemical reactor that degrades the quality of urban water. Reducing the in-sewer pollution stocks would effectively control urban runoff pollution.
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Sediment type affects competition between a native and an exotic species in coastal China.
Li, Hong-Li; Wang, Yong-Yang; An, Shu-Qing; Zhi, Ying-Biao; Lei, Guang-Chun; Zhang, Ming-Xiang
2014-10-23
Different types of sediments in salt marsh have different physical and chemical characters. Thus sediment type plays a role in plant competition and growth in salt marsh ecosystems. Spartina anglica populations have been increasingly confined to upper elevation gradients of clay, and the niche sediment has changed. Because the niches of S. anglica and the native species Scirpus triqueter overlap, we conducted a greenhouse experiment to test the hypothesis that plant competition has changed under different types of sediments. Biomass and asexual reproduction were analyzed, and inter- and intraspecific competition was measured by log response ratio for the two species in both monoculture and combination under three sediment types (sand, clay and mixture of sand and clay). For S. anglica, biomass, ramet number and rhizome length in combination declined significantly compared with those in monoculture, and the intensity of interspecific competition was significantly higher than that of intraspecific competition under all sediments. For S. triqueter, the intensities of intra- and interspecific competition were not significantly different. This indicates that S. triqueter exerts an asymmetric competitive advantage over S. anglica across all sediments, but especially clay. Thus the sediment type changes competition between S. anglica and S. triqueter.
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Sediment Type Affects Competition between a Native and an Exotic Species in Coastal China
Li, Hong-Li; Wang, Yong-Yang; An, Shu-Qing; Zhi, Ying-Biao; Lei, Guang-Chun; Zhang, Ming-Xiang
2014-01-01
Different types of sediments in salt marsh have different physical and chemical characters. Thus sediment type plays a role in plant competition and growth in salt marsh ecosystems. Spartina anglica populations have been increasingly confined to upper elevation gradients of clay, and the niche sediment has changed. Because the niches of S. anglica and the native species Scirpus triqueter overlap, we conducted a greenhouse experiment to test the hypothesis that plant competition has changed under different types of sediments. Biomass and asexual reproduction were analyzed, and inter- and intraspecific competition was measured by log response ratio for the two species in both monoculture and combination under three sediment types (sand, clay and mixture of sand and clay). For S. anglica, biomass, ramet number and rhizome length in combination declined significantly compared with those in monoculture, and the intensity of interspecific competition was significantly higher than that of intraspecific competition under all sediments. For S. triqueter, the intensities of intra- and interspecific competition were not significantly different. This indicates that S. triqueter exerts an asymmetric competitive advantage over S. anglica across all sediments, but especially clay. Thus the sediment type changes competition between S. anglica and S. triqueter. PMID:25339574
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NASA Astrophysics Data System (ADS)
Sobolev, S. V.; Brown, M.
2017-12-01
Plate tectonics (PT) is the most important geological process operating on Earth, making it unique among the rocky planets in the Solar System. The question of how PT was initiated and which factors controlled its evolution over Earth's history are widely discussed, but remain controversial. It is broadly accepted that a necessary condition for initiation and stable operation of PT is maintaining low strength along plate boundaries, particularly along the subduction zone interfaces in the subduction channels. Examples from the South American Andes and other convergent margins show that unconsolidated continental sediments in trenches serve as an efficient lubricant for subduction; if these are lacking, friction in the subduction channel and strength of the plate boundary are significantly increased. We suggest that lubrication of subduction by accumulation of continental sediments in trenches played a crucial role during the evolution of PT on Earth since the mid-Mesoarchean. We posit that continental emergence and enhanced surface erosion caused an increasing flux of sediments into the oceans, which in turn lubricated subduction channels and intensified PT. Thus, peaks in orogenesis, as confirmed by several proxies, during periods of supercraton/supercontinent assembly represent periods of vigorous subduction and continental sedimentation in trenches prior to terminal collision. Conversely, a decrease in plate boundary length and a reduction in continental sediment accumulation in trenches during periods of stability after supercraton/supercontinent assembly is the likely reason for periods of lower PT vigor, including the so called `boring billion' between 1.8 and 0.8 Ga. The largest surface erosion and subduction-lubrication event occurred at the end of the `snowball' Earth epoch in the Neoproterozoic and likely accelerated the most recent episode of vigorous PT. Based on analysis of various geological observations, we suggest that the cyclic behavior of PT on Earth since the mid-Mesoarchean (the so-called `supercontinent cycle') can be interpreted in terms of the balance of power between PT, driven by slab pull and controlled by the temperature of the upper mantle, and the efficiency of lubrication in the subduction zones, controlled by accumulation of continental sediment in the trenches.
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Hepatitis E virus capsid protein assembles in 4M urea in the presence of salts.
Yang, Chunyan; Pan, Huirong; Wei, Minxi; Zhang, Xiao; Wang, Nan; Gu, Ying; Du, Hailian; Zhang, Jun; Li, Shaowei; Xia, Ningshao
2013-03-01
The hepatitis E virus (HEV) capsid protein has been demonstrated to be able to assemble into particles in vitro. However, this process and the mechanism of protein-protein interactions during particle assembly remain unclear. In this study, we investigated the assembly mechanism of HEV structural protein subunits, the capsid protein p239 (aa368-606), using analytical ultracentrifugation. It was the first to observe that the p239 can form particles in 4M urea as a result of supplementation with salt, including ammonium sulfate [(NH₄)₂SO₄], sodium sulfate (Na₂SO₄), sodium chloride (NaCl), and ammonium chloride (NH₄Cl). Interestingly, it is the ionic strength that determines the efficiency of promoting particle assembly. The assembly rate was affected by temperature and salt concentration. When (NH₄)₂SO₄ was used, assembling intermediates of p239 with sedimentation coefficient values of approximately 5 S, which were mostly dodecamers, were identified for the first time. A highly conserved 28-aa region (aa368-395) of p239 was found to be critical for particle assembly, and the hydrophobic residues Leu³⁷², Leu³⁷⁵, and Leu³⁹⁵ of p239 was found to be critical for particle assembly, which was revealed by site-directed mutagenesis. This study provides new insights into the assembly mechanism of native HEV, and contributes a valuable basis for further investigations of protein assembly by hydrophobic interactions under denaturing conditions. Copyright © 2012 The Protein Society.
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NASA Astrophysics Data System (ADS)
Smith, J. P.; Owens, P. N.; Gaspar, L.; Lobb, D. A.; Petticrew, E. L.
2015-12-01
An understanding of sediment redistribution processes and the main sediment sources within a watershed is needed to support watershed management strategies. The fingerprinting technique is increasingly being recognized as a method for establishing the source of the sediment transported within watersheds. However, the different behaviour of the various fingerprinting properties has been recognized as a major limitation of the technique, and the uncertainty associated with tracer selection needs to be addressed. There are also questions associated with which modelling approach (frequentist or Bayesian) is the best to unmix complex environmental mixtures, such as river sediment. This study aims to compare and evaluate the differences between fingerprinting predictions provided by a Bayesian unmixing model (MixSIAR) using different groups of tracer properties for use in sediment source identification. We used fallout radionuclides (e.g. 137Cs) and geochemical elements (e.g. As) as conventional fingerprinting properties, and colour parameters as emerging properties; both alone and in combination. These fingerprinting properties are being used (i.e. Koiter et al., 2013; Barthod et al., 2015) to determine the proportional contributions of fine sediment in the South Tobacco Creek Watershed, an agricultural watershed located in Manitoba, Canada. We show that the unmixing model using a combination of fallout radionuclides and geochemical tracers gave similar results to the model based on colour parameters. Furthermore, we show that a model that combines all tracers (i.e. radionuclide/geochemical and colour) gave similar results, showing that sediment sources change from predominantly topsoil in the upper reaches of the watershed to channel bank and bedrock outcrop material in the lower reaches. Barthod LRM et al. (2015). Selecting color-based tracers and classifying sediment sources in the assessment of sediment dynamics using sediment source fingerprinting. J Environ Qual. Doi:10.2134/jeq2015.01.0043 Koiter AJ et al. (2013). Investigating the role of connectivity and scale in assessing the sources of sediment in an agricultural watershed in the Canadian prairies using sediment source fingerprinting. J Soils Sediments, 13, 1676-1691.
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Lindh, Markus V; Maillot, Brianne M; Smith, Craig R; Church, Matthew J
2018-04-01
Deep-sea mining of commercially valuable polymetallic nodule fields will generate a seabed sediment plume into the water column. Yet, the response of bacterioplankton communities, critical in regulating energy and matter fluxes in marine ecosystems, to such disturbances is unknown. Metacommunity theory, traditionally used in general ecology for macroorganisms, offers mechanistic understanding on the relative role of spatial differences compared with local environmental conditions (habitat filtering) for community assembly. We examined bacterioplankton metacommunities using 16S rRNA amplicons from the Clarion-Clipperton Zone (CCZ) in the eastern Pacific Ocean and in global ocean transect samples to determine sensitivity of these assemblages to environmental perturbations. Habitat filtering was the main assembly mechanism of bacterioplankton community composition in the epi- and mesopelagic waters of the CCZ and the Tara Oceans transect. Bathy- and abyssopelagic bacterioplankton assemblages were mainly assembled by undetermined metacommunity types or neutral and dispersal-driven patch-dynamics for the CCZ and the Malaspina transect. Environmental disturbances may alter the structure of upper-ocean microbial assemblages, with potentially even more substantial, yet unknown, impact on deep-sea communities. Predicting such responses in bacterioplankton assemblage dynamics can improve our understanding of microbially-mediated regulation of ecosystem services in the abyssal seabed likely to be exploited by future deep-sea mining operations. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Chen, Weidong; Pan, Yongbo; Yu, Lingyu; Yang, Jun; Zhang, Wenjing
2017-01-01
Microeukaryotes play key roles in the structure and functioning of marine ecosystems. Little is known about the relative importance of the processes that drive planktonic and benthic microeukaryotic biogeography in subtropical offshore areas. This study compares the microeukaryotic community compositions (MCCs) from offshore waters (n = 12) and intertidal sediments (n = 12) around Xiamen Island, southern China, using high-throughput sequencing of 18S rDNA. This work further quantifies the relative contributions of spatial and environmental variables on the distribution of marine MCCs (including total, dominant, rare and conditionally rare taxa). Our results showed that planktonic and benthic MCCs were significantly different, and the benthic richness (6627 OTUs) was much higher than that for plankton (4044 OTUs) with the same sequencing effort. Further, we found that benthic MCCs exhibited a significant distance-decay relationship, whereas the planktonic communities did not. After removing two unique sites (N2 and N3), however, 72% variation in planktonic community was explained well by stochastic processes. More importantly, both the environmental and spatial factors played significant roles in influencing the biogeography of total and dominant planktonic and benthic microeukaryotic communities, although their relative effects on these community variations were different. However, a high proportion of unexplained variation in the rare taxa (78.1–97.4%) and conditionally rare taxa (49.0–81.0%) indicated that more complex mechanisms may influence the assembly of the rare subcommunity. These results demonstrate that patterns and processes in marine microeukaryotic community assembly differ among the different habitats (coastal water vs. intertidal sediment) and different communities (total, dominant, rare and conditionally rare microeukaryotes), and provide novel insight on the microeukaryotic biogeography and ecological mechanisms in coastal waters and intertidal sediments at local scale. PMID:29075237
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Tansel, Berrin; Boglaienko, Daria
2017-01-01
Contaminant fate and transport studies and models include transport mechanisms for colloidal particles and dissolved ions which can be easily moved with water currents. However, mobilization of much larger contaminated granular particles (i.e., sand) in sediments have not been considered as a possible mechanism due to the relatively larger size of sand particles and their high bulk density. We conducted experiments to demonstrate that oil contaminated granular particles (which exhibit hydrophobic characteristics) can attach on gas bubbles to form granular shells and transfer from the sediment phase to the water column. The interactions and conditions necessary for the oil contaminated granular particles to self assemble as tightly packed granular shells on the gas bubbles which transfer from sediment phase to the water column were evaluated both experimentally and theoretically for South Louisiana crude oil and quartz sand particles. Analyses showed that buoyancy forces can be adequate to move the granular shell forming around the air bubbles if the bubble radius is above 0.001mm for the sand particles with 0.28mm diameter. Relatively high magnitude of the Hamaker constant for the oil film between sand and air (5.81×10 -20 J for air-oil-sand) indicates that air bubbles have high affinity to attach on the oil film that is on the sand particles in comparison to attaching to the sand particles without the oil film in water (1.60×10 -20 J for air-water-sand). The mobilization mechanism of the contaminated granular particles with gas bubbles can occur in natural environments resulting in transfer of granular particles from sediments to the water column. Copyright © 2016 Elsevier B.V. All rights reserved.
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Edwards, B.D.
2002-01-01
The storm-protected continental shelf of Monterey Bay, part of the Monterey Bay National Marine Sanctuary, north-central California, is subject to abundant, episodic sediment input from fluvial sources. North of Monterey Bay, conditions of reduced sediment supply combined with the exposed nature of the shelf provide an effective laboratory for studying the contrasting effects of storm- versus fluvial-dominated conditions on modern sedimentation. Textural analyses performed on surface sediment samples collected from more than 380 box cores and MultiCores??? document the existence of a clearly defined mud belt occupying the mid-shelf throughout the region. Inshore sands combined with these mid-shelf muds represent deposits from modern sedimentation processes. In Monterey Bay, where episodic fluvial input from winter storms dominates sedimentation, the mid-shelf mud belt extends across the shelf to the shelf break. North of Monterey Bay, where sediment loads are reduced and both oceanographic and storm processes dominate, the mid-shelf mud belt is bordered by relict sediments occupying the outer shelf. In the study area, mass accumulation rates established by radiochemical studies support the contention that storm-induced along-shelf processes result in northward transport of sediment within the mud belt. The continuity of transport, however, is interrupted by topographic highs which are barriers or inhibitors to sediment transport created by wrench-style tectonics associated with the San Andreas fault system.
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Zeng, Xiangfeng; Twardowska, Irena; Wei, Shuhe; Sun, Lina; Wang, Jun; Zhu, Jianyu; Cai, Jianchao
2015-05-15
Bioleaching by Aspergillus niger strain SY1 combined with Fenton-like reaction was optimized to improve trace metal removal and dewaterability of dredged sediments. The major optimized parameters were the duration of bioleaching and H₂O₂ dose in Fenton-like process (5 days and 2g H₂O₂/L, respectively). Bioleaching resulted in the removal of ≈90% of Cd, ≈60% of Zn and Cu, ≈20% of Pb, and in decrease of sediment pH from 6.6 to 2.5 due to organic acids produced by A. niger. After addition of H₂O₂, Fenton-like reaction was initiated and further metal removal occurred. Overall efficiency of the combined process comprised: (i) reduction of Cd content in sediment by 99.5%, Cu and Zn by >70% and Pb by 39% as a result of metal release bound in all mobilizable fractions; (ii) decrease of sediment capillary suction time (CST) from 98.2s to 10.1s (by 89.8%) and specific resistance to filtration (SRF) from 37.4×10(12)m/kg to 6.2×10(12)m/kg (by 83.8%), due to reducing amount of extracellular polymeric substances (EPS) by 68.7% and bound water content by 79.1%. The combined process was found to be an efficient method to remove trace metals and improve dewaterability of contaminated dredged sediments. Copyright © 2015 Elsevier B.V. All rights reserved.
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Rapid formation of hyperpycnal sediment gravity currents offshore of a semi-arid California river
Warrick, J.A.; Xu, Jie; Noble, M.A.; Lee, H.J.
2008-01-01
Observations of sediment dispersal from the Santa Clara River of southern California during two moderately sized river discharge events suggest that river sediment rapidly formed a negatively buoyant (hyperpycnal) bottom plume along the seabed within hours of peak discharge. An array of acoustic and optical sensors were placed at three stations 1 km from the Santa Clara River mouth in 10-m water depth during January-February 2004. These combined observations suggest that fluid mud concentrations of suspended sediment (>10 g/l) and across-shore gravity currents (???5 cm/s) were observed in the lower 20-40 cm of the water column 4-6 h after discharge events. Gravity currents were wave dominated, rather than auto-suspending, and appeared to consist of silt-to-clay sized sediment from the river. Sediment mass balances suggest that 25-50% of the discharged river sediment was transported by these hyperpycnal currents. Sediment settling purely by flocs (???1 mm/s) cannot explain the formation of the observed hyperpycnal plumes, therefore we suggest that some enhanced sediment settling from mixing, convective instabilities, or diverging plumes occurred that would explain the formation of the gravity currents. These combined results provide field evidence that high suspended-sediment concentrations from rivers (>1 g/l) may rapidly form hyperpycnal sediment gravity currents immediately offshore of river mouths, and these pathways can explain a significant portion of the river-margin sediment budget. The fate of this sediment will be strongly influenced by bathymetry, whereas the fate of the remaining sediment will be much more influenced by ocean currents.
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The influence of a semi-arid sub-catchment on suspended sediments in the Mara River, Kenya
2018-01-01
The Mara River Basin in East Africa is a trans-boundary basin of international significance experiencing excessive levels of sediment loads. Sediment levels in this river are extremely high (turbidities as high as 6,000 NTU) and appear to be increasing over time. Large wildlife populations, unregulated livestock grazing, and agricultural land conversion are all potential factors increasing sediment loads in the semi-arid portion of the basin. The basin is well-known for its annual wildebeest (Connochaetes taurinus) migration of approximately 1.3 million individuals, but it also has a growing population of hippopotami (Hippopotamus amphibius), which reside within the river and may contribute to the flux of suspended sediments. We used in situ pressure transducers and turbidity sensors to quantify the sediment flux at two sites for the Mara River and investigate the origin of riverine suspended sediment. We found that the combined Middle Mara—Talek catchment, a relatively flat but semi-arid region with large populations of wildlife and domestic cattle, is responsible for 2/3 of the sediment flux. The sediment yield from the combined Middle Mara–Talek catchment is approximately the same as the headwaters, despite receiving less rainfall. There was high monthly variability in suspended sediment fluxes. Although hippopotamus pools are not a major source of suspended sediments under baseflow, they do contribute to short-term variability in suspended sediments. This research identified sources of suspended sediments in the Mara River and important regions of the catchment to target for conservation, and suggests hippopotami may influence riverine sediment dynamics. PMID:29420624
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Modelling of sedimentation and remobilization in in-line storage sewers for stormwater treatment.
Frehmann, T; Flores, C; Luekewille, F; Mietzel, T; Spengler, B; Geiger, W F
2005-01-01
A special arrangement of combined sewer overflow tanks is the in-line storage sewer with downstream discharge (ISS-down). This layout has the advantage that, besides the sewer system, no other structures are required for stormwater treatment. The verification of the efficiency with respect to the processes of sedimentation and remobilization of sediment within the in-line storage sewer with downstream discharge is carried out in a combination of a field and a pilot plant study. The model study was carried out using a pilot plant model scaled 1:13. The following is intended to present some results of the pilot plant study and the mathematical empirical modelling of the sedimentation and remobilization process.
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NASA Astrophysics Data System (ADS)
Jiang, Jingtao; Sui, Rendong; Shi, Yan; Li, Furong; Hu, Caiqi
In this paper 3-D models of combined fixture elements are designed, classified by their functions, and saved in computer as supporting elements library, jointing elements library, basic elements library, localization elements library, clamping elements library, and adjusting elements library etc. Then automatic assembly of 3-D combined checking fixture for auto-body part is presented based on modularization theory. And in virtual auto-body assembly space, Locating constraint mapping technique and assembly rule-based reasoning technique are used to calculate the position of modular elements according to localization points and clamp points of auto-body part. Auto-body part model is transformed from itself coordinate system space to virtual assembly space by homogeneous transformation matrix. Automatic assembly of different functional fixture elements and auto-body part is implemented with API function based on the second development of UG. It is proven in practice that the method in this paper is feasible and high efficiency.
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Bradshaw, Clare; Strid, Anna; von Stedingk, Hans; Gustafsson, Kerstin
2015-06-01
The authors studied the fate of the brominated flame retardant hexabromocyclododecane (HBCDD) added in a particulate suspension to experimental ecosystems assembled from brackish (Baltic Sea) coastal bays. Two experiments examined how benthic macrofauna (over 21 d) and increased temperature (14 d) affected HBCDD concentrations and fractionation of α, β, and γ diastereomers in the water, sediment, and biota. A third experiment run over 3 seasons (231 d), studied the effect of HBCDD dose on the same endpoints. In all treatments of the 3 experiments, HBCDD partitioned mainly to the sediment, and this proportion increased with time. Presence of macrofauna tended to increase the HBCDD concentration in the sediment and decreased its concentration in the water. Increased temperature (+ 5°C) decreased the amount of HBCDD in sediment and water but not in the filter- and deposit-feeding infaunal bivalves (Macoma balthica). The partitioning between water, sediment, and biota was not concentration dependent. In all treatments, sediment became enriched in γ-HBCDD, M. balthica in α-HBCDD, and water in α- and β-HBCDD. Bioaccumulation of HBCDD in M. balthica was high in all experiments (log biota-sediment accumulation factor [BSAF] > 1.25), the α diastereomer contributing the most (log BSAF 2.1-5.2). There is a risk of trophic transfer of HBCDD from benthic to pelagic food webs, as well as secondary poisoning of marine consumers. © 2015 SETAC.
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Chaton, Catherine T.
2017-01-01
Sedimentation velocity analytical ultracentrifugation (SV-AUC) has seen a resurgence in popularity as a technique for characterizing macromolecules and complexes in solution. SV-AUC is a particularly powerful tool for studying protein conformation, complex stoichiometry, and interacting systems in general. Deconvoluting velocity data to determine a sedimentation coefficient distribution c(s) allows for the study of either individual proteins or multi-component mixtures. The standard c(s) approach estimates molar masses of the sedimenting species based on determination of the frictional ratio (f/f0) from boundary shapes. The frictional ratio in this case is a weight-averaged parameter, which can lead to distortion of mass estimates and loss of information when attempting to analyze mixtures of macromolecules with different shapes. A two-dimensional extension of the c(s) analysis approach provides size-and-shape distributions that describe the data in terms of a sedimentation coefficient and frictional ratio grid. This allows for better resolution of species with very distinct shapes that may co-sediment and provides better molar mass determinations for multi-component mixtures. An example case is illustrated using globular and non-globular proteins of different masses with nearly identical sedimentation coefficients that could only be resolved using the size-and-shape distribution. Other applications of this analytical approach to complex biological systems are presented, focusing on proteins involved in the innate immune response to cytosolic microbial DNA. PMID:26412652
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Battery-Powered Field Filtration Assembly Using an Inexpensive Mini-Compressor.
ERIC Educational Resources Information Center
Corbett, Robert G.; Quick, Thomas J.
1986-01-01
Suggests how modifications on a mini-compressor can result in a low-cost vacuum filtration system for use with suspended sediments in the field or laboratory. Explains and illustrates the changes needed to make the apparatus efficient and servicable for providing data for mass balance, geochemical exploration, and environmental studies. (ML)
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NASA Astrophysics Data System (ADS)
Li, Yichen; Zhou, Lan; Liu, Guojin; Chai, Liqin; Fan, Qinguo; Shao, Jianzhong
2018-06-01
The Silica/Poly(methylmethacrylate-butylacrylate)[SiO2/P(MMA-BA)] photonic crystals(PCs) with brilliant structural colors were fabricated on fabric substrates by co-sedimentation self-assembly, in which the relatively smaller P(MMA-BA) copolymer particles filled in the interstices among the larger SiO2 microspheres. The fabricated composite PCs were mechanically robust and strongly bonded to the substrate because of the cementing effect caused by the soft P(MMA-BA) copolymer particles filling in the interstices of the SiO2 microspheres like cement filling in the gap and tightly holding stones in a sturdy cement wall. The volume fraction and the size ratios of the two components significantly influenced the structural colors of the composite PCs, and the larger volume fraction could improve the structural stability of the composite PCs, while the smaller size ratios could enhance the brightness of the structural colors of the composite PCs. The composite PCs with both high structural stability and brilliant structural colors have great application prospect for structural coloration of textiles.
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Entropically Driven Self-Assembly of Colloidal Crystals on Templates in Space
NASA Technical Reports Server (NTRS)
Yodh, Arjun G.; Zimmerli, Gregory A.
2002-01-01
These experiments aim to create new colloidal crystalline materials, to study the assembly and thermodynamics of these materials, to measure the optical properties of these materials. and to fix the resulting structures so that they can be brought back and studied on earth. In microgravity, the elimination of particle sedimentation effects creates a purely "thermodynamic" environment for colloidal suspensions wherein particle size, volume fraction, and interparticle interactions are the primary determinants of the assembled structures. We will control the colloidal assembly process using attractive, entropic particle interactions brought about by the depletion effect. By using attractive interactions for colloidal assembly we create conditions for growth that resemble those associated with "conventional" microscopic systems such as atoms and molecules. This approach differs qualitatively from the more common "space-filling" mode of colloidal crystal growth that is driven purely by packing constraints. It is anticipated that at least some of the solidified structures will survive reentry to earth's gravitational field, and that their optical, magnetic, and electrical properties can then be studied in detail upon return.
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Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.
Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C
2016-01-01
Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.
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NASA Astrophysics Data System (ADS)
Felbauer, Lucia; Pöppl, Ronald
2016-04-01
Global warming results in an ongoing retreat of glaciers in the Alps, leaving behind large amounts of easily erodible sediments. In addition, the debuttressing of rock-walls and the decay of permafrost in the high mountain regions facilitates mass movements of potential disastrous consequences, such as rock falls, landslides and debris flows. Therefore, it is highly important to quantify the amount of sediments that are supplied from the different compartments and to investigate how glacial retreat influences sediment dynamics in proglacial areas. In the presented work glacier retreat and associated sediment dynamics were investigated in the Kromer valley (Silvretta Alps, Austria) by analyzing remote sensing data. Glacial retreat from the period of 1950 to 2012 was documented by interpreting aerial photographs. By digitizing the different stages of the glaciers for six time frames, changes in glacier area and length were mapped and quantified. In order to identify, characterize and quantify sediment dynamics in the proglacial areas a high resolution DEM of difference (DoD) between 2007 and 2012 was created and analyzed, further differentiating between different zones (e.g. valley bottom, hillslope) and types of geomorphic processes (e.g. fluvial, gravitational). First results will be presented at the EGU General Assembly 2016.
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Crankshaft position sensing with combined starter alternator
Brandenburg, Larry Raymond; Miller, John Michael
2000-06-13
A crankshaft position sensing apparatus for use with an engine (16) having a combined starter/alternator assembly (18). The crankshaft position sensing apparatus includes a tone ring (38) with a sensor (36) and bandpass filter (46), having a cylinder identification input from a camshaft sensor (48), and a gain limiter (54). The sensing apparatus mounts near the rotor (30) of the combined starter/alternator assembly (18). The filtered crankshaft position signal can then be input into a vehicle system controller (58) and an inner loop controller (60). The starter/alternator assembly (18) in combination with an internal combustion engine is particularly useful for a hybrid electric vehicle system.
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Humanes, Adriana; Ricardo, Gerard F; Willis, Bette L; Fabricius, Katharina E; Negri, Andrew P
2017-03-10
Coral reproduction is vulnerable to both declining water quality and warming temperatures, with simultaneous exposures likely compounding the negative impact of each stressor. We investigated how early life processes of the coral Acropora tenuis respond to increasing levels of suspended sediments in combination with temperature or organic nutrients. Fertilization success and embryo development were more sensitive to suspended sediments than to high temperatures or nutrient enrichment, while larval development (after acquisition of cilia) and settlement success were predominantly affected by thermal stress. Fertilization success was reduced 80% by suspended sediments, and up to 24% by temperature, while the addition of nutrients to suspended sediments had no further impact. Larval survivorship was unaffected by any of these treatments. However, settlement success of larvae developing from treatment-exposed embryos was negatively affected by all three stressors (e.g. up to 55% by suspended sediments), while exposure only during later larval stages predominantly responded to temperature stress. Environmentally relevant levels of suspended sediments and temperature had the greatest impacts, affecting more processes than the combined impacts of sediments and nutrients. These results suggest that management strategies to maintain suspended sediments at low concentrations during coral spawning events will benefit coral recruitment, especially with warming climate.
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Luo, Lian-Cong; Qin, Bo-Qiang; Zhu, Guang-Wei
2004-01-01
Investigation was made into sediment depth at 723 irregularly scattered measurement points which cover all the regions in Taihu Lake, China. The combination of successive correction scheme and geostatistical method was used to get all the values of recent sediment thickness at the 69 x 69 grids in the whole lake. The results showed that there is the significant difference in sediment depth between the eastern area and the western region, and most of the sediments are located in the western shore-line and northern regimes but just a little in the center and eastern parts. The notable exception is the patch between the center and Xishan Island where the maximum sediment depth is more than 4.0 m. This sediment distribution pattern is more than likely related to the current circulation pattern induced by the prevailing wind-forcing in Taihu Lake. The numerical simulation of hydrodynamics can strong support the conclusion. Sediment effects on water quality was also studied and the results showed that the concentrations of TP, TN and SS in the western part are obviously larger than those in the eastern regime, which suggested that more nutrients can be released from thicker sediment areas.
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NASA Astrophysics Data System (ADS)
Humanes, Adriana; Ricardo, Gerard F.; Willis, Bette L.; Fabricius, Katharina E.; Negri, Andrew P.
2017-03-01
Coral reproduction is vulnerable to both declining water quality and warming temperatures, with simultaneous exposures likely compounding the negative impact of each stressor. We investigated how early life processes of the coral Acropora tenuis respond to increasing levels of suspended sediments in combination with temperature or organic nutrients. Fertilization success and embryo development were more sensitive to suspended sediments than to high temperatures or nutrient enrichment, while larval development (after acquisition of cilia) and settlement success were predominantly affected by thermal stress. Fertilization success was reduced 80% by suspended sediments, and up to 24% by temperature, while the addition of nutrients to suspended sediments had no further impact. Larval survivorship was unaffected by any of these treatments. However, settlement success of larvae developing from treatment-exposed embryos was negatively affected by all three stressors (e.g. up to 55% by suspended sediments), while exposure only during later larval stages predominantly responded to temperature stress. Environmentally relevant levels of suspended sediments and temperature had the greatest impacts, affecting more processes than the combined impacts of sediments and nutrients. These results suggest that management strategies to maintain suspended sediments at low concentrations during coral spawning events will benefit coral recruitment, especially with warming climate.
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Capturing sediment and nutrients in irrigated terraced landscapes
NASA Astrophysics Data System (ADS)
Slaets, Johanna; Schmitter, Petra; Hilger, Thomas; Piepho, Hans-Peter; Dercon, Gerd; Cadisch, Georg
2016-04-01
Terraces are often promoted as green filters in landscapes, buffering discharge and constituent peaks. For irrigated rice terraces, however, this mitigating potential has not been assessed at the landscape level. Additionally, sediment and nutrient inputs potentially affect soil fertility in agricultural terraces and therefore yield - the extent of the impact depending on the quality and quantity of the captured material. Quantifying such upland-lowland linkages is particularly important in intensely cultivated landscapes, as declining upland soil fertility could alter beneficial hydrological connectivity between terraces and surrounding landscapes. In this study, we therefore quantified the sediment, sediment-associated organic carbon and nitrogen inputs and losses for a 13 ha paddy rice area, surrounded by upland maize cultivation in Northwest Vietnam in 2010 and 2011. Turbidity sensors were used in combination with a linear mixed model in order to obtain continuous predictions of the constituent concentrations. Sediment texture was determined using mid-infrared spectroscopy. Uncertainty on annual load estimates was quantified by calculating 95% confidence intervals with a bootstrap approach. Sediment inputs from irrigation water to the rice area amounted to 48 Mg ha-1 a-1 and runoff during rainfall events contributed an additional 16 Mg ha-1 a-1. Export from the rice terraces equalled 63 Mg ha-1 a-1 of sediments, resulting in a net balance of 28 Mg ha-1 a-1 or a trapping of almost half of the annual sediment inputs. Runoff contributed one third of the sand inputs, while irrigated sediments were predominantly silty. As paddy outflow contained almost exclusively silt- and clay-sized material, 24 Mg ha-1 a-1 of captured sediments consisted of sand. The sediment-associated organic carbon resulted in a deposit of 1.09 Mg ha-1 a-1. For sediment-associated nitrogen, 0.68 Mg ha-1 a-1 was trapped in the terraces. Combining both sediment-associated and dissolved nitrogen, irrigation water provided a total input of 1.11 Mg ha-1 a-1, of which 54% was in the plant-available forms of ammonium and nitrate - an input larger than the recommended application of chemical fertilizer. Rice terraces were net traps for sediment and protected downstream areas by filtering coarse sediments. Combined with the importance of irrigation water as a source of organic carbon and nitrogen for the rice, this connectivity underscores the vulnerability of agricultural terraces to changes in surrounding land use.
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Schnell, Sabine; Olivares, Alba; Piña, Benjamin; Echavarri-Erasun, Beatriz; Lacorte, Silvia; Porte, Cinta
2013-12-15
Sediment contamination poses a potential risk for both ecosystems and human health. Risk assessment is troublesome as sediments contain complex mixtures of toxicants, and traditional chemical analyses can neither provide information about potential hazards to organisms nor identify and measure all present contaminants. This work combines the use of the PLHC-1 cell line and the recombinant yeast assay (RYA) to assess the environmental quality of estuarine and coastal sediments. The application of multiple endpoints (cytotoxicity, generation of oxidative stress, presence of CYP1A inducing agents, micronucleus formation and estrogenicity) revealed that the organic extracts of those sediments affected by industrial activities or collected near harbours and untreated urban discharges showed significant cytotoxicity, micronuclei and CYP1A induction. The study highlights the usefulness of the applied bioassays to identify those sediments that could pose risk to aquatic organisms and that require further action to improve their environmental quality. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Wei, Guangshan; Li, Mingcong; Li, Fenge; Li, Han; Gao, Zheng
2016-11-01
There are close exchanges between sediment and water in estuaries; however, the patterns of prokaryotic community assembly in these two habitat types are still unclear. This study investigated the bacterial and archaeal abundance, diversity, and community composition in the sediment and the overlying water of the Yellow River estuary. Notably higher prokaryotic abundance and diversity were detected in the sediment than in the water, and bacterial abundance and diversity were remarkably higher than those of archaea. Furthermore, the ratio of bacterial to archaeal 16S rRNA gene abundance was significantly lower in the sediment than in the water. Bacterial communities at different taxonomic levels were apparently distinct between the sediment and water, but archaeal communities were not. The most dominant bacteria were affiliated with Deltaproteobacteria and Gammaproteobacteria in sediment and with Alphaproteobacteria and Betaproteobacteria in water. Euryarchaeota and Thaumarchaeota were the most abundant archaea in both habitats. Although distinct prokaryotic distribution patterns were observed, most of the dominant bacteria and archaea present were related to carbon, nitrogen, and sulfur cycling processes, such as methanogenesis, ammonia oxidation, and sulfate reduction. Unexpectedly, prokaryotes from the water showed a higher sensitivity to environmental factors, while only a few factors affected sediment communities. Additionally, some potential co-occurrence relationships between prokaryotes were also found in this study. These results suggested distinct distribution patterns of bacterial and archaeal communities between sediment and overlying water in this important temperate estuary, which may serve as a useful community model for the further ecological and evolutionary study of prokaryotes in estuarine ecosystems.
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Medrano, María; Fuertes, Miguel Ángel; Valbuena, Alejandro; Carrillo, Pablo J P; Rodríguez-Huete, Alicia; Mateu, Mauricio G
2016-11-30
Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.
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The legacy of contaminated sediments in Boston Harbor
Manheim, Frank T.
Scientists at the U.S. Geological Survey (USGS) have assembled a significant body of data that is now in a usable form. The USGS adopted an interdisciplinary approach to begin the pioneering effort at data rescue. This work involved collaboration with the Environmental Protection Agency (EPA), the U.S. Army Corps of Engineers (USACE), the Massachusetts Water Resources Authority (MWRA), Massachusetts Coastal Zone Management, and the National Oceanic and Atmospheric Administration (NOAA). More than 100,000 sediment chemistry analyses from over 1,500 samples were gleaned from 500 references, compiled, and scientifically edited by the USGS and other workers for use in studies of the distribution and fate of contaminants.
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2007-09-30
combined with measured sediment properties, to test the validity of sediment acoustic models , and in particular the poroelastic (Biot) model . Addressing...TERM GOALS 1. Development of accurate models for acoustic scattering from, penetration into, and propagation within shallow water ocean sediments...2. Development of reliable methods for modeling acoustic detection of buried objects at subcritical grazing angles. 3. Improving our
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NASA Astrophysics Data System (ADS)
Yuan, Wenhao; Yin, Daowei; Finlayson, Brian; Chen, Zhongyuan
2012-04-01
The geomorphic impacts of dams on downstream river channels are complex, not readily predictable for specific cases, but widely reported in the literature. For the Three Gorges Dam on the Yangtze (Changjiang) River in China, no studies of the impact of the changed flow and sediment conditions below the dam on the behaviour of the channel were included in the pre-dam feasibility report. We have assembled a database of flow and sediment data for the middle Yangtze River from Yichang to Hankou and used this to analyse changes following the closure of the dam. While total flow is little affected, the operating strategy for the dam that provides for storage of part of the summer high flows to maintain hydroelectric power generation in winter (the low flow season) is reflected in changes to the seasonal distribution of flow below the dam. We calculated potential sediment carrying capacity and compared it with measured sediment concentrations for both pre- and post-dam conditions. While channel sedimentation is indicated along the middle Yangtze for pre-dam conditions, scour is indicated for post-dam conditions, highest at Yichang immediately below the dam and decreasing downstream.
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The advanced receiver 2: Telemetry test results in CTA 21
NASA Technical Reports Server (NTRS)
Hinedi, S.; Bevan, R.; Marina, M.
1991-01-01
Telemetry tests with the Advanced Receiver II (ARX II) in Compatibility Test Area 21 are described. The ARX II was operated in parallel with a Block-III Receiver/baseband processor assembly combination (BLK-III/BPA) and a Block III Receiver/subcarrier demodulation assembly/symbol synchronization assembly combination (BLK-III/SDA/SSA). The telemetry simulator assembly provided the test signal for all three configurations, and the symbol signal to noise ratio as well as the symbol error rates were measured and compared. Furthermore, bit error rates were also measured by the system performance test computer for all three systems. Results indicate that the ARX-II telemetry performance is comparable and sometimes superior to the BLK-III/BPA and BLK-III/SDA/SSA combinations.
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Rendigs, Richard R.; Anderson, Roger Y.; Xu, Jingping; Davis, Raymond E.; Bergeron, Emile M.
2009-01-01
This manual illustrates the development of a programmable instrument designed to deploy a series of wafer-shaped discs (partitions) into the collection tube of a sediment trap in various aquatic environments. These hydrodynamically shaped discs are deployed at discrete time intervals from the Intervalometer and provide markers that delineate time intervals within the sediments that accumulate in the collection tube. The timer and mechanical system are lodged in an air-filled, water-tight pressure housing that is vertically hung within the confines of a cone-shaped sediment trap. The instrumentation has been operationally pressure tested to an equivalent water depth of approximately 1 km. Flaws discovered during extensive laboratory and pressure testing resulted in the implementation of several mechanical modifications (such as a redesign of the rotor and the discs) that improved the operation of the rotor assembly as well as the release of discs through the end cap. These results also identified a preferred azimuth placement of the rotor disc relative to the drop hole of the end cap. In the initial field trial, five sediment traps and coupled Intervalometers were attached to moored arrays and deployed at two sites off the coast of Southern California for approximately 8 months. Each of the instruments released 18 discs at the programmed 10 day intervals, except one unit, which experienced a malfunction after approximately 4 months. Most of the discs oriented in a near-horizontal position upon the surface of the sediment in the collection tubes. Sampling of the sediments for geochemical analyses was improved by these clearly defined markers, which indicated the changes in the flux and nature of sediments accumulated during the deployment period of each sediment trap.
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Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.; ...
2017-02-03
Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less
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Smith, Benjamin D.; Fichthorn, Kristen A.; Kirby, David J.; Quimby, Lisa M.; Triplett, Derek A.; González, Pedro; Hernández, Darimar; Keating, Christine D.
2014-01-01
Understanding how micro- and nanoparticles interact is important for achieving bottom-up assembly of desired structures. Here, we examine the self-assembly of two-component, compositionally asymmetric nanocylinders that sediment from solution onto a solid surface. These particles spontaneously formed smectic arrays. Within the rows of an array, nanocylinders tended to assemble such that neighboring particles had the same orientation of their segments. As a probe of interparticle interactions, we classified nanocylinder alignments by measuring the segment orientations of many sets of neighboring particles. Monte Carlo simulations incorporating an exact expression for the van der Waals (vdW) energy indicate that differences in the vdW interactions, even when small, are the key factor in producing observed segment alignment. These results point to asymmetrical vdW interactions as a potentially powerful means of controlling orientation in multicomponent cylinder arrays, and suggest that designing for these interactions could yield new ways to control self-assembly. PMID:24308771
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Enhancement of dynamin polymerization and GTPase activity by Arc/Arg3.1
Byers, Christopher E.; Barylko, Barbara; Ross, Justin A.; Southworth, Daniel R.; James, Nicholas G.; Taylor, Clinton A.; Wang, Lei; Collins, Katie A.; Estrada, Armando; Waung, Maggie; Tassin, Tara C.; Huber, Kimberly M.; Jameson, David.M.; Albanesi, Joseph P.
2015-01-01
BACKGROUND The Activity-regulated cytoskeleton-associated protein, Arc, is an immediate-early gene product implicated in various forms of synaptic plasticity. Arc promotes endocytosis of AMPA type glutamate receptors and regulates cytoskeletal assembly in neuronal dendrites. Its role in endocytosis may be mediated by its reported interaction with dynamin 2 (Dyn2), a 100 kDa GTPase that polymerizes around the necks of budding vesicles and catalyzes membrane scission. METHODS Enzymatic and turbidity assays are used in this study to monitor effects of Arc on dynamin activity and polymerization. Arc oligomerization is measured using a combination of approaches, including size exclusion chromatography, sedimentation analysis, dynamic light scattering, fluorescence correlation spectroscopy, and electron microscopy. RESULTS We present evidence that bacterially-expressed His6-Arc facilitates the polymerization of Dyn2 and stimulates its GTPase activity under physiologic conditions (37°C and 100 mM NaCl). At lower ionic strength Arc also stabilizes pre-formed Dyn2 polymers against GTP-dependent disassembly, thereby prolonging assembly-dependent GTP hydrolysis catalyzed by Dyn2. Arc also increases the GTPase activity of Dyn3, an isoform of implicated in dendrite remodeling, but does not affect the activity of Dyn1, a neuron-specific isoform involved in synaptic vesicle recycling. We further show in this study that Arc (either His6-tagged or untagged) has a tendency to form large soluble oligomers, which may function as a scaffold for dynamin assembly and activation. CONCLUSIONS and GENERAL SIGNIFICANCE The ability of Arc to enhance dynamin polymerization and GTPase activation may provide a mechanism to explain Arc-mediated endocytosis of AMPA receptors and the accompanying effects on synaptic plasticity. This study represents the first detailed characterization of the physical properties of Arc. PMID:25783003
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Enhancement of dynamin polymerization and GTPase activity by Arc/Arg3.1.
Byers, Christopher E; Barylko, Barbara; Ross, Justin A; Southworth, Daniel R; James, Nicholas G; Taylor, Clinton A; Wang, Lei; Collins, Katie A; Estrada, Armando; Waung, Maggie; Tassin, Tara C; Huber, Kimberly M; Jameson, David M; Albanesi, Joseph P
2015-06-01
The Activity-regulated cytoskeleton-associated protein, Arc, is an immediate-early gene product implicated in various forms of synaptic plasticity. Arc promotes endocytosis of AMPA type glutamate receptors and regulates cytoskeletal assembly in neuronal dendrites. Its role in endocytosis may be mediated by its reported interaction with dynamin 2, a 100 kDa GTPase that polymerizes around the necks of budding vesicles and catalyzes membrane scission. Enzymatic and turbidity assays are used in this study to monitor effects of Arc on dynamin activity and polymerization. Arc oligomerization is measured using a combination of approaches, including size exclusion chromatography, sedimentation analysis, dynamic light scattering, fluorescence correlation spectroscopy, and electron microscopy. We present evidence that bacterially-expressed His6-Arc facilitates the polymerization of dynamin 2 and stimulates its GTPase activity under physiologic conditions (37°C and 100mM NaCl). At lower ionic strength Arc also stabilizes pre-formed dynamin 2 polymers against GTP-dependent disassembly, thereby prolonging assembly-dependent GTP hydrolysis catalyzed by dynamin 2. Arc also increases the GTPase activity of dynamin 3, an isoform of implicated in dendrite remodeling, but does not affect the activity of dynamin 1, a neuron-specific isoform involved in synaptic vesicle recycling. We further show in this study that Arc (either His6-tagged or untagged) has a tendency to form large soluble oligomers, which may function as a scaffold for dynamin assembly and activation. The ability of Arc to enhance dynamin polymerization and GTPase activation may provide a mechanism to explain Arc-mediated endocytosis of AMPA receptors and the accompanying effects on synaptic plasticity. Copyright © 2015 Elsevier B.V. All rights reserved.
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Performance of ultrafiltration membrane process combined with coagulation/sedimentation.
Jang, N Y; Watanabe, Y; Minegishi, S
2005-01-01
Effects of coagulation/sedimentation as a pre-treatment on the dead-end ultrafiltration (UF) membrane process were studied in terms of membrane fouling and removal efficiency of natural dissolved organic matter, using Chitose River water. Two types of experiment were carried out. One was a bench scale membrane filtration with jar-test and the other was membrane filtration pilot plant combined with the Jet Mixed Separator (JMS) as a pre-coagulation/sedimentation unit. In the bench scale experiment, the effects of coagulant dosage, pH and membrane operating pressure on the membrane fouling and removal efficiency of natural dissolved organic matter were investigated. In the pilot plant experiment, we also investigated the effect of pre-coagulation/sedimentation on the membrane fouling and the removal efficiency of natural dissolved organic matter. Coagulation/sedimentation prior to membrane filtration process controlled the membrane fouling and increased the removal efficiency of natural dissolved organic matter.
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Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto
2015-10-14
The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.
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New element for optimizing the functioning of sediment traps
NASA Astrophysics Data System (ADS)
Schwindt, Sebastian; Franca, Mário; Schleiss, Anton
2017-04-01
Sediment traps protect urban areas against excessive sediment transport during hazardous floods and consist typically of a retention basin with an open sediment check dam at the downstream end. The design, as well as the morphological processes within the retention basin, were analyzed by several authors. With regard to open sediment check dams two types of triggering mechanisms for the initiation of sediment retention can be distinguished: (1) mechanical and (2) hydraulic clogging of the structure. Recent studies have shown that outlet structures combining both clogging principles may be considered to avoid undesired self-flushing. Further elements of check dams are conceivable, e.g. for retaining or conveying driftwood. This study analyses experimentally working principles and design criteria of standard elements of sediment traps. Furthermore, it introduces a new structural element to the sediment trap design with a guiding channel in the retention reservoir. Taking into account the natural shape of mountain rivers, the guiding channel has a trapezoidal cross-section shape and a rough but fixed bed. The effect of the guiding channel on sediment deposition pattern and re-mobilization are studied by means of physical model experiments with a standardized hydrograph and variable sediment supply. The results are evaluated by means of zenithal pictures and bedload transport rate, measured at the downstream end of the model. Major advantages of the combined use of both clogging principles include an improved control of the initiation of sediment deposition in order to allow for sediment transfer for small floods and a reduction of hazards related to self-flushing.
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Methods to measure sedimentation of spawning gravels
Thomas E. Lisle; Rand E. Eads
1991-01-01
Sediment transport occurring after spawning can cause scour of incubating embryos and infiltration of fine sediment into spawning gravel, decreasing intergravel flow and preventing hatched fry from emerging from the gravel. Documentation of these effects requires measuring gravel conditions before and after high flow periods and combining methods to record scour and...
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HYDRAULIC CHARACTERISTICS OF SEWER SEDIMENT GATE FLUSHING TANKS: LABORATORY FLUME STUDIES
The objective of this study was to test the performance of gate flushing tanks, simulated in a laboratory flume, to remove sediments from combined sewers and storage tanks. A significant amount of sediment/debris/sludge may accumulate at the bottom of a sewer during dry weather o...
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HYDRAULIC CHARACTERISTICS OF SEWER SEDIMENT GATE-FLUSHING TANKS: LABORATORY FLUME STUDIES
The objective of this study was to test the performance of gate-flushing tanks, simulated in a laboratory flume, to remove sediments from combined sewers and storage tanks. A significant amount of sediment/debris/sludge may accumulate at the bottom of a sewer during dry weather o...
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Formation of polymeric toroidal-spiral particles.
Sharma, Vishal; Szymusiak, Magdalena; Shen, Hao; Nitsche, Ludwig C; Liu, Ying
2012-01-10
Compared to spherical matrices, particles with well-defined internal structure provide large surface to volume ratio and predictable release kinetics for the encapsulated payloads. We describe self-assembly of polymeric particles, whereby competitive kinetics of viscous sedimentation, diffusion, and cross-linking yield a controllable toroidal-spiral (T-S) structure. Precursor polymeric droplets are splashed through the surface of a less dense, miscible solution, after which viscous forces entrain the surrounding bulk solution into the sedimenting polymer drop to form T-S channels. The intricate structure forms because low interfacial tension between the two miscible solutions is dominated by viscous forces. The biocompatible polymer, poly(ethylene glycol) diacrylate (PEG-DA), is used to demonstrate the solidification of the T-S shapes at various configurational stages by UV-triggered cross-linking. The dimensions of the channels are controlled by Weber number during impact on the surface, and Reynolds number and viscosity ratio during subsequent sedimentation. We anticipate applications of the T-S particle in drug delivery, wherein diffusion through these T-S channels and the polymer matrix would offer parallel release pathways for molecules of different sizes. Polyphosphate, as a model macromolecule, is entrained in T-S particles during their formation. The in vitro release kinetics of polyphosphate from the T-S particles with various channel length and width is reported. In addition, self-assembly of T-S particles occurs in a single step under benign conditions for delicate macromolecules, and appears conducive to scaleup.
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DECONTAMINATION AND BENEFICIAL USE OF DREDGED MATERIALS.
DOE Office of Scientific and Technical Information (OSTI.GOV)
STERN, E.A.; LODGE, J.; JONES, K.W.
2000-12-03
Our group is leading a large-sale demonstration of dredged material decontamination technologies for the New York/New Jersey Harbor. The goal of the project is to assemble a complete system for economic transformation of contaminated dredged material into an environmentally-benign material used in the manufacture of a variety of beneficial use products. This requires the integration of scientific, engineering, business, and policy issues on matters that include basic knowledge of sediment properties, contaminant distribution visualization, sediment toxicity, dredging and dewatering techniques, decontamination technologies, and product manufacturing technologies and marketing. A summary of the present status of the system demonstrations including themore » use of both existing and new manufacturing facilities is given here. These decontamination systems should serve as a model for use in dredged material management plans of regions other than NY/NJ Harbor, such as Long Island Sound, where new approaches to the handling of contaminated sediments are desirable.« less
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Book review: Geomagnetism of baked clays and recent sediments
Mankinen, Edward A.
1984-01-01
This book is an outgrowth of the symposium entitled “Time Scales of Geomagnetic Secular Variations,” which was held at the 4th Assembly of the International Association of Geomagnetism and Aeronomy (Edinburgh, U.K., August 1981). The volume includes many of the papers presented, which described paleomagnetic results from both archeologic materials and Holocene geologic deposits, as well as contributions solicited from other researchers in the fields of archeomagnetism and paleomagnetism. In a remarkably short time after the conclusion of the symposium the editors were able to elicit, edit, and assemble a large body of material from 40 individuals into a thoughtful, wellorganized product.
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The MARVEL assembly for neutron multiplication.
Chichester, David L; Kinlaw, Mathew T
2013-10-01
A new multiplying test assembly is under development at Idaho National Laboratory to support research, validation, evaluation, and learning. The item is comprised of three stacked, highly-enriched uranium (HEU) cylinders, each 11.4 cm in diameter and having a combined height of up to 11.7 cm. The combined mass of all three cylinders is 20.3 kg of HEU. Calculations for the bare configuration of the assembly indicate a multiplication level of >3.5 (k(eff)=0.72). Reflected configurations of the assembly, using either polyethylene or tungsten, are possible and have the capability of raising the assembly's multiplication level to greater than 10. This paper describes simulations performed to assess the assembly's multiplication level under different conditions and describes the resources available at INL to support the use of these materials. We also describe some preliminary calculations and test activities using the assembly to study neutron multiplication. Copyright © 2013 Elsevier Ltd. All rights reserved.
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De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman
2017-04-07
The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Ae aegypti and Culex quinquefasciatus , each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species. Copyright © 2017, American Association for the Advancement of Science.
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Barjhoux, Iris; Clérandeau, Christelle; Menach, Karyn Le; Anschutz, Pierre; Gonzalez, Patrice; Budzinski, Hélène; Morin, Bénédicte; Baudrimont, Magalie; Cachot, Jérôme
2017-08-01
Sediment compartment is a long term sink for pollutants and a secondary source of contamination for aquatic species. The abiotic factors controlling the bioavailability and thus the toxicity of complex mixtures of pollutants accumulated in sediments are poorly documented. To highlight the different factors influencing sediment toxicity, we identified and analyzed the physico-chemical properties, micro-pollutant contents, and toxicity level of six contrasted sediments in the Lot-Garonne continuum. Sediment toxicity was evaluated using the recently described Japanese medaka (Oryzias latipes) embryo-larval assay with direct exposure to whole sediment (MELAc). Multiple toxicity endpoints including embryotoxicity, developmental defects and DNA damage were analyzed in exposed embryos. Chemical analyses revealed significant variations in the nature and contamination profile of sediments, mainly impacted by metallic trace elements and, unexpectedly, polycyclic aromatic hydrocarbons. Exposure to sediments induced different toxic impacts on medaka early life stages when compared with the reference site. Principal component analysis showed that the toxic responses following exposure to sediments from the Lot River and its tributary were associated with micro-pollutant contamination: biometric measurements, hatching success, genotoxicity, craniofacial deformities and yolk sac malabsorption were specifically correlated to metallic and organic contaminants. Conversely, the main biological responses following exposure to the Garonne River sediments were more likely related to their physico-chemical properties than to their contamination level. Time to hatch, cardiovascular injuries and spinal deformities were correlated to organic matter content, fine particles and dissolved oxygen levels. These results emphasize the necessity of combining physico-chemical analysis of sediment with toxicity assessment to accurately evaluate the environmental risks associated with sediment contamination. Copyright © 2017 Elsevier Inc. All rights reserved.
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Zabaleta, Ane; Meaurio, Maite; Ruiz, Estilita; Antigüedad, Iñaki
2014-01-01
Climate change is likely to have an impact on runoff and fluvial sediments in watersheds. These factors are among those used to characterize water bodies in relation to the European Water Framework Directive (WFD). Hence, it is important to investigate the extent to which climate change may hinder the achievement of the objectives of the WFD. We explored the potential impact of climate change on runoff and sediment yield for the Aixola watershed using the Soil and Water Assessment Tool (SWAT). The model calibration (2007-2010) and validation (2005-2006) results were rated as satisfactory. Subsequently, simulations were run for four climate change model-scenario combinations based on two general circulation models (CGCM2 and ECHAM4) under two emissions scenarios (A2 and B2) from 2011 to 2100. All combinations predicted that runoff and sediment yield would decrease compared with baseline (1961-1990). Three combinations suggested that runoff and sediments would decrease by 0.13 to 0.45 m s and 0.11 to 0.43 t every year from 2011 to 2100. However, the CGCM2-B2 scenario resulted in an "extremely likely" increase in runoff and sediments of 0.94 m s and 0.57 t every year. These variations in annual sediment yield are closely related to changes in precipitation. The high degree of uncertainty in the results must be considered when assessing potential impacts and making decisions about adaptation measures. Nevertheless, this first attempt to estimate future sediment yields in our region could be a useful starting point to explore future hydrological impacts in the area. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
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7 CFR 58.634 - Assembling and combining mix ingredients.
Code of Federal Regulations, 2010 CFR
2010-01-01
... 7 Agriculture 3 2010-01-01 2010-01-01 false Assembling and combining mix ingredients. 58.634 Section 58.634 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) REGULATIONS...
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7 CFR 58.634 - Assembling and combining mix ingredients.
Code of Federal Regulations, 2011 CFR
2011-01-01
... 7 Agriculture 3 2011-01-01 2011-01-01 false Assembling and combining mix ingredients. 58.634 Section 58.634 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) REGULATIONS...
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15N indicates an active N-cycling microbial community in low carbon, freshwater sediments.
NASA Astrophysics Data System (ADS)
Sheik, C.
2017-12-01
Earth's large lakes are unique aquatic ecosystems, but we know little of the microbial life driving sedimentary biogeochemical cycles and ultimately the isotopic record. In several of these large lakes, water column productivity is constrained by element limitation, such as phosphorus and iron, creating oligotrophic water column conditions that drive low organic matter content in sediments. Yet, these sediments are biogeochemically active and have been shown to have oxygen consumption rates akin to pelagic ocean sediments and complex sulfur cycling dynamics. Thus, large oligotrophic lakes provide unique and interesting biogeochemical contrast to highly productive freshwater and coastal marine systems. Using Lake Superior as our study site, we found microbial community structure followed patterns in bulk sediment carbon and nitrogen concentrations. These observed patterns were loosely driven by land proximity, as some stations are more coastal and have higher rates of sedimentation, allochthonous carbon inputs and productivity than pelagic sites. Interestingly, upper sediment carbon and nitrogen stable isotopes were quite different from water column. Sediment carbon and nitrogen isotopes correlated significantly with microbial community structure. However, 15N showed much stronger correlation than 13C, and became heavier with core depth. Coinciding with the increase in 15N values, we see evidence of both denitrification and anammox processes in 16S rRNA gene libraries and metagenome assembled genomes. Given that microorganisms prefer light isotopes and that these N-cycling processes both contribute to N2 production and efflux from the sediment, the increase in 15N with sediment depth suggests microbial turnover. Abundance of these genomes also varies with depth suggesting these novel microorganisms are partitioning into specific sediment geochemical zones. Additionally, several of these genomes contain genes involved in sulphur cycling, suggesting a dual biogeochemical role and potential for a cryptic sulfur cycle. Together, Lake Superior sediments offer a glimpse into microbial metabolism in carbon limited environments. Further the pervasiveness of co-metabolic pathways suggests interpretation of isotopic records may be messier than previously thought.
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Morphological processes in permeable sediment traps with check dams
NASA Astrophysics Data System (ADS)
Schwindt, S.; Franca, M. J.; Schleiss, A. J.
2017-12-01
Sediment traps serve for the retention of sediment in the case of major floods, but the retention of sediment is not wanted up to smaller frequent floods which are important to the morphodynamics of rivers. A new concept for the sediment traps that enables sediment transfer for frequent floods and safely retains sediment in the case of important floods was recently developed and experimentally tested. The tests were performed using a standardized hydrograph and different barrier types for the mechanically or hydraulically controlled retention of sediments. The deposition pattern was measured at the end of every experimental run using a motion sensing camera. These measurements show that the shape of the deposits varies as a function of the retention control type (mechanical or hydraulic) and particularly as a function of the barrier height. Deposits were large when a high barrier was applied that was not overflown, and when both control types were combined. The deposition slope was shallow in the case of the high barrier, steeper for combined controls and steepest when mechanical control only was tested. The study enables a better understanding for the optimization of the shape of artificial deposition areas upstream of partially permeable check dams to enhance the tradeoff between eco-morphological and economical aspects of flood protection.
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In situ observation of the water-sediment interface in combined sewers, using endoscopy.
Oms, C; Gromaire, M C; Chebbo, G
2003-01-01
A new method for water-sediment interface observation has been designed. This system is based on a small diameter endoscope protected by a graduated plastic tube. It makes it possible to visualise in a non-destructive manner the sediments and the water-sediment interface. The endoscope was used to investigate Le Marais catchment (Paris): an immobile organic layer was observed at the water-sediment interface. This layer appears in pools of gross bed sediment, at the upstream of collectors, in zones where velocity is slow and where bed shear stress is less than 0.03 N/m2.
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Functional evaluation of pollutant transformation in sediment from combined sewer system.
Shi, Xuan; Ngo, Huu Hao; Sang, Langtao; Jin, Pengkang; Wang, Xiaochang C; Wang, Guanghua
2018-07-01
In this study, a pilot combined sewer system was constructed to characterize the pollutant transformation in sewer sediment. The results showed that particulate contaminants deposited from sewage could be transformed into dissolved matter by distinct pollutant transformation pathways. Although the oxidation-reduction potential (ORP) was varied from -80 mV to -340 mV in different region of the sediment, the fermentation was the dominant process in all regions of the sediment, which induced hydrolysis and decomposition of particulate contaminants. As a result, the accumulation of dissolved organic matter and the variation of ORP values along the sediment depth led to the depth-dependent reproduction characteristics of methanogens and sulfate-reducing bacteria, which were existed in the middle and deep layer of the sediment respectively. However, the diversity of nitrifying and polyphosphate-accumulating bacteria was low in sewer sediment and those microbial communities showed a non-significant correlation with nitrogen and phosphorus contaminants, which indicated that the enrichment of nitrogen and phosphorus contaminants was mainly caused by physical deposition process. Thus, this study proposed a promising pathway to evaluate pollutant transformation and can help provide theoretical foundation for urban sewer improvement. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Bosch, Carme; Olivares, Alba; Faria, Melissa; Navas, Jose M; del Olmo, Iván; Grimalt, Joan O; Piña, Benjamín; Barata, Carlos
2009-08-13
A combination of cost effective sublethal Daphnia magna feeding tests, yeast- and cell culture-based bioassays and Toxicity Identification Evaluation (TIE) procedures was used to characterize toxic compounds within sediments collected in a river area under the influence of the effluents from a chlor-alkali industry (Ebro River, NE Spain). Tests were designed to measure and identify toxic compounds in the particulate and filtered water fractions of sediment elutriates. The combined use of bioassays responding to elutriates and dioxin-like compounds evidenced the existence of three major groups of hazardous contaminants in the most contaminated site: (A) metals such as cadmium and mercury bound to sediment fine particles that could be easily resuspended and moved downstream, (B) soluble compounds (presumably, lye) able to alkalinize water to toxic levels, and (C) organochlorine compounds with high dioxin-like activity. These results provided evidence that elutriate D. magna feeding responses can be used as surrogate assays for more tedious chronic whole sediment tests, and that the incorporation of such tests in sediment TIE procedures may improve the ability to identify the toxicity of particle-bound and water-soluble contaminants in sediments.
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Impacts of chemical gradients on microbial community structure
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less
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Impacts of chemical gradients on microbial community structure
Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.; ...
2017-01-17
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less
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Impacts of chemical gradients on microbial community structure
Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc
2017-01-01
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems. PMID:28094795
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Impacts of chemical gradients on microbial community structure.
Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc
2017-04-01
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.
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Sze, Sing-Hoi; Parrott, Jonathan J; Tarone, Aaron M
2017-12-06
While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. Our divide-and-conquer strategy allows memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies.
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Relation of waterfowl poisoning to sediment lead concentrations in the Coeur d'Alene River Basin
Beyer, W.N.; Audet, D.J.; Heinz, G.H.; Hoffman, D.J.; Day, D.
2000-01-01
For many years, waterfowl have been poisoned by lead after ingesting contaminated sediment in the Coeur d'Alene River Basin, in Idaho. Results of studies on waterfowl experimentally fed this sediment were combined with results from field studies conducted in the Basin to relate sediment lead concentration to injury to waterfowl. The first step in the model estimated exposure as the relation of sediment lead concentration to blood lead concentration in mute swans (Cygnus olor), ingesting 22% sediment in a rice diet. That rate corresponded to the 90th percentile of sediment ingestion estimated from analyses of feces of tundra swans (Olor columbianus) in the Basin. Then, with additional laboratory studies on Canada geese (Branta canadensis) and mallards (Anas platyrhynchos) fed the sediment, we developed the general relation of blood lead to injury in waterfowl. Injury was quantified by blood lead concentrations, ALAD (-aminolevulinic acid dehydratase) activity, protoporphyrin concentrations, hemoglobin concentrations, hepatic lead concentrations, and the prevalence of renal nuclear inclusion bodies. Putting the exposure and injury relations together provided a powerful tool for assessing hazards to wildlife in the Basin. The no effect concentration of sediment lead was estimated as 24 mg/kg and the lowest effect level as 530 mg/kg. By combining our exposure equation with data on blood lead concentrations measured in moribund tundra swans in the Basin, we estimated that some mortality would occur at a sediment lead concentration as low as 1800 mg/kg.
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NASA Astrophysics Data System (ADS)
Glud, Ronnie Nøhr; Jensen, Kim; Revsbech, Niels Peter
1995-01-01
Diffusional characteristics of two biologically active surface sediments were determined by use of a combined N 2O-O 2 microsensor. By analyzing changes in the N2O-gradients in these sediments, it was possible to determine the product ( φDs) for this species with submillimetre depth resolution, where φ is the porosity and Ds the substrate diffusion coefficient. The ( φDs)-value for O 2 could be calculated then from ( φDs)-value for N 2O, because the diffusivity of the two molecules were modified in the same way within the sediment. Both sediments exhibited fine-scale horizontal and vertical variability in diffusion characteristics, and this must be accounted for when analyzing microprofile data. The average ( φDs)-value for N 2O at 20°C for an estuarine surface sediment was 0.93 × 10 -5 cm2 s -1 (at 0-4 mm depth), while the value for the upper 2 mm of a stream sediment covered by a microbial mat was 1.42 × 10 -5 cm 2 s -1. Biological inactivation and oxidation by exposure to an O 2 atmosphere had no effect on the measured ( φDs) for the estuarine sediment; however, the value for the sediment covered by a microbial mat, with dense populations of meiofauna, decreased by 20%. The method presented is ideal for measurements of diffusivity at a high spatial resolution in surficial sediments and densely packed microbial communities.
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Formation of Heterogeneous Toroidal-Spiral Particles -- by Drop Sedimentation and Interaction
NASA Astrophysics Data System (ADS)
Liu, Ying; Nitsche, Ludwig; Gemeinhart, Richard; Sharma, Vishal; Szymusiak, Magdalena; Shen, Hao
2013-03-01
We describe self-assembly of polymeric particles, whereby competitive kinetics of viscous sedimentation, diffusion, and cross-linking yield a controllable toroidal-spiral (TS) structure. Precursor polymeric droplets are splashed through the surface of a less dense, miscible solution, after which viscous forces entrain the surrounding bulk solution into the sedimenting polymer drop to form TS channels. The intricate structure forms because low interfacial tension between the two miscible solutions is dominated by viscous forces. The biocompatible polymer, poly(ethylene glycol) diacrylate (PEG-DA), is used to demonstrate the solidification of the TS shapes at various configurational stages by UV-triggered cross-linking. The dimensions of the channels are controlled by Weber number during impact on the surface, and Reynolds number and viscosity ratio during subsequent sedimentation. Within the critical separation distance, interaction of multiple drops generates similar structure with more flexibility. Furthermore, the understanding of multiple drop interaction is essential for mass production of TS particles by using parallel and sequential arrays of drops. This work was supported by NSF CBET Grant CBET-1039531.
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NASA Astrophysics Data System (ADS)
Strode, Evita; Jansons, Mintauts; Purina, Ingrida; Balode, Maija; Berezina, Nadezhda A.
2017-08-01
The aim of this study was to assess the toxicity of bottom sediment and to estimate the potential effects of contaminated sediment on health of benthic organisms in the Gulf of Riga (eastern Baltic Sea). Two endpoints were used: survival rate (acute toxicity test) of five crustacean amphipod species and frequency of embryo malformation (samples were collected from the field) in the two species. Toxic resistance of living animals to sediment quality was measured as survival rate (%) at 25 study sites from 2010-2012. Significant differences in the toxic resistance between species were found: 80-100% for Monoporeia affinis, 70-95% for Corophium volutator, 38-88% for Pontogammarus robustoides, 38-100% for Bathyporeia pilosa and 60-100% for Hyalella azteca. Reproductive disorders, measured as percentage (%) of malformed embryos per female, varied in the ranges of 0.0-9.5% in deep water species M. affinis and 0.3-7.5% in littoral species P. robustoides. Both the acute toxicity test and embryo malformation test (only M. affinis was used) indicated moderate and poor sediment quality at 20% and 12% accordingly in the study sites, low toxicity of sediment was estimated in 64% of cases, and no toxicity was recorded in the rest of the cases (4%). Additionally, sediment toxicity test using aquatic organisms was combined with sediment chemical analysis (trace metals) and the Benthic Quality Index (macrozoobenthos) was based on data collected from 13 sites in the Gulf of Riga in 2010 and used for triad sediment quality assessment. According to this combined approach, 23% of the bottom sediments were classified as likely impacted and 23% as possibly impacted (central and southern part of the Gulf). However, the remaining 54% was identified as likely un-impacted. The sediment quality assessment with single survival test or chemical analyses showed better sediment quality in the Gulf than the triad method. The embryo malformation test appeared to be more sensitive to pollution than acute toxicity survival test, that allow us to recommend the inclusion of this novel biomarker in environmental monitoring, while combining it with other tests. In general, our results indicate good or moderate states of sediments and minimal effects of the toxic contamination in them on the Gulf of Riga ecosystem.
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Anaya, Roberto; Braun, Christopher L.; Kuniansky, Eve L.
2000-01-01
A shallow alluvial aquifer at the Naval Weapons Industrial Reserve Plant near Dallas, Texas, has been contaminated by organic solvents used in the fabrication and assembly of aircraft and aircraft parts. Natural gamma-ray and electromagnetic-induction log data collected during 1997 from 162 wells were integrated with existing lithologic and cone-penetrometer test log data to improve characterization of the subsurface alluvium at the site. The alluvium, consisting of mostly fine-grained, low-permeability sediments, was classified into low, intermediate, and high clay-content sediments on the basis of the gamma-ray logs. Low clay-content sediments were interpreted as being relatively permeable, whereas high clay-content sediments were interpreted as being relatively impermeable. Gamma-ray logs, cone-penetrometer test logs, and electromagnetic-induction logs were used to develop a series of intersecting sections to delineate the spatial distribution of low, intermediate, and high clay-content sediments and to delineate zones of potentially contaminated sediments. The sections indicate three major sedimentary units in the shallow alluvial aquifer at NWIRP. The lower unit consists of relatively permeable, low clay-content sediments and is absent over the southeastern and northwestern part of the site. Permeable zones in the complex, discontinuous middle unit are present mostly in the western part of the site. In the eastern and southeastern part of the site, the upper unit has been eroded away and replaced by fill material. Zones of potentially contaminated sediments are generally within the uppermost clay layer or fill material. In addition, the zones tend to be local occurrences.
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Sediment accumulation and mixing in the Penobscot River and estuary, Maine.
Yeager, K M; Schwehr, K A; Schindler, K J; Santschi, P H
2018-04-16
Mercury (Hg) was discharged in the late 1960s into the Penobscot River by the Holtra-Chem chlor-alkali production facility, which was in operation from 1967 to 2000. To assess the transport and distribution of total Hg, and recovery of the river and estuary system from Hg pollution, physical and radiochemical data were assembled from sediment cores collected from 58 of 72 coring stations sampled in 2009. These stations were located throughout the lower Penobscot River, and included four principal study regions, the Penobscot River (PBR), Mendall Marsh (MM), the Orland River (OR), and the Penobscot estuary (ES). To provide the geochronology required to evaluate sedimentary total Hg profiles, 58 of 72 sediment cores were dated using the atmospheric radionuclide tracers 137 Cs, 210 Pb, and 239,240 Pu. Sediment cores were assessed for depths of mixing, and for the determination of sediment accumulation rates using both geochemical (total Hg) and radiochemical data. At most stations, evidence for significant vertical mixing, derived from profiles of 7 Be (where possible) and porosity, was restricted to the upper ~1-3cm. Thus, historic profiles of both total Hg and radionuclides were only minimally distorted, allowing a reconstruction of their depositional history. The pulse input tracers 137 Cs and 239,240 Pu used to assess sediment accumulation rates agreed well, while the steady state tracer 210 Pb exhibited weaker agreement, likely due to irregular lateral sediment inputs. Copyright © 2018. Published by Elsevier B.V.
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Moll, Karen M; Zhou, Peng; Ramaraj, Thiruvarangan; Fajardo, Diego; Devitt, Nicholas P; Sadowsky, Michael J; Stupar, Robert M; Tiffin, Peter; Miller, Jason R; Young, Nevin D; Silverstein, Kevin A T; Mudge, Joann
2017-08-04
Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.
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Measuring suspended sediment in small mountain streams
Robert B. Thomas
1985-01-01
Measuring suspended sediment concentration in streams provides a way of monitoring the effects of forest management activities on water quality. Collecting data on suspended sediment is an act of sampling. The nature of the delivery process and the circumstances under which data are collected combine to produce highly variable results that are difficult to analyze and...
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Zill, Julie A; Gil, Michael A; Osenberg, Craig W
2017-03-01
Environmental stressors often interact, but most studies of multiple stressors have focused on combinations of abiotic stressors. Here we examined the potential interaction between a biotic stressor, the vermetid snail Ceraesignum maximum , and an abiotic stressor, high sedimentation, on the growth of reef-building corals. In a field experiment, we subjected juvenile massive Porites corals to four treatments: (i) neither stressor, (ii) sedimentation, (iii) vermetids or (iv) both stressors. Unexpectedly, we found no effect of either stressor in isolation, but a significant decrease in coral growth in the presence of both stressors. Additionally, seven times more sediment remained on corals in the presence (versus absence) of vermetids, likely owing to adhesion of sediments to corals via vermetid mucus. Thus, vermetid snails and high sedimentation can interact to drive deleterious effects on reef-building corals. More generally, our study illustrates that environmental factors can combine to have negative interactive effects even when individual effects are not detectable. Such 'ecological surprises' may be easily overlooked, leading to environmental degradation that cannot be anticipated through the study of isolated factors. © 2017 The Author(s).
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The Self- and Directed Assembly of Nanowires
NASA Astrophysics Data System (ADS)
Smith, Benjamin David
This thesis explores the self- and directed assembly of nanowires. Specifically, we examine the driving forces behind nanowire self-assembly and the macro-structures that are formed. Particle-dense, oriented nanowire structures show promise in the fields of photonics, energy, sensing, catalysis, and electronics. Arrays of spherical particles have already found uses in electronic inks, sensing arrays, and many other commercial applications; but, it is a challenge to create specific arrays of morphologically and/or compositionally anisotropic particles. The following chapters illuminate the interactions that drive the assembly of anisotropic particles in high density solutions in the absence of applied fields or solution drying. Special emphasis is placed on the structures that are formed. The properties of micro- and nanoparticles and their assembly are introduced in Chapter 1. In particular, the properties of shape and material anisotropic particles are highlighted, while challenges in producing desired arrays are discussed. In this thesis, metallic nanowires of increasing complexity were used to examine the self-assembly behavior of both shape and material anisotropic particles. Nanowires were synthesized through templated electrodeposition. In this process, porous alumina membranes served as a template in which metal salts were reduced to form particles. Upon template dissolution, billions of nominally identical particles were released. We specifically focused on segmented, metallic nanowires 2-13 mum in length and 180 to 350 nm in diameter. Since these particles have strong van der Waals (VDWs) attractions, an electrostatically repulsive coating was necessary to prevent aggregation; we used small molecule, DNA, or amorphous silica coatings. Nanowires and their coatings were characterized by electron microscopy. In order to study self-assembly behavior, particle-dense aqueous suspensions were placed within an assembly chamber defined by a silicone spacer. The nanowires rapidly sedimented due to gravity onto a glass cover slip to concentrate and form a dense film. Particles and assemblies were imaged using inverted optical microscopy. We quantitatively analyzed the images and movies captured in order to track and classify particles and classify the overall arrays formed. We then correlated how particle characteristics, e.g., materials, size, segmentation, etc. changed the ordering and alignment observed. With that knowledge, we hope to be able to form new and interesting structures. We began our studies by examining the assembly of single component nanowires. Chapter 2 describes this work, in which solid Au nanowires measuring 2-7 mum in length and 290 nm in diameter self-assembled into smectic rows. By both experiment and theory, we determined that these rows formed due to a balance of electrostatic repulsions and van der Waals attractions. Final assemblies were stable for at least several days. Monte Carlo methods were used to simulate assemblies and showed structures that mirrored those experimentally observed. Simulations indicated that the smectic phase was preferred over others, i.e., nematic, when an additional small charge was added to the ends of the nanowires. Our particles have rough tips, which might create these additional electrostatic repulsions. To increase the particle and array complexity, two-component, metallic nanowire assembly was explored in Chapter 3. We examined numerous types of nanowires by changing the segment length, ratio, and material, the nanowire length, the surface coating, and the presence of small third segments. These segmented nanowires were generally Au-Ag and also ordered into smectic rows. Segmented wires arranged in rows, however, can be aligned in two possible ways with respect to a neighboring particle. The Au segments on neighboring particles can be oriented in the same direction or opposed to each other. Orientation was quantified in terms of an order parameter that took into account alignment with respect to nearest neighbor particles. All experiments showed order parameters indicating a slight preference for orientational ordering that was relatively insensitive to segment size, nanowire size, and nanowire coating. Monte Carlo simulations pointed towards this alignment as a consequence of small differences in the van der Waals attractions between the segments. Experimentally, ordering might to be limited by the large size of the nanowires, which results in kinetically trapped structures. In an attempt to obtain better ordering within rows, silica coated nanowires with partial Au cores were made. The synthesis involved silica-coating the nanowires and selectively etching a Ag segment. These particles have extremely different VDWs attractions between their segments, as the Au cores are much more attractive than the solvent-filled etched ends. The assembly of these partially etched nanowires (PENs) is detailed in Chapters 4, 5, and 6. When allowed to self-assemble, we observed the formation of either vertically or horizontally oriented arrays depending on PEN composition. The formation of vertically oriented arrays of anisotropic particles is important, since not many methods to produce these structures are currently available for particles of this size. We examined the effects of PEN length, PEN diameter, and the size, number, and location of the core segments. Our findings showed a large etched segment at one end (which resulted in a large offset in the center of mass and concentrated the VDWs attractions to one end of the particle) resulted in the best columnar assemblies. These vertically orientated arrays formed in a two part process. First, after PENs sedimented, they fell flat and oriented parallel to the surface. These PENs then sampled many orientations, including rotating out of the surface plane. When higher surface concentrations of particles built as more PENs fell to the surface of the cover slip, neighboring particles stabilized vertical orientations. Second, particles fell oriented vertically and when the surface concentrations were high, they retained this orientation upon reaching the substrate. Since vertically aligned PENs supported each other, assembly into vertical arrays was highly dependent on the surface concentration. But, oriented arrays could be easily formed on larger or smaller substrates, provided a particle concentration scaled to the substrate were used. The mixing of these particles to form heterogeneous arrays was examined. The overall array structure favored that of particles which sedimented more quickly and/or were present in higher amounts. The semi-automated counting of PENs in images by software is used heavily in Chapters 4 and 5. Appendix A describes the use, development, and validation of macros within Image-Pro. The structure, syntax, and use are specifically examined for three nanowire counting macros. The counting results; including: number of particles in an image, number of horizontally vs. vertically oriented PENs, and PENs in microwells; are compared with manual hand counts. Chapter 7 examines the overall conclusions and future directions for this research. By combining our assembly techniques with known directing forces (e.g., electric or magnetic fields) more specific alignment and/or positioning could be achieved. We have also begun to explore directing assembly through lithographic microwells. Further work needs to explore the integration of arrays into devices and the use of functional materials. Then, high density, oriented arrays could be created for photonic, energy, sensing, catalytic, and electronic applications.
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Linnik, V G; Brown, J E; Dowdall, M; Potapov, V N; Surkov, V V; Korobova, E M; Volosov, A G; Vakulovsky, S M; Tertyshnik, E G
2005-03-01
The radioactive contamination of a riverine floodplain, heavily influenced by discharges from Krasnoyarsk-26, has been studied with respect to sedimentation processes and the geomorphology of the Upper Yenisey floodplain. The study was effected by implementation of a regime of in situ observations and measurements, sampling, and the interpretation of satellite images. The results of the study indicate that on the Balchug Bypass Floodplain, radionuclide contamination is primarily influenced by the thickness of the deposited sediments, and the area can be considered as two depositional environments. The Balchug floodplain area was contaminated due to sedimentation of radionuclide-contaminated alluvium, whose depositional regime significantly changed after the construction of a hydroelectric power station in 1967. Contamination levels are lower on the upstream part of the floodplain where sediment depth is less than 0.2-0.3 m, and this contamination started to accumulate in 1967, while the downstream part of the floodplain, exhibiting deeper deposits, displays higher levels of radionuclide contamination because radionuclides began to deposit here in 1958 when the Krasnoyarsk-26 Mining and Chemical Combine (KMCC) commenced operation. Radionuclide contamination of the floodplain is also related to the elevation of the floodplain, higher regions of the floodplain typically having lower contamination than low-lying areas, which tend to be frequently inundated with sediments being deposited during such inundations. Local relief, its orientation, and vegetation cover have also combined to form sediment traps with significantly higher radionuclide contamination. Lithological analysis combined with radiometric assay indicates a total 137Cs floodplain inventory of 33.7 GBq.
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Electrolytic oxide reduction system
Wiedmeyer, Stanley G; Barnes, Laurel A; Williamson, Mark A; Willit, James L; Berger, John F
2015-04-28
An electrolytic oxide reduction system according to a non-limiting embodiment of the present invention may include a plurality of anode assemblies, a plurality of cathode assemblies, and a lift system configured to engage the anode and cathode assemblies. The cathode assemblies may be alternately arranged with the anode assemblies such that each cathode assembly is flanked by two anode assemblies. The lift system may be configured to selectively engage the anode and cathode assemblies so as to allow the simultaneous lifting of any combination of the anode and cathode assemblies (whether adjacent or non-adjacent).
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Fluvial sediment supply to a mega-delta reduced by shifting tropical-cyclone activity.
Darby, Stephen E; Hackney, Christopher R; Leyland, Julian; Kummu, Matti; Lauri, Hannu; Parsons, Daniel R; Best, James L; Nicholas, Andrew P; Aalto, Rolf
2016-11-10
The world's rivers deliver 19 billion tonnes of sediment to the coastal zone annually, with a considerable fraction being sequestered in large deltas, home to over 500 million people. Most (more than 70 per cent) large deltas are under threat from a combination of rising sea levels, ground surface subsidence and anthropogenic sediment trapping, and a sustainable supply of fluvial sediment is therefore critical to prevent deltas being 'drowned' by rising relative sea levels. Here we combine suspended sediment load data from the Mekong River with hydrological model simulations to isolate the role of tropical cyclones in transmitting suspended sediment to one of the world's great deltas. We demonstrate that spatial variations in the Mekong's suspended sediment load are correlated (r = 0.765, P < 0.1) with observed variations in tropical-cyclone climatology, and that a substantial portion (32 per cent) of the suspended sediment load reaching the delta is delivered by runoff generated by rainfall associated with tropical cyclones. Furthermore, we estimate that the suspended load to the delta has declined by 52.6 ± 10.2 megatonnes over recent years (1981-2005), of which 33.0 ± 7.1 megatonnes is due to a shift in tropical-cyclone climatology. Consequently, tropical cyclones have a key role in controlling the magnitude of, and variability in, transmission of suspended sediment to the coast. It is likely that anthropogenic sediment trapping in upstream reservoirs is a dominant factor in explaining past, and anticipating future, declines in suspended sediment loads reaching the world's major deltas. However, our study shows that changes in tropical-cyclone climatology affect trends in fluvial suspended sediment loads and thus are also key to fully assessing the risk posed to vulnerable coastal systems.
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Zhao, Liangyuan; Jiang, Jinhui; Chen, Chuanhong; Zhan, Shuie; Yang, Jiaoyan; Yang, Shao
2017-05-01
Phytoremediation is an economic and promising technique for removing toxic pollutants from the environment. Freshwater sediments are regarded as the ultimate sink of the widely used PBDE congener decabromodiphenyl ether (BDE-209) in the environment. In the study, the aquatic macrophyte Scirpus validus was selected to remove BDE-209 from three types of sediments (silt, clay, and sand) at an environmentally relevant concentration. After 18 months of phytoremediation experiment, S. validus significantly enhanced the dissipation rates of BDE-209 in all the sediments compared to the controls. Average removal rates of BDE-209 in the three treatments of silt, clay, and sandy sediments with S. validus were respectively 92.84, 84.04, and 72.22%, which were 148, 197, and 233% higher than that in the control sediments without S. validus. In the phytoremediation process, the macrophyte-rhizosphere microbe combined degradation was the main pathway of BDE-209 removal. Sixteen lower brominated PBDE congeners (di- to nona-) were detected in the sediments and plant tissues, confirming metabolic debromination of BDE-209 in S. validus. A relatively higher proportion of penta- and di-BDE congeners among the metabolites in plant tissues than that in the sediments indicated further debromination of PBDEs within plants. The populations and activities of microorganisms in the sediments were greatly promoted by S. validus. Bacterial community structure in BDE-209-contaminated rhizosphere sediments was different from that in the control rhizosphere sediment, as indicated by the dominant proportions of β-proteobacteria, δ-proteobacteria, α-proteobacteria, Acidobacteria, and Chloroflexi in the microbial flora. All these results suggested that S. validus was effective in phytoremediation of BDE-209 by the macrophyte-rhizosphere microbe combined degradation in aquatic sediments.
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Performance of the dipstick screening test as a predictor of negative urine culture
Marques, Alexandre Gimenes; Doi, André Mario; Pasternak, Jacyr; Damascena, Márcio dos Santos; França, Carolina Nunes; Martino, Marinês Dalla Valle
2017-01-01
ABSTRACT Objective To investigate whether the urine dipstick screening test can be used to predict urine culture results. Methods A retrospective study conducted between January and December 2014 based on data from 8,587 patients with a medical order for urine dipstick test, urine sediment analysis and urine culture. Sensitivity, specificity, positive and negative predictive values were determined and ROC curve analysis was performed. Results The percentage of positive cultures was 17.5%. Nitrite had 28% sensitivity and 99% specificity, with positive and negative predictive values of 89% and 87%, respectively. Leukocyte esterase had 79% sensitivity and 84% specificity, with positive and negative predictive values of 51% and 95%, respectively. The combination of positive nitrite or positive leukocyte esterase tests had 85% sensitivity and 84% specificity, with positive and negative predictive values of 53% and 96%, respectively. Positive urinary sediment (more than ten leukocytes per microliter) had 92% sensitivity and 71% specificity, with positive and negative predictive values of 40% and 98%, respectively. The combination of nitrite positive test and positive urinary sediment had 82% sensitivity and 99% specificity, with positive and negative predictive values of 91% and 98%, respectively. The combination of nitrite or leukocyte esterase positive tests and positive urinary sediment had the highest sensitivity (94%) and specificity (84%), with positive and negative predictive values of 58% and 99%, respectively. Based on ROC curve analysis, the best indicator of positive urine culture was the combination of positives leukocyte esterase or nitrite tests and positive urinary sediment, followed by positives leukocyte and nitrite tests, positive urinary sediment alone, positive leukocyte esterase test alone, positive nitrite test alone and finally association of positives nitrite and urinary sediment (AUC: 0.845, 0.844, 0.817, 0.814, 0.635 and 0.626, respectively). Conclusion A negative urine culture can be predicted by negative dipstick test results. Therefore, this test may be a reliable predictor of negative urine culture. PMID:28444086
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Baptista, Rodrigo P; Reis-Cunha, Joao Luis; DeBarry, Jeremy D; Chiari, Egler; Kissinger, Jessica C; Bartholomeu, Daniella C; Macedo, Andrea M
2018-02-14
Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.
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Martínez Belmonte, Marta; Wezenberg, Sander J; Haak, Robert M; Anselmo, Daniele; Escudero-Adán, Eduardo C; Benet-Buchholz, Jordi; Kleij, Arjan W
2010-05-21
The self-assembly features of a series of (non)symmetrical Zn(salphen) complexes have been studied in detail by X-ray crystallography, NMR and UV-vis techniques. The combined data demonstrate that the stability of these dimeric assemblies and the relative position of each monomeric unit within the dinuclear structure depend on the location and combination of the aromatic ring substituents.
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Fractal dimension of microbead assemblies used for protein detection.
Hecht, Ariel; Commiskey, Patrick; Lazaridis, Filippos; Argyrakis, Panos; Kopelman, Raoul
2014-11-10
We use fractal analysis to calculate the protein concentration in a rotating magnetic assembly of microbeads of size 1 μm, which has optimized parameters of sedimentation, binding sites and magnetic volume. We utilize the original Forrest-Witten method, but due to the relatively small number of bead particles, which is of the order of 500, we use a large number of origins and also a large number of algorithm iterations. We find a value of the fractal dimension in the range 1.70-1.90, as a function of the thrombin concentration, which plays the role of binding the microbeads together. This is in good agreement with previous results from magnetorotation studies. The calculation of the fractal dimension using multiple points of reference can be used for any assembly with a relatively small number of particles. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Girardclos, S.; Baster, I.; Wildi, W.; Pugin, A.; Rachoud-Schneider, A. -M.
2003-01-01
The Late-Glacial and Holocene sedimentary history of the Hauts-Monts area (western Lake Geneva, Switzerland) is reconstructed combining high resolution seismic stratigraphy and well-dated sedimentary cores. Six reflections and seismic units are defined and represented by individual isopach maps, which are further combined to obtain a three-dimensional age-depth model. Slumps, blank areas and various geometries are identified using these seismic data. The sediment depositional areas have substantially changed throughout the lake during the end of the Late-Glacial and the Holocene. These changes are interpreted as the result of variations in the intensity of deep lake currents and the frequency of strong winds determining the distribution of sediment input from the Versoix River and from reworking of previously deposited sediments within the lacustrine basin. The identified changes in sediment distribution allowed us to reconstruct the lake's deep-current history and the evolution of dominant strong wind regimes from the Preboreal to present times.
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Three-dimensional cell to tissue assembly process
NASA Technical Reports Server (NTRS)
Wolf, David A. (Inventor); Schwarz, Ray P. (Inventor); Lewis, Marian L. (Inventor); Cross, John H. (Inventor); Huls, Mary H. (Inventor)
1992-01-01
The present invention relates a 3-dimensional cell to tissue and maintenance process, more particularly to methods of culturing cells in a culture environment, either in space or in a gravity field, with minimum fluid shear stress, freedom for 3-dimensional spatial orientation of the suspended particles and localization of particles with differing or similar sedimentation properties in a similar spatial region.
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NASA Technical Reports Server (NTRS)
Sukharev, S. I.; Schroeder, M. J.; McCaslin, D. R.
1999-01-01
MscL, a 15 kDa transmembrane protein, is the only component involved in the formation of a 3 nS channel in the inner membrane of Escherichia coli that opens in response to mechanical or osmotic stress. While previous data had suggested that the functional MscL complex might be a hexamer, a recent crystallographic study of the MscL homologue from M. tuberculosis reveals a pentameric structure. The present work further examines the stoichiometry of the E. coli MscL using a variety of biochemical approaches. Detergent-purified 6His-MscL in solution and MscL in the membrane could be chemically crosslinked with the products displaying ladderlike patterns on SDS gels. Three crosslinking agents (EDC, DMS, and DMA) used at saturating concentrations invariably generated pentamers as the largest product. DSS produced additional bands corresponding to larger complexes although the pentamer band appeared to be the predominant product at high levels of crosslinker. It is not clear whether these extra bands reflect a difference in the crosslinking chemistry of DSS or whether its spacer arm is the longest of those used, or a combination of both facts. For the detergent-solubilized 6His-MscL both sedimentation equilibrium and gel chromatography showed the presence of multiple species. Thus the longer spacer arm could permit both intra- and intercomplex linkages. Nonetheless, the patterns obtained with all agents are consistent with and strongly suggest a pentameric organization for the MscL channel. Expression of MscL as genetically engineered double or triple subunit tandems yields low numbers of functional channels as compared to expressed monomers. The double-tandem assemblies must have an even number of subunits and crosslinking in the membrane confirmed hexamerization. Gel chromatography clearly demonstrated that the channels formed from the double tandems were larger than those formed from WT MscL, consistent with the native channel being pentameric. The observation that both double and triple tandems form channels of normal conductance implies that the pentameric assembly is to some degree independent of the number of subunit repeats in the polypeptide precursor. The channel is thus a pentameric core with the 'extra' subunits left out of the functional complex. From sedimentation equilibrium and size-exclusion chromatography, we also conclude that MscL complexes are not in a dynamic equilibrium with monomers, but are pre-assembled; and thus, their gating properties must result from changes in the conformation of the entire complex induced by the mechanical stress.
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Sukharev, S I; Schroeder, M J; McCaslin, D R
1999-10-01
MscL, a 15 kDa transmembrane protein, is the only component involved in the formation of a 3 nS channel in the inner membrane of Escherichia coli that opens in response to mechanical or osmotic stress. While previous data had suggested that the functional MscL complex might be a hexamer, a recent crystallographic study of the MscL homologue from M. tuberculosis reveals a pentameric structure. The present work further examines the stoichiometry of the E. coli MscL using a variety of biochemical approaches. Detergent-purified 6His-MscL in solution and MscL in the membrane could be chemically crosslinked with the products displaying ladderlike patterns on SDS gels. Three crosslinking agents (EDC, DMS, and DMA) used at saturating concentrations invariably generated pentamers as the largest product. DSS produced additional bands corresponding to larger complexes although the pentamer band appeared to be the predominant product at high levels of crosslinker. It is not clear whether these extra bands reflect a difference in the crosslinking chemistry of DSS or whether its spacer arm is the longest of those used, or a combination of both facts. For the detergent-solubilized 6His-MscL both sedimentation equilibrium and gel chromatography showed the presence of multiple species. Thus the longer spacer arm could permit both intra- and intercomplex linkages. Nonetheless, the patterns obtained with all agents are consistent with and strongly suggest a pentameric organization for the MscL channel. Expression of MscL as genetically engineered double or triple subunit tandems yields low numbers of functional channels as compared to expressed monomers. The double-tandem assemblies must have an even number of subunits and crosslinking in the membrane confirmed hexamerization. Gel chromatography clearly demonstrated that the channels formed from the double tandems were larger than those formed from WT MscL, consistent with the native channel being pentameric. The observation that both double and triple tandems form channels of normal conductance implies that the pentameric assembly is to some degree independent of the number of subunit repeats in the polypeptide precursor. The channel is thus a pentameric core with the 'extra' subunits left out of the functional complex. From sedimentation equilibrium and size-exclusion chromatography, we also conclude that MscL complexes are not in a dynamic equilibrium with monomers, but are pre-assembled; and thus, their gating properties must result from changes in the conformation of the entire complex induced by the mechanical stress.
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Runoff and sediment yield from proxy records: Upper Animas Creek Basin, New Mexico
W. R. Osterkamp
1999-01-01
Analyses of water- and sediment-yield records from the Walnut Gulch Experimental Watershed, the San Simon Wash Basin, and the Jornada Experimental Range, combined with observations of regional variations in climate, geology and soils, vegetation, topography, fire frequency, and land-use history, allow estimates of present conditions of water and sediment discharges in...
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, Chongxuan; Shang, Jianying; Shan, Huimei
2014-02-04
The effect of subgrid heterogeneity in sediment properties on the rate of uranyl[U(VI)] desorption was investigated using a sediment collected from the US Department of Energy Hanford site. The sediment was sieved into 7 grain size fractions that each exhibited different U(VI) desorption properties. Six columns were assembled using the sediment with its grain size fractions arranged in different spatial configurations to mimic subgrid heterogeneity in reactive transport properties. The apparent rate of U(VI) desorption varied significantly in the columns. Those columns with sediment structures leading to preferential transport had much lower rates of U(VI) desorption than those with relativelymore » homogeneous transport. Modeling analysis indicated that the U(VI) desorption model and parameters characterized from well-mixed reactors significantly over-predicted the measured U(VI) desorption in the columns with preferential transport. A dual domain model, which operationally separates reactive transport properties into two subgrid domains improved the predictions significantly. A similar effect of subgrid heterogeneity, albeit at a less degree, was observed for denitrification, which also occurred in the columns. The results imply that subgrid heterogeneity is an important consideration in extrapolating reaction rates from the laboratory to field.« less
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Ascribing soil erosion of hillslope components to river sediment yield.
Nosrati, Kazem
2017-06-01
In recent decades, soil erosion has increased in catchments of Iran. It is, therefore, necessary to understand soil erosion processes and sources in order to mitigate this problem. Geomorphic landforms play an important role in influencing water erosion. Therefore, ascribing hillslope components soil erosion to river sediment yield could be useful for soil and sediment management in order to decrease the off-site effects related to downstream sedimentation areas. The main objectives of this study were to apply radionuclide tracers and soil organic carbon to determine relative contributions of hillslope component sediment sources in two land use types (forest and crop field) by using a Bayesian-mixing model, as well as to estimate the uncertainty in sediment fingerprinting in a mountainous catchment of western Iran. In this analysis, 137 Cs, 40 K, 238 U, 226 Ra, 232 Th and soil organic carbon tracers were measured in 32 different sampling sites from four hillslope component sediment sources (summit, shoulder, backslope, and toeslope) in forested and crop fields along with six bed sediment samples at the downstream reach of the catchment. To quantify the sediment source proportions, the Bayesian mixing model was based on (1) primary sediment sources and (2) combined primary and secondary sediment sources. The results of both approaches indicated that erosion from crop field shoulder dominated the sources of river sediments. The estimated contribution of crop field shoulder for all river samples was 63.7% (32.4-79.8%) for primary sediment sources approach, and 67% (15.3%-81.7%) for the combined primary and secondary sources approach. The Bayesian mixing model, based on an optimum set of tracers, estimated that the highest contribution of soil erosion in crop field land use and shoulder-component landforms constituted the most important land-use factor. This technique could, therefore, be a useful tool for soil and sediment control management strategies. Copyright © 2016 Elsevier Ltd. All rights reserved.
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De Lange, H J; Van Griethuysen, C; Koelmans, A A
2008-01-01
Sediment treatment and sediment storage may alter sediment toxicity, and consequently biotic response. Purpose of our study was to combine these three aspects (treatment-toxicity-biotic response) in one integrated approach. We used Acid Volatile Sulfide (AVS) concentrations as a proxy of the disturbance of the sediment. AVS and Simultaneously Extracted Metal (SEM) concentrations were compared to bioassay responses with the freshwater benthic macroinvertebrate Asellus aquaticus. Storage conditions and sediment treatment affected AVS but not SEM levels. AVS can be used as a proxy for sediment disturbance. The best way to pretreat the sediment for use in a bioassay in order to maintain initial AVS conditions was to sample the sediment with an Ekman grab, immediately store it in a jar without headspace, and freeze it as soon as possible. In a survey using seven different sediments, bioassay responses of A. aquaticus were correlated with SEM and AVS characteristics.
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Shi, Zhenyu; Wedd, Anthony G.; Gras, Sally L.
2013-01-01
The development of synthetic biology requires rapid batch construction of large gene networks from combinations of smaller units. Despite the availability of computational predictions for well-characterized enzymes, the optimization of most synthetic biology projects requires combinational constructions and tests. A new building-brick-style parallel DNA assembly framework for simple and flexible batch construction is presented here. It is based on robust recombination steps and allows a variety of DNA assembly techniques to be organized for complex constructions (with or without scars). The assembly of five DNA fragments into a host genome was performed as an experimental demonstration. PMID:23468883
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Large-scale suspended sediment transport and sediment deposition in the Mekong Delta
NASA Astrophysics Data System (ADS)
Manh, N. V.; Dung, N. V.; Hung, N. N.; Merz, B.; Apel, H.
2014-08-01
Sediment dynamics play a major role in the agricultural and fishery productivity of the Mekong Delta. However, the understanding of sediment dynamics in the delta, one of the most complex river deltas in the world, is very limited. This is a consequence of its large extent, the intricate system of rivers, channels and floodplains, and the scarcity of observations. This study quantifies, for the first time, the suspended sediment transport and sediment deposition in the whole Mekong Delta. To this end, a quasi-2D hydrodynamic model is combined with a cohesive sediment transport model. The combined model is calibrated using six objective functions to represent the different aspects of the hydraulic and sediment transport components. The model is calibrated for the extreme flood season in 2011 and shows good performance for 2 validation years with very different flood characteristics. It is shown how sediment transport and sediment deposition is differentiated from Kratie at the entrance of the delta on its way to the coast. The main factors influencing the spatial sediment dynamics are the river and channel system, dike rings, sluice gate operations, the magnitude of the floods, and tidal influences. The superposition of these factors leads to high spatial variability of sediment transport, in particular in the Vietnamese floodplains. Depending on the flood magnitude, annual sediment loads reaching the coast vary from 48 to 60% of the sediment load at Kratie. Deposited sediment varies from 19 to 23% of the annual load at Kratie in Cambodian floodplains, and from 1 to 6% in the compartmented and diked floodplains in Vietnam. Annual deposited nutrients (N, P, K), which are associated with the sediment deposition, provide on average more than 50% of mineral fertilizers typically applied for rice crops in non-flooded ring dike floodplains in Vietnam. Through the quantification of sediment and related nutrient input, the presented study provides a quantitative basis for estimating the benefits of annual Mekong floods for agriculture and fishery, and is an important piece of information with regard to the assessment of the impacts of deltaic subsidence and climate-change-related sea level rise on delta morphology.
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McGuire, Luke; Kean, Jason W.; Staley, Dennis M.; Rengers, Francis K.; Wasklewicz, Thad A.
2016-01-01
Mountain watersheds recently burned by wildfire often experience greater amounts of runoff and increased rates of sediment transport relative to similar unburned areas. Given the sedimentation and debris flow threats caused by increases in erosion, more work is needed to better understand the physical mechanisms responsible for the observed increase in sediment transport in burned environments and the time scale over which a heightened geomorphic response can be expected. In this study, we quantified the relative importance of different hillslope erosion mechanisms during two postwildfire rainstorms at a drainage basin in Southern California by combining terrestrial laser scanner-derived maps of topographic change, field measurements, and numerical modeling of overland flow and sediment transport. Numerous debris flows were initiated by runoff at our study area during a long-duration storm of relatively modest intensity. Despite the presence of a well-developed rill network, numerical model results suggest that the majority of eroded hillslope sediment during this long-duration rainstorm was transported by raindrop-induced sediment transport processes, highlighting the importance of raindrop-driven processes in supplying channels with potential debris flow material. We also used the numerical model to explore relationships between postwildfire storm characteristics, vegetation cover, soil infiltration capacity, and the total volume of eroded sediment from a synthetic hillslope for different end-member erosion regimes. This study adds to our understanding of sediment transport in steep, postwildfire landscapes and shows how data from field monitoring can be combined with numerical modeling of sediment transport to isolate the processes leading to increased erosion in burned areas.
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NASA Astrophysics Data System (ADS)
Corrigan, A.; Silins, U.; Stone, M.
2016-12-01
Best management practices (BMPs) and associated erosion control measures for mitigating sediment impacts from forestry roads and road-stream crossings are well documented. While rapid road decommissioning after forestry operations may serve to limit broader impacts on sediment production in high value headwater streams, few studies have evaluated the combined effects of accelerated harvest operations and rapid retirement of logging roads and road-stream crossings on stream sediment. The objectives of this study were to evaluate the initial impacts of these strategies on fine sediment loading and fate during a short duration harvesting operation in 3 headwater sub-catchments in the southwestern Rocky Mountains of Alberta, Canada. A multi-pronged sampling approach (ISCOs, event focused grab sampling, continuous wash load sampling, and stream bed sediment intrusion measurements) was used to measure sediment loading and deposition in streambeds upstream and downstream of road-stream bridge crossings during harvest operations (2015) and after road and bridge crossing retirement (2016). Sediment production from forestry roads was generally much lower than has been reported from other studies in similar settings. Average total suspended solids (TSS) downstream of the bridge crossings were actually lower (-3.28 g/L; -0.704 g/L) than upstream of two bridge crossings while in-stream sediment sources contributed to elevated sediment downstream of a third road-stream crossing. Minimal in stream sediment impacts from forest harvest and road-stream crossings was likely a reflection of combined factors including a) employment of erosion control BMPs to roads and bridge crossings, b) rapid decommissioning of roads and crossings to limit exposure of linear land disturbance features, and c) drier El Niño climatic conditions during the study.
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Magnetic assembly and annealing of colloidal lattices and superlattices.
Tierno, Pietro
2014-07-08
The ability to assemble mesoscopic colloidal lattices above a surface is important for fundamental studies related with nucleation and crystallization but also for a variety of technological applications in photonics and microengineering. Current techniques based on particle sedimentation above a lithographic template are limited by a slow deposition process and by the use of static templates, which make difficult to implement fast annealing procedures. Here it is demonstrated a method to realize and anneal a series of colloidal lattices displaying triangular, honeycomb, or kagome-like symmetry above a structure magnetic substrate. By using a binary mixture of particles, superlattices can be realized increasing further the variety and complexity of the colloidal patterns which can be produced.
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Bersinger, T; Le Hécho, I; Bareille, G; Pigot, T
2015-01-01
Eroded sewer sediments are a significant source of organic matter discharge by combined sewer overflows. Many authors have studied the erosion and sedimentation processes at the scale of a section of sewer pipe and over short time periods. The objective of this study was to assess these processes at the scale of an entire sewer network and over 1 month, to understand whether phenomena observed on a small scale of space and time are still valid on a larger scale. To achieve this objective the continuous monitoring of turbidity was used. First, the study of successive rain events allows observation of the reduction of the available sediment and highlights the widely different erosion resistance for the different sediment layers. Secondly, calculation of daily chemical oxygen demand (COD) fluxes during the entire month was performed showing that sediment storage in the sewer pipe after a rain period is important and stops after 5 days. Nevertheless, during rainfall events, the eroded fluxes are more important than the whole sewer sediment accumulated during a dry weather period. This means that the COD fluxes promoted by runoff are substantial. This work confirms, with online monitoring, most of the conclusions from other studies on a smaller scale.
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Intelligent Augmented Reality Training for Motherboard Assembly
ERIC Educational Resources Information Center
Westerfield, Giles; Mitrovic, Antonija; Billinghurst, Mark
2015-01-01
We investigate the combination of Augmented Reality (AR) with Intelligent Tutoring Systems (ITS) to assist with training for manual assembly tasks. Our approach combines AR graphics with adaptive guidance from the ITS to provide a more effective learning experience. We have developed a modular software framework for intelligent AR training…
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Beam, Jacob P; Jay, Zackary J; Kozubal, Mark A; Inskeep, William P
2014-01-01
Novel lineages of the phylum Thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. The primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65–72 °C), acidic (pH∼3) iron oxide and sulfur sediment environments of Yellowstone National Park (YNP). Metabolic reconstruction was coupled with detailed geochemical measurements of each geothermal habitat and reverse-transcriptase PCR to confirm the in situ activity of these populations. Phylogenetic analyses of ribosomal and housekeeping proteins place these archaea near the root of the thaumarchaeal branch. Metabolic reconstruction suggests that these populations are chemoorganotrophic and couple growth with the reduction of oxygen or nitrate in iron oxide habitats, or sulfur in hypoxic sulfur sediments. The iron oxide population has the potential for growth via the oxidation of sulfide to sulfate using a novel reverse sulfate reduction pathway. Possible carbon sources include aromatic compounds (for example, 4-hydroxyphenylacetate), complex carbohydrates (for example, starch), oligopeptides and amino acids. Both populations contain a type III ribulose bisphosphate carboxylase/oxygenase used for carbon dioxide fixation or adenosine monophosphate salvage. No evidence for the oxidation of ammonia was obtained from de novo sequence assemblies. Our results show that thermoacidophilic Thaumarchaeota from oxic iron mats and hypoxic sulfur sediments exhibit different respiratory machinery depending on the presence of oxygen versus sulfide, represent deeply rooted lineages within the phylum Thaumarchaeota and are endemic to numerous sites in YNP. PMID:24196321
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NASA Astrophysics Data System (ADS)
Ohlendorf, Christian; Gebhardt, Catalina; Hahn, Annette; Kliem, Pierre; Zolitschka, Bernd
2011-07-01
Using the ICDP (International Continental Scientific Drilling Program) deep lake drilling expedition no. 5022 as an example, we describe core processing and sampling procedures as well as new tools developed for subsampling. A manual core splitter is presented that is (1) mobile, (2) able to cut plastic core liners lengthwise without producing swarf of liner material and (3) consists of off-the-shelf components. In order to improve the sampling of sediment cores, a new device, the core sampling assembly (CSA), was developed that meets the following targets: (1) the partitioning of the sediment into discs of equal thickness is fast and precise, (2) disturbed sediment at the inner surface of the liner is discarded during this sampling process, (3) usage of the available sediment is optimised, (4) subsamples are volumetric and oriented, and (5) identical subsamples are taken. The CSA can be applied to D-shaped split sediment cores of any diameter and consists of a divider and a D-shaped scoop. The sampling plan applied for ICDP expedition 5022 is illustrated and may be used as a guideline for planning the efficient partitioning of sediment amongst different lake research groups involved in multidisciplinary projects. For every subsample, the use of quality flags is suggested (1) to document the sample condition, (2) to give a first sediment classification and (3) to guarantee a precise adjustment of logging and scanning data with data determined on individual samples. Based on this, we propose a protocol that might be applied across lake drilling projects in order to facilitate planning and documentation of sampling campaigns and to ensure a better comparability of results.
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Unravelling the relative contribution of bed and suspended sediment load on a large alluvial river
NASA Astrophysics Data System (ADS)
Darby, S. E.; Hackney, C. R.; Parsons, D. R.; Leyland, J.; Aalto, R. E.; Nicholas, A. P.; Best, J.
2017-12-01
The world's largest rivers transport 19 billion tonnes of sediment to the coastal zone annually, often supporting large deltas that rely on this sediment load to maintain their elevation in the face of rising sea level, and to sustain high levels of agricultural productivity and biodiversity. However, the majority of estimates of sediment delivery to coastal regions pertain solely to the suspended fraction of the sediment load, with the bedload fraction often being neglected due to the difficulty in estimating bedload flux and the assumption that bedload contributes a minor (<10%) fraction of the total sediment load. In large rivers, capturing accurate estimates of the suspended- and bed- load fractions is difficult given the large channel widths and depths and the intrusive nature of typical methodologies. Yet, for the successful implementation of sustainable river, and delta, management plans, improved estimates of all fractions of the sediment load are essential. Recent advances in non-intrusive, high-resolution, technology have begun to enable more accurate estimates of bedload transport rates. However, the characterisation of the holistic sediment transport regime of large alluvial rivers is still lacking. Here, we develop a sediment transport rating curve, combining both suspended- and bed- load sediment fractions, for the Lower Mekong River. We define suspended sediment rating curves using the inversion of acoustic return data from a series of acoustic Doppler current profiler surveys conducted through the Lower Mekong River in Cambodia, and into the bifurcating channels of the Mekong delta in Vietnam. Additionally, we detail estimates of bed-load sediment transport determined using repeat multibeam echo sounder surveys of the channel bed. By combining estimates of both fractions of the sediment load, we show the spatial and temporal contribution of bedload to the total sediment load of the Mekong and refine estimates of sediment transport to the Mekong delta. Our results indicate that the time-averaged suspended load transport rates for the Mekong River are 87 MT/yr, whilst bedload transport forms c. < 5% of the total sediment load within the Mekong River. Such estimates are integral to future channel management within this highly threatened river basin.
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X-DRAIN and XDS: a simplified road erosion prediction method
William J. Elliot; David E. Hall; S. R. Graves
1998-01-01
To develop a simple road sediment delivery tool, the WEPP program modeled sedimentation from forest roads for more than 50,000 combinations of distance between cross drains, road gradient, soil texture, distance from stream, steepness of the buffer between the road and the stream, and climate. The sediment yield prediction from each of these runs was stored in a data...
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Long-distance electron transport occurs globally in marine sediments
NASA Astrophysics Data System (ADS)
Burdorf, Laurine D. W.; Tramper, Anton; Seitaj, Dorina; Meire, Lorenz; Hidalgo-Martinez, Silvia; Zetsche, Eva-Maria; Boschker, Henricus T. S.; Meysman, Filip J. R.
2017-02-01
Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements.
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Gellis, Allen C.; Noe, Gregory B.; Clune, John W.; Myers, Michael K.; Hupp, Cliff R.; Schenk, Edward R.; Schwarz, Gregory E.
2015-01-01
Management implications of this study indicate that both agriculture and streambanks are important sources of sediment in Linganore Creek where the delivery of agriculture sediment was 4 percent and the delivery of streambank sediment was 44 percent. Fourth order streambanks, on average, had the highest rates of bank erosion. Combining the sediment fingerprinting and sediment budget results indicates that 96 percent of the eroded fine-grained sediment from agriculture went into storage. Flood plains and ponds are effective storage sites of sediment in the Linganore Creek watershed. Flood plains stored 8 percent of all eroded sediment with 4th and 5th order flood plains, on average, storing the most sediment. Small ponds in the Linganore Creek watershed, which drained 16 percent of the total watershed area, stored 15 percent of all eroded sediment. Channel beds were relatively stable with the greatest erosion generally occurring in 4th and 5th order streams.
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NASA Astrophysics Data System (ADS)
Sherwood, Christopher R.; Aretxabaleta, Alfredo L.; Harris, Courtney K.; Rinehimer, J. Paul; Verney, Romaric; Ferré, Bénédicte
2018-05-01
We describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean-Atmosphere-Wave-Sediment Transport Modeling System (COAWST Subversion repository revision 1234). These include the following: floc dynamics (aggregation and disaggregation in the water column); changes in floc characteristics in the seabed; erosion and deposition of cohesive and mixed (combination of cohesive and non-cohesive) sediment; and biodiffusive mixing of bed sediment. These routines supplement existing non-cohesive sediment modules, thereby increasing our ability to model fine-grained and mixed-sediment environments. Additionally, we describe changes to the sediment bed layering scheme that improve the fidelity of the modeled stratigraphic record. Finally, we provide examples of these modules implemented in idealized test cases and a realistic application.
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Tracing sediment dispersal on nourished beaches: Two case studies
Thieler, E. Robert; Gayes, Paul T.; Schwab, William C.; Harris, M. Scott
1999-01-01
The event- to decade-scale patterns of sediment dispersal on two artificially nourished beaches have been mapped using a combination of geophysical surveys, closely-spaced vibracores, and repeated beach profiles. At both Wrightsville Beach, NC and Folly Island, SC the sediment used for beach nourishment is macroscopically distinct from native sediment and can be used to identify sediment transport pathways and infer mechanisms for across-shelf transport. The data from both sites demonstrate that significant quantities of nourishment sediment are being transported seaward onto the inner continental shelf. The time and space scales of this transport are of engineering interest for the planning, design and long-term maintenance of nourished beaches.
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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.
Tørresen, Ole K; Star, Bastiaan; Jentoft, Sissel; Reinar, William B; Grove, Harald; Miller, Jason R; Walenz, Brian P; Knight, James; Ekholm, Jenny M; Peluso, Paul; Edvardsen, Rolf B; Tooming-Klunderud, Ave; Skage, Morten; Lien, Sigbjørn; Jakobsen, Kjetill S; Nederbragt, Alexander J
2017-01-18
The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.
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1981-01-01
Meteorological Parameters at Meteorological Station 1, 31 May 1980 ........................ 68 $24 Relationship of Jubai. Port Datum to Tide Table Datum. .70 25...around which was a circular weight with two handles. Once assembled, the device was nositioned vertically at the point to be sampled and manually...limited use for sampling very fluid or unconsolidated sand or shell. In the former case, the upper few centimeters of cohesive sediment became embedded
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Yin, Shuangye
2012-06-01
Shuangye Yin on "Finished prokaryotic genome assemblies from a low-cost combination of short and long reads"; at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
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NASA Astrophysics Data System (ADS)
Pulley, Simon; Ian, Foster; Paula, Antunes
2014-05-01
In recent years, sediment fingerprinting methodologies have gained widespread adoption when tracing sediment provenance in geomorphological research. A wide variety of tracers have been employed in the published literature, with corrections for particle size and organic matter applied when the researcher judged them necessary. This paper aims to explore the errors associated with tracer use by a comparison of fingerprinting results obtained using fallout and lithogenic radionuclides, geochemical, and mineral magnetic tracers in a range of environments located in the Nene basin, UK. Specifically, fingerprinting was undertaken on lake, reservoir and floodplain sediment cores, on actively transported suspended sediment and on overbank and channel bed sediment deposits. Tracer groups were investigated both alone and in combination to determine the differences between their sediment provenance predictions and potential causes of these differences. Additionally, simple organic and particle size corrections were applied to determine if they improve the agreement between the tracer group predictions. Key results showed that when fingerprinting contributions from channel banks to actively transported or recently deposited sediments the tracer group predictions varied by 24% on average. These differences could not be clearly attributed to changes in the sediment during erosion or transport. Instead, the most likely cause of differences was the pre-existing spatial variability in tracer concentrations within sediment sources, combined with highly localised erosion. This resulted in the collected sediment source samples not being representative of the actual sediment sources. Average differences in provenance predictions between the different tracer groups in lake, reservoir and floodplain sediment cores were lowest in the reservoir core at 19% and highest in some floodplain cores, with differences in predictions in excess of 50%. In these latter samples organic enrichment of the sediment, selective transport of fine particles and post-depositional chemical changes to the sediment were determined to be the likely cause of the differences. It was determined that organic and particle size corrections made the differences between tracer groups larger in most cases, although differences between tracer group predictions were reduced in two of the four floodplain cores.
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Changes in bathymetry for Lake Katherine and Wood Lake, Richland County, South Carolina, 1989-93
Patterson, Glenn G.
1995-01-01
Bathymetric surveys of Lake Katherine and Wood Lake, small residential lakes in Columbia, South Carolina, were made in 1989 and 1993. During this period the combined volume of the lakes decreased by 519,000 cubic feet (11.9 acre-feet). Most of the decrease in volume occurred in the northern part of Lake Katherine where deltaic sediment deposits at the mouth of Gills Creek increased in thickness during the 4-year period. The sediment was derived from a combination of sources in the Gills Creek Basin upstream from the lakes. Construction of a highway and a housing development in the Basin were significant factors in the sedimentation.
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Clean-up and disposal process of polluted sediments from urban rivers.
He, P J; Shao, L M; Gu, G W; Bian, C L; Xu, C
2001-10-01
In this paper, the discussion is concentrated on the properties of the polluted sediments and the combination of clean-up and disposal process for the upper layer heavily polluted sediments with good flowability. Based on the systematic analyses of various clean-up processes, a suitable engineering process has been evaluated and recommended. The process has been applied to the river reclamation in Yangpu District of Shanghai City, China. An improved centrifuge is used for dewatering the dredged sludge, which plays an important role in the combination of clean-up and disposal process. The assessment of the engineering process shows its environmental and technical economy feasibility, which is much better than that of traditional dredging-disposal processes.
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Oyane, Ayako; Araki, Hiroko; Nakamura, Maki; Shimizu, Yoshiki; Shubhra, Quazi T H; Ito, Atsuo; Tsurushima, Hideo
2016-05-01
Surface-mediated gene delivery systems have many potential applications in tissue engineering. We recently fabricated an assembly consisting of DNA-amorphous calcium phosphate (DNA-ACP) nanocomposite spheres on a polymer substrate via coprecipitation in a labile supersaturated calcium phosphate (CaP) solution and demonstrated the assembly's high gene delivery efficacy. In this study, we conducted a detailed investigation of the coprecipitation process in solution and revealed that the negatively charged DNA molecules were immobilized in the ACP spheres during the initial stage of coprecipitation and functioned as both sphere-dispersing and size-regulating agents. As a result, the DNA-ACP nanocomposites grew into size-regulated submicrospheres in solution and assembled onto the substrate via gravity sedimentation. The assembled nanocomposite spheres were chemically anchored to the substrate surface through an intermediate layer of CaP-based nanoparticles that was formed heterogeneously at the substrate surface. The coprecipitation conditions, i.e., coprecipitation time and Ca and P concentrations in solution, greatly affected the state of assembly of the nanocomposite spheres, thereby influencing the gene expression level of the cells cultured on the substrate. Increasing the number density and decreasing the size of the nanocomposite spheres did not always increase the assembly's gene delivery efficacy (per surface area of the substrate) due to adverse effects on cellular viability. As demonstrated herein, controlling the coprecipitation conditions is important for designing a cell-stimulating and biocompatible scaffold surface consisting of an assembly of DNA-ACP nanocomposite spheres. Copyright © 2016 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fisher, A.T.; Becker, K.; Narasimhan, T.
1990-06-01
Pore fluids are passively convecting through young oceanic sediments and crust around Deep Sea Drilling Project (DSDP) site 504 on the southern flank of the Costa Rica Rift, as inferred from a variety of geological, geochemical, and geothermal observations. The presence of a fluid circulation system is supported by new data collected on Ocean Drilling Program (ODP) Leg 111 and a predrilling survey cruise over the heavily sedimented, 5.9 Ma site; during the latter, elongated heat flow anomalies were mapped subparallel to structural strike, with individual measurements of twice the regional mean value, and large lateral and vertical geochemical gradientsmore » were detected in pore waters squeezed from sediment cores. Also, there is a strong correlation between heat flow, bathymetry, sediment thickness, and inferred fluid velocities up through the sediments. On an earlier DSDP leg, an 8-bar underpressure was measured in the upper 200 m of basement beneath thick sediment cover. The widely varied geothermal and hydrogeological observations near site 504 are readily explained by a model that combines (1) basement relief, (2) irregular sediment drape, (3) largely conductive heat transfer through the sediments overlying the crust, and (4) thermal and geochemical homogenization of pore fluids at the sediment/basement interface, which results from (5) topographically induced, passive hydrothermal circulation with large aspect ratio, convection cells. This convection involves mainly the permeable, upper 200-300 m of crust; the deeper crust is not involved. This convection is induced through a combination of buoyancy fluxes, owing to heating from below, and topographic variations on the seafloor and at the basement-sediment interface.« less
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NASA Astrophysics Data System (ADS)
Downs, Peter W.; Dusterhoff, Scott R.; Sears, William A.
2013-05-01
Understanding the cumulative impact of natural and human influences on the sensitivity of channel morphodynamics, a relative measure between the drivers for change and the magnitude of channel response, requires an approach that accommodates spatial and temporal variability in the suite of primary stressors. Multiple historical data sources were assembled to provide a reach-scale analysis of the lower Santa Clara River (LSCR) in Ventura County, California, USA. Sediment supply is naturally high due to tectonic activity, earthquake-generated landslides, wildfires, and high magnitude flow events during El Niño years. Somewhat typically for the region, the catchment has been subject to four reasonably distinct land use and resource management combinations since European-American settlement. When combined with analysis of channel morphological response (quantifiable since ca. 1930), reach-scale and temporal differences in channel sensitivity become apparent. Downstream reaches have incised on average 2.4 m and become narrower by almost 50% with changes focused in a period of highly sensitive response after about 1950 followed by forced insensitivity caused by structural flood embankments and a significant grade control structure. In contrast, the middle reaches have been responsive but are morphologically resilient, and the upstream reaches show a mildly sensitive aggradational trend. Superimposing the natural and human drivers for change reveals that large scale stressors (related to ranching and irrigation) have been replaced over time by a suite of stressors operating at multiple spatial scales. Lower reaches have been sensitive primarily to 'local' scale impacts (urban growth, flood control, and aggregate mining) whereas, upstream, catchment-scale influences still prevail (including flow regulation and climate-driven sediment supply factors). These factors illustrate the complexity inherent to cumulative impact assessment in fluvial systems, provide evidence for a distinct Anthropocene fluvial response, and underpin the enormity of the challenge faced in trying to sustainably manage and restore rivers.
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24 CFR 3280.702 - Definitions.
Code of Federal Regulations, 2011 CFR
2011-04-01
... conditioning self contained system means a comfort cooling appliance combining the condenser section... assembly composed of listed factory-built components assembled in accordance with the terms of listing to... means that portion of a manufactured home heater flue or vent assembly, including the cap, insulating...
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Peña-Icart, Mirella; Pereira-Filho, Edenir Rodrigues; Lopes Fialho, Lucimar; Nóbrega, Joaquim A; Alonso-Hernández, Carlos; Bolaños-Alvarez, Yoelvis; Pomares-Alfonso, Mario S
2017-02-01
The purpose of the present work was to combine several tools for assessing metal pollution in marine sediments from Cienfuegos Bay. Fourteen surface sediments collected in 2013 were evaluated. Concentrations of As, Cu, Ni, Zn and V decreased respect to those previous reported. The metal contamination was spatially distributed in the north and south parts of the bay. According to the contamination factor (CF) enrichment factor (EF) and index of geoaccumulation (I geo ), Cd and Cu were classified in that order as the most contaminated elements in most sediment. Comparison of the total metal concentrations with the threshold (TELs) and probable (PELs) effect levels in sediment quality guidelines suggested a more worrisome situation for Cu, of which concentrations were occasional associated with adverse biological effects in thirteen sediments, followed by Ni in nine sediments; while adverse effects were rarely associated with Cd. Probably, Cu could be considered as the most dangerous in the whole bay because it was classified in the high contamination levels by all indexes and, simultaneously, associated to occasional adverse effects in most samples. Despite the bioavailability was partially evaluated with the HCl method, the low extraction of Ni (<3% in all samples) and Cu (<55%, except sample 3) and the relative high extraction of Cd (50% or more, except sample 14) could be considered as an attenuating (Ni and Cu) or increasing (Cd) factor in the risk assessment of those element. Copyright © 2016. Published by Elsevier Ltd.
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Shayanfar, Noushin; Tobler, Ulrich; von Eckardstein, Arnold; Bestmann, Lukas
2007-01-01
Automated analysis of insoluble urine components can reduce the workload of conventional microscopic examination of urine sediment and is possibly helpful for standardization. We compared the diagnostic performance of two automated urine sediment analyzers and combined dipstick/automated urine analysis with that of the traditional dipstick/microscopy algorithm. A total of 332 specimens were collected and analyzed for insoluble urine components by microscopy and automated analyzers, namely the Iris iQ200 (Iris Diagnostics) and the UF-100 flow cytometer (Sysmex). The coefficients of variation for day-to-day quality control of the iQ200 and UF-100 analyzers were 6.5% and 5.5%, respectively, for red blood cells. We reached accuracy ranging from 68% (bacteria) to 97% (yeast) for the iQ200 and from 42% (bacteria) to 93% (yeast) for the UF-100. The combination of dipstick and automated urine sediment analysis increased the sensitivity of screening to approximately 98%. We conclude that automated urine sediment analysis is sufficiently precise and improves the workflow in a routine laboratory. In addition, it allows sediment analysis of all urine samples and thereby helps to detect pathological samples that would have been missed in the conventional two-step procedure according to the European guidelines. Although it is not a substitute for microscopic sediment examination, it can, when combined with dipstick testing, reduce the number of specimens submitted to microscopy. Visual microscopy is still required for some samples, namely, dysmorphic erythrocytes, yeasts, Trichomonas, oval fat bodies, differentiation of casts and certain crystals.
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NASA Astrophysics Data System (ADS)
Schwendel, Arved; Aalto, Rolf; Nicholas, Andrew
2014-05-01
Lowland floodplains in subsiding basins form major depocentres responsible for the storage and cycling of large quantities of fine sediment and associated nutrients and contaminants. Obtaining reliable estimates of sediment storage in such environments is problematic due to the high degree of spatial and temporal variability exhibited by overbank sediment accumulation rates, combined with the logistical difficulties inherent in sampling locations far away from the channel. Further complexity is added by the high channel mobility, which recycles sediment and reconfigures the relationships between channel and floodplain morphology, sediment transport and overbank sedimentation. Estimates of floodplain accretion can be derived using a range of numerical sedimentation models of varying complexity. However, data required for model calibration are rarely available for the vast floodplains associated with tropical rivers. We present results from a study of channel-floodplain sediment exchange fluxes on the Rio Beni, a highly dynamic, tropical sand-bed tributary of the Amazon in northern Bolivia. The Beni transports high concentrations of suspended sediment, generated in the river's Andean headwaters, and disperses this material across an extensive floodplain wetland that experiences annual inundation over an area of up to 40000 km2. We utilise estimates of overbank sedimentation rates over the past century derived from 210Pb analysis of floodplain sediment cores collected along a 375 km length of channel, including sampling a range of channel-floodplain configurations within the channel belt and on the distal floodplain (up to 60 km from the channel). These data are used to investigate spatial and temporal variations in rates of floodplain sediment accumulation for a range of grain sizes. Specifically, we examine relationships between sedimentation rate and distance from the channel, and characterise within channel belt variability in sedimentation linked to patterns of channel migration and associated levee reworking. Field data are used to inform a hydrodynamically-driven model of overbank sedimentation and to derive uncertainty-bounded estimates of total floodplain sediment accumulation. Sediment exchange due to planform channel mobility is quantified using a numerical model of meander migration, calibrated using analysis of remote sensing imagery to determine rates and geometry of channel migration. Our combined data and model analysis allows the construction of a mean annual sediment budget for the Beni, which suggests channel-sediment exchange fluxes in the order of 100 Mt a-1, equivalent to 10% of the sediment load of the mainstem Amazon.
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NASA Astrophysics Data System (ADS)
Guzmán, Gema; Laguna, Ana; Cañasveras, Juan Carlos; Boulal, Hakim; Barrón, Vidal; Gómez-Macpherson, Helena; Giráldez, Juan Vicente; Gómez, José Alfonso
2015-05-01
Although soil erosion is one of the main threats to agriculture sustainability in many areas of the world, its processes are difficult to measure and still need a better characterization. The use of iron oxides as sediment tracers, combined with erosion and mixing models opens up a pathway for improving the knowledge of the erosion and redistribution of soil, determining sediment sources and sinks. In this study, magnetite and a multivariate mixing model were used in rainfall simulations at the micro-plot scale to determine the source of the sediment at different stages of a furrow-ridge system both with (+T) and without (-T) wheel tracks. At a plot scale, magnetite, hematite and goethite combined with two soil erosion models based on the kinematic wave approach were used in a sprinkler irrigation test to study trends in sediment transport and tracer dynamics along furrow lengths under a wide range of scenarios. In the absence of any stubble cover, sediment contribution from the ridges was larger than the furrow bed one, almost 90%, while an opposite trend was observed with stubble, with a smaller contribution from the ridge (32%) than that of the bed, at the micro-plot trials. Furthermore, at a plot scale, the tracer concentration analysis showed an exponentially decreasing trend with the downstream distance both for sediment detachment along furrows and soil source contribution from tagged segments. The parameters of the distributed model KINEROS2 have been estimated using the PEST Model to obtain a more accurate evaluation. Afterwards, this model was used to simulate a broad range of common scenarios of topography and rainfall from commercial farms in southern Spain. Higher slopes had a significant influence on sediment yields while long furrow distances allowed a more efficient water use. For the control of runoff, and therefore soil loss, an equilibrium between irrigation design (intensity, duration, water pattern) and hydric needs of the crops should be defined in order to establish a sustainable management strategy.
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Vertical variation of mixing within porous sediment beds below turbulent flows
Chandler, I. D.; Pearson, J. M.; van Egmond, R.
2016-01-01
Abstract River ecosystems are influenced by contaminants in the water column, in the pore water and adsorbed to sediment particles. When exchange across the sediment‐water interface (hyporheic exchange) is included in modeling, the mixing coefficient is often assumed to be constant with depth below the interface. Novel fiber‐optic fluorometers have been developed and combined with a modified EROSIMESS system to quantify the vertical variation in mixing coefficient with depth below the sediment‐water interface. The study considered a range of particle diameters and bed shear velocities, with the permeability Péclet number, PeK between 1000 and 77,000 and the shear Reynolds number, Re*, between 5 and 600. Different parameterization of both an interface exchange coefficient and a spatially variable in‐sediment mixing coefficient are explored. The variation of in‐sediment mixing is described by an exponential function applicable over the full range of parameter combinations tested. The empirical relationship enables estimates of the depth to which concentrations of pollutants will penetrate into the bed sediment, allowing the region where exchange will occur faster than molecular diffusion to be determined. PMID:27635104
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Reynolds, Richard L.; Rosenbaum, Joseph G.; Thompson, Robert S.
2008-01-01
We describe here results of magnetic susceptibility (MS) measurements and magnetic mineralogy of sediments sampled in three cores from the south basin of Great Salt Lake. The cores were obtained in 1996 with a Kullenburg-type piston corer at sites in close proximity: core 96-4 at 41 deg 01.00' N, 112 deg 28.00' W and cores 96-5 and 96-6 at 41 deg 00.09' N, 112 deg 23.05' W. Cores 96-5 (2.16 m long) and -6 combine to make a composite 11.31-m sediment record. Sediments in core 96-4 (5.54 m long) correspond to the approximate depth interval of 3.9-9.6 m in the composite core of 96-5 and -6 based on similarities in the MS records as described below. The central goal of the research was to provide a sediment record of paleoenvironmental change in the northeastern Basin and Range Province over the past 40,000 years. Specific targets included a sedimentologic record of lake-level change combined with a pollen record of climatic change.
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McCormick, Norman J.
1976-01-01
For use in the identification of failed fuel assemblies in a nuclear reactor, the ratios of the tag gas isotopic concentrations are located on curved surfaces to enable the ratios corresponding to failure of a single fuel assembly to be distinguished from those formed from any combination of two or more failed assemblies.
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Regional regression models of watershed suspended-sediment discharge for the eastern United States
NASA Astrophysics Data System (ADS)
Roman, David C.; Vogel, Richard M.; Schwarz, Gregory E.
2012-11-01
SummaryEstimates of mean annual watershed sediment discharge, derived from long-term measurements of suspended-sediment concentration and streamflow, often are not available at locations of interest. The goal of this study was to develop multivariate regression models to enable prediction of mean annual suspended-sediment discharge from available basin characteristics useful for most ungaged river locations in the eastern United States. The models are based on long-term mean sediment discharge estimates and explanatory variables obtained from a combined dataset of 1201 US Geological Survey (USGS) stations derived from a SPAtially Referenced Regression on Watershed attributes (SPARROW) study and the Geospatial Attributes of Gages for Evaluating Streamflow (GAGES) database. The resulting regional regression models summarized for major US water resources regions 1-8, exhibited prediction R2 values ranging from 76.9% to 92.7% and corresponding average model prediction errors ranging from 56.5% to 124.3%. Results from cross-validation experiments suggest that a majority of the models will perform similarly to calibration runs. The 36-parameter regional regression models also outperformed a 16-parameter national SPARROW model of suspended-sediment discharge and indicate that mean annual sediment loads in the eastern United States generally correlates with a combination of basin area, land use patterns, seasonal precipitation, soil composition, hydrologic modification, and to a lesser extent, topography.
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Regional regression models of watershed suspended-sediment discharge for the eastern United States
Roman, David C.; Vogel, Richard M.; Schwarz, Gregory E.
2012-01-01
Estimates of mean annual watershed sediment discharge, derived from long-term measurements of suspended-sediment concentration and streamflow, often are not available at locations of interest. The goal of this study was to develop multivariate regression models to enable prediction of mean annual suspended-sediment discharge from available basin characteristics useful for most ungaged river locations in the eastern United States. The models are based on long-term mean sediment discharge estimates and explanatory variables obtained from a combined dataset of 1201 US Geological Survey (USGS) stations derived from a SPAtially Referenced Regression on Watershed attributes (SPARROW) study and the Geospatial Attributes of Gages for Evaluating Streamflow (GAGES) database. The resulting regional regression models summarized for major US water resources regions 1–8, exhibited prediction R2 values ranging from 76.9% to 92.7% and corresponding average model prediction errors ranging from 56.5% to 124.3%. Results from cross-validation experiments suggest that a majority of the models will perform similarly to calibration runs. The 36-parameter regional regression models also outperformed a 16-parameter national SPARROW model of suspended-sediment discharge and indicate that mean annual sediment loads in the eastern United States generally correlates with a combination of basin area, land use patterns, seasonal precipitation, soil composition, hydrologic modification, and to a lesser extent, topography.
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Kuijpers, Niels GA; Chroumpi, Soultana; Vos, Tim; Solis-Escalante, Daniel; Bosman, Lizanne; Pronk, Jack T; Daran, Jean-Marc; Daran-Lapujade, Pascale
2013-01-01
In vivo assembly of overlapping fragments by homologous recombination in Saccharomyces cerevisiae is a powerful method to engineer large DNA constructs. Whereas most in vivo assembly methods reported to date result in circular vectors, stable integrated constructs are often preferred for metabolic engineering as they are required for large-scale industrial application. The present study explores the potential of combining in vivo assembly of large, multigene expression constructs with their targeted chromosomal integration in S. cerevisiae. Combined assembly and targeted integration of a ten-fragment 22-kb construct to a single chromosomal locus was successfully achieved in a single transformation process, but with low efficiency (5% of the analyzed transformants contained the correctly assembled construct). The meganuclease I-SceI was therefore used to introduce a double-strand break at the targeted chromosomal locus, thus to facilitate integration of the assembled construct. I-SceI-assisted integration dramatically increased the efficiency of assembly and integration of the same construct to 95%. This study paves the way for the fast, efficient, and stable integration of large DNA constructs in S. cerevisiae chromosomes. PMID:24028550
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Utturkar, Sagar M.; Klingeman, Dawn Marie; Land, Miriam L.; ...
2014-06-14
Our motivation with this work was to assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. Our results show Illumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as anmore » additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies. As to availability and implementation–all assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.« less
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Self-assembly of nucleic acids, silk and hybrid materials thereof.
Humenik, Martin; Scheibel, Thomas
2014-12-17
Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here,we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.
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Self-assembly of nucleic acids, silk and hybrid materials thereof
NASA Astrophysics Data System (ADS)
Humenik, Martin; Scheibel, Thomas
2014-12-01
Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here, we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.
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1984-01-01
transferred -. to a 2.8-f wide mouth erlenmeyer flask. Sufficient distiLled deionized 1 38 -... 3 .° - . N,. 0 a V0 1- f I. S.0 cc SL ’S. 0 *1’*, -E C) C 5...water-to- dry -sediment weight ratio of 15:1. The sediment-water mixtures were kept in suspension by continuous stirring with a magnetic stirrer. Sediment...pH 5.0, pit 6.5, and pH 8.0). Each Eh-pH combination was amended with 75 Wg of As(V)/g dry weight of sediment as sodium arsenate and 25 wg Sb/g dry
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NASA Astrophysics Data System (ADS)
Bates, B.; Lowell, T. V.; Diefendorf, A. F.; Freimuth, E. J.; Stewart, A. K.
2017-12-01
Plant wax compounds preserved in lake sediments are used as proxies for paleohydrologic reconstructions. Despite their presence in lake sediments, little is known about their transport from plants to their deposition in lake sediments. By drawing on the leaf and pollen taphonomy literature combined with sediment focusing models, it is possible to develop several working hypotheses for the transport and deposition of plant waxes in lake sediments. An improved understanding of plant wax transport and deposition into lake sediments is necessary to increase the accuracy of paleohydrologic reconstructions. To better understand the controls on plant wax transport and deposition in lake sediment, we analyzed the sedimentary plant waxes from 3 lakes in the Adirondack Mountains of New York. These lakes were chosen to capture a range of basin-specific properties to evaluate their influences on the transport and deposition of plant wax compounds in surface sediments. We spatially characterized sediment properties with surface sediment samples and high-resolution underwater imaging, acoustically profiled the sub-bottom, and measured temperature profiles. From each site, we measured n-alkanes, bulk organic content (loss-on-ignition), bulk carbon and nitrogen concentrations, C:N ratios, and bulk carbon isotopes. Preliminary n-alkane concentrations and chain length distributions, as well as bulk carbon isotopes, are variable within each lake basin suggesting a mix of aquatic and terrestrial sources. The bulk carbon isotope values for two of the three lakes show a similar range of -2‰ compared to a range of -6.3‰ at the third lake. Likewise, the range of total n-alkane concentrations is much higher in the third lake suggesting that the controls on the distribution of n-alkanes and organic carbon are different between lakes. For terrestrial plant waxes, we find low n-alkane concentrations in sandy nearshore sediments relative to higher n-alkane concentrations in deeper fine-grained sediments. Combined, this information suggests that littoral processes focus organic compounds and fine sediments towards the main depo-center of the lake. These and other observations highlight important relationships between basin-specific properties and processes controlling the transport and deposition of plant wax compounds.
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Bayesian analysis for erosion modelling of sediments in combined sewer systems.
Kanso, A; Chebbo, G; Tassin, B
2005-01-01
Previous research has confirmed that the sediments at the bed of combined sewer systems are the main source of particulate and organic pollution during rain events contributing to combined sewer overflows. However, existing urban stormwater models utilize inappropriate sediment transport formulas initially developed from alluvial hydrodynamics. Recently, a model has been formulated and profoundly assessed based on laboratory experiments to simulate the erosion of sediments in sewer pipes taking into account the increase in strength with depth in the weak layer of deposits. In order to objectively evaluate this model, this paper presents a Bayesian analysis of the model using field data collected in sewer pipes in Paris under known hydraulic conditions. The test has been performed using a MCMC sampling method for calibration and uncertainty assessment. Results demonstrate the capacity of the model to reproduce erosion as a direct response to the increase in bed shear stress. This is due to the model description of the erosional strength in the deposits and to the shape of the measured bed shear stress. However, large uncertainties in some of the model parameters suggest that the model could be over-parameterised and necessitates a large amount of informative data for its calibration.
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ERIC Educational Resources Information Center
Hung, Y.-C.
2012-01-01
This paper investigates the impact of combining self explaining (SE) with computer architecture diagrams to help novice students learn assembly language programming. Pre- and post-test scores for the experimental and control groups were compared and subjected to covariance (ANCOVA) statistical analysis. Results indicate that the SE-plus-diagram…
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NASA Astrophysics Data System (ADS)
Trowbridge, J. H.; Butman, B.; Limeburner, R.
1994-08-01
Time-series measurements of current velocity, optical attenuation and surface wave intensity obtained during the Sediment Transport Events on Shelves and Slopes (STRESS) experiments, combined with shipboard measurements of conductivity, temperature and optical attenuation obtained during the Shelf Mixed Layer Experiment (SMILE), provide a description of the sediment concentration field over the central and outer shelf off northern California. The questions addressed are: (1) existence and characteristics of bottom nepheloid layers and their relationship to bottom mixed layers; (2) characteristics of temporal fluctuations in sediment concentration and their relationship to waves and currents; (3) spatial scales over which suspended sediment concentrations vary horizontally; and (4) vertical distribution of suspended sediment.
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Analysis of PKR-RNA interactions by sedimentation velocity
Wong, C. Jason; Launer-Felty, Katherine; Cole, James L.
2010-01-01
PKR is an interferon-induced kinase that plays a pivotal role in the innate immunity pathway for defense against viral infection. PKR is activated to undergo autophosphorylation upon binding to RNAs that contain duplex regions. Some highly structured viral RNAs do not activate and function as PKR inhibitors. In order to define the mechanisms of activation and inhibition of PKR by RNA it is necessary to characterize the stoichiometries, affinities and free energy couplings governing the assembly of the relevant complexes. We have found sedimentation velocity analytical ultracentrifugation to be particularly useful in the study of PKR-RNA interactions. Here, we describe protocols for designing and analyzing sedimentation velocity experiments that are generally applicable to studies of protein-nucleic interactions. Initially, velocity data obtained at multiple protein:RNA ratios are analyzed using the dc/dt method to define the association model and to test whether the system is kinetically limited. The sedimentation velocity data obtained at multiple loading concentrations are then globally fit to this model to determine the relevant association constants. The frictional ratios of the complexes are calculated using the fitted sedimentation coefficients to determine whether the hydrodynamic properties are physically reasonable. We demonstrate the utility of this approach using examples from our studies of PKR interactions with simple dsRNAs, the HIV TAR RNA and the VAI RNA from Adenovirus. PMID:21195224
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Bioavailability of sediment-bound contaminants to marine organisms
DOE Office of Scientific and Technical Information (OSTI.GOV)
Brown, B.; Neff, J.
1993-09-01
The bioavailability of sediment-bound contaminants to marine organisms indicates that there exists a potential for transfer of these contaminants through marine food webs to commercial fisheries products consumed by humans. However, there has been relatively little effort to combine and synthesize data on chemical/biological interactions between benthic animals and seagrasses and the sediments in which they reside on the one hand, and on the chemistry of bioaccumulation on the other. This report provides a conceptual basis for an approach to bioavailability and biomagnification of sediment-bound contaminants that reviews biological and chemical approaches.
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PHOTOTOXIC POLYCYCLIC AROMATIC HYDROCARBONS IN SEDIMENTS: A MODEL-BASED APPROACH FOR ASSESSING RISK
Over the past five years we have developed a number of models which will be combined in an integrated framework with chemical-monitoring information to assess the potential for widespread risk of phototoxic PAHs in sediments.
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Old River Control Complex Sedimentation Investigation
2015-06-01
efforts to describe the shoaling processes and sediment transport in the two-river system. Geomorphic analysis The geomorphic assessment utilized...District, New Orleans. The investigation was conducted via a combination of field data collection and laboratory analysis, geomorphic assessments, and...6 Geomorphic analysis
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Fuel and oxidizer valve assembly employs single solenoid actuator
NASA Technical Reports Server (NTRS)
1966-01-01
Valve assembly simultaneously starts or stops the flow of oxidizer and fuel from separate inlet channels to reaction control motors. The assembly combines an oxidizer shutoff valve and a fuel shutoff valve which are mechanically linked and operated by a single high-speed solenoid actuator.
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Stavrianakou, Maria; Perez, Ricardo; Wu, Cheng; Sachs, Matthew S; Aramayo, Rodolfo; Harlow, Mark
2017-08-14
The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ. Sequencing yielded 102 million paired-end 100 bp reads. De novo Trinity assembly was performed at Kmer 25 (default) and Kmers 27, 29, and 31. Trinity, generated around 103,000 transcripts, and 78,000 genes per assembly. Assemblies were evaluated based on the number of bases/transcripts assembled, RSEM-EVAL scores and informational content and completeness. We found that different assemblies scored differently according to the evaluation criteria used, and that while each individual assembly contained unique information, much of the assembly information was shared by all assemblies. To generate the presynaptic transcriptome (electric lobe), while capturing all information, assemblies were first clustered and then combined with postsynaptic transcripts (electric organ) downloaded from NCBI. The completness of the resulting clustered predicted MetaProteome was rigorously evaluated by comparing its information against the predicted proteomes from Homo sapiens, Callorhinchus milli, and the Transporter Classification Database (TCDB). In summary, we obtained a MetaProteome containing 92%, 88.5%, and 66% of the expected set of ultra-conserved sequences (i.e., BUSCOs), expected to be found for Eukaryotes, Metazoa, and Vertebrata, respectively. We cross-annotated the conserved set of proteins shared between the T. californica MetaProteome and the proteomes of H. sapiens and C. milli, using the H. sapiens genome as a reference. This information was used to predict the position in human pathways of the conserved members of the T. californica MetaProteome. We found proteins not detected before in T. californica, corresponding to processes involved in synaptic vesicle biology. Finally, we identified 42 transporter proteins in TCDB that were detected by the T. californica MetaProteome (electric fish) and not selected by a control proteome consisting of the combined proteomes of 12 widely diverse non-electric fishes by Reverse-Blast-Hit Blast. Combined, the information provided here is not only a unique tool for the study of cholinergic neurotransmission, but it is also a starting point for understanding the evolution of early vertebrates.
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Hierarchical nanoparticle assemblies formed by decorating breath figures.
Böker, Alexander; Lin, Yao; Chiapperini, Kristen; Horowitz, Reina; Thompson, Mike; Carreon, Vincent; Xu, Ting; Abetz, Clarissa; Skaff, Habib; Dinsmore, A D; Emrick, Todd; Russell, Thomas P
2004-05-01
The combination of two self-assembly processes on different length scales leads to the formation of hierarchically structured nanoparticle arrays. Here, the formation of spherical cavities, or 'breath figures'-made by the condensation of micrometre-sized water droplets on the surface of a polymer solution-that self-assemble into a well-ordered hexagonal array, is combined with the self-assembly of CdSe nanoparticles at the polymer solution-water droplet interface. Complete evaporation of the solvent and water confines the particle assembly to an array of spherical cavities and allows for ex situ investigation. Fluorescence confocal, transmission electron and scanning electron microscope images show the preferential segregation of the CdSe nanoparticles to the polymer solution-water interface where they form a 5-7-nm-thick layer, thus functionalizing the walls of the holes. This process opens a new route to fabricating highly functionalized ordered microarrays of nanoparticles, potentially useful in sensory, separation membrane or catalytic applications.
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Self-assembled biomimetic nanoreactors I: Polymeric template
NASA Astrophysics Data System (ADS)
McTaggart, Matt; Malardier-Jugroot, Cecile; Jugroot, Manish
2015-09-01
The variety of nanoarchitectures made feasible by the self-assembly of alternating copolymers opens new avenues for biomimicry. Indeed, self-assembled structures allow the development of nanoreactors which combine the efficiency of high surface area metal active centres to the effect of confinement due to the very small cavities generated by the self-assembly process. A novel self-assembly of high molecular weight alternating copolymers is characterized in the present study. The self-assembly is shown to organize into nanosheets, providing a 2 nm hydrophobic cavity with a 1D confinement.
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Ferrer, I.; Heine, C.E.; Thurman, E.M.
2004-01-01
Diphenhydramine (Benadryl) is a popular over-the-counter antihistaminic medication used for the treatment of allergies. After consumption, excretion, and subsequent discharge from wastewater treatment plants, it is possible that diphenhydramine will be found in environmental sediments due to its hydrophobicity (log P = 3.27). This work describes a methodology for the first unequivocal determination of diphenhydramine bound to environmental sediments. The drug is removed from the sediments by accelerated solvent extraction and then analyzed by liquid chromatography with a time-of-flight mass spectrometer and an ion trap mass spectrometer. This combination of techniques provided unequivocal identification and confirmation of diphenhydramine in two sediment samples. The accurate mass measurements of the protonated molecules were m/z 256.1703 and 256.1696 compared to the calculated mass of m/z 256.1701, resulting in errors of 0.8 and 2.3 ppm. This mass accuracy was sufficient to verify the elemental composition of diphenhydramine in each sample. Furthermore, accurate mass measurements of the primary fragment ion were obtained. This work is the first application of time-of-flight mass spectrometry for the identification of diphenhydramine and shows the accumulation of an over-the-counter medication in aquatic sediments at five different locations.
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León-Muñoz, Jorge; Echeverría, Cristian; Marcé, Rafael; Riss, Wolfgang; Sherman, Bradford; Iriarte, Jose Luis
2013-10-15
Water and sediment quality in North Patagonia's large, oligotrophic lakes are expected to suffer as native forest continues to be fragmented and degraded by its conversion to cropping and pasture land uses. These changes in land use are expected to increase diffuse nutrient loads to the region's lakes. In addition, these lakes are home to the world's second largest salmon aquaculture industry which provides additional point sources of nutrients within the lakes. We studied the combined influences of land use change and salmon farming on the nutrient concentrations in a North Patagonian lake (Lake Rupanco, 233 km(2) water surface, 163 m average depth) in four sub-watersheds ranging in disturbance from near-pristine forest to 53% converted to cropping and pasture. Nitrogen exports from the tributary sub-watersheds increased from 33 kg TN/km(2)/y to 621 kg TN/km(2)/y as the proportion of crop and pasture land increased. The combined nutrient load from land use change and salmon farming has led to significant differences in the nitrogen concentrations of the lake's water column and sediments in the near-shore zones across the lake. Total nitrogen concentrations in the sediments varied from 37 ± 18 mg/kg in near-pristine sub-watersheds without salmon farming to 6400 ± 698 mg/kg where the sub-watershed was dominated by crop and pasture lands combined with the presence of salmon farming. These results demonstrate the importance of considering the impacts of both salmon farming and land use on water and sediment quality for future environmental planning, management and decision making. Copyright © 2013 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Groehn, Franziska; Duering, Jasmin; Moldenhauer, Daniel; Interdisciplinary CenterMolecular Materials Team
2013-03-01
Recently we have introduced a novel type of self-assembled ``nano-objects'' in solution: From the association of macroions and multivalent counterions well-defined and stable structures in the shape of spheres, rod, rings, hollow spheres and networks can form in solution. Using light-addressable counterions, it is possible to switch the particle size through UV irradiation. Building blocks can be of organic or inorganic nature: Using gold or cadmium sulphide nanoclusters results in hybrid assemblies which also functionally combine nanoparticle and dye. Thermodynamic studies in combination with a detailed structural characterization yield insight into driving forces and structural control in the self-assembly process. Crucial is the delicate interplay of ionic, π - π , and Hamaker interaction. The concept is particularly attractive, as it relies on general physical effects - that is the combination of different non-covalent interactions - and hence is very versatile. Great potential of the structures presented lies in areas such as catalysis and energy conversion.
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NASA Astrophysics Data System (ADS)
Ishmukhametov, Robert R.; Russell, Aidan N.; Berry, Richard M.
2016-10-01
An important goal in synthetic biology is the assembly of biomimetic cell-like structures, which combine multiple biological components in synthetic lipid vesicles. A key limiting assembly step is the incorporation of membrane proteins into the lipid bilayer of the vesicles. Here we present a simple method for delivery of membrane proteins into a lipid bilayer within 5 min. Fusogenic proteoliposomes, containing charged lipids and membrane proteins, fuse with oppositely charged bilayers, with no requirement for detergent or fusion-promoting proteins, and deliver large, fragile membrane protein complexes into the target bilayers. We demonstrate the feasibility of our method by assembling a minimal electron transport chain capable of adenosine triphosphate (ATP) synthesis, combining Escherichia coli F1Fo ATP-synthase and the primary proton pump bo3-oxidase, into synthetic lipid vesicles with sizes ranging from 100 nm to ~10 μm. This provides a platform for the combination of multiple sets of membrane protein complexes into cell-like artificial structures.
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NASA Astrophysics Data System (ADS)
Schrott, Lothar; Hufschmidt, Gabi; Hankammer, Martin; Hoffmann, Thomas; Dikau, Richard
2003-09-01
Spatial patterns of sediment storage types and associated volumes using a novel approach for quantifying valley fill deposits are presented for a small alpine catchment (17 km 2) in the Bavarian Alps. The different sediment storage types were analysed with respect to geomorphic coupling and sediment flux activity. The most landforms in the valley in terms of surface area were found to be talus slopes (sheets and cones) followed by rockfall deposits and alluvial fans and plains. More than two-thirds of the talus slopes are relict landforms, completely decoupled from the geomorphic system. Notable sediment transport is limited to avalanche tracks, debris flows, and along floodplains. Sediment volumes were calculated using a combination of polynomial functions of cross sections, seismic refraction, and GIS modelling. A total of, 66 seismic refraction profiles were carried out throughout the valley for a more precise determination of sediment thicknesses and to check the bedrock data generated from geomorphometric analysis. We calculated the overall sediment volume of the valley fill deposits to be 0.07 km 3. This corresponds to a mean sediment thickness of 23.3 m. The seismic refraction data showed that large floodplains and sedimentation areas, which have been developed through damming effects from large rockfalls, are in general characterised by shallow sediment thicknesses (<20 m). By contrast, the thickness of several talus slopes is more than twice as much. For some locations (e.g., narrow sections of valley), the polynomial-generated cross sections resulted in overestimations of up to one order of magnitude; whereas in sections with a moderate valley shape, the modelled cross sections are in good accordance with the obtained seismic data. For the quantification of valley fill deposits, a combined application of bedrock data derived from polynomials and geophysical prospecting is highly recommended.
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Marvin-Dipasquale, Mark; Lutz, Michelle A; Brigham, Mark E; Krabbenhoft, David P; Aiken, George R; Orem, William H; Hall, Britt D
2009-04-15
Mercury speciation, controls on methylmercury (MeHg) production, and bed sediment-pore water partitioning of total Hg (THg) and MeHg were examined in bed sediment from eight geochemically diverse streams where atmospheric deposition was the predominant Hg input. Across all streams, sediment THg concentrations were best described as a combined function of sediment percent fines (%fines; particles < 63 microm) and organic content. MeHg concentrations were best described as a combined function of organic content and the activity of the Hg(II)-methylating microbial community and were comparable to MeHg concentrations in streams with Hg inputs from industrial and mining sources. Whole sediment tin-reducible inorganic reactive Hg (Hg(II)R) was used as a proxy measure for the Hg(II) pool available for microbial methylation. In conjunction with radiotracer-derived rate constants of 203Hg(II) methylation, Hg(II)R was used to calculate MeHg production potential rates and to explain the spatial variability in MeHg concentration. The %Hg(II)R (of THg) was low (2.1 +/- 5.7%) and was inversely related to both microbial sulfate reduction rates and sediment total reduced sulfur concentration. While sediment THg concentrations were higher in urban streams, %MeHg and %Hg(II)R were higher in nonurban streams. Sediment pore water distribution coefficients (log Kd's) for both THg and MeHg were inversely related to the log-transformed ratio of pore water dissolved organic carbon (DOC) to bed sediment %fines. The stream with the highest drainage basin wetland density also had the highest pore water DOC concentration and the lowest log Kd's for both THg and MeHg. No significant relationship existed between overlying water MeHg concentrations and those in bed sediment or pore water, suggesting upstream sources of MeHg production may be more important than local streambed production as a driver of water column MeHg concentration in drainage basins that receive Hg inputs primarily from atmospheric sources.
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Mtibaa, Slim; Hotta, Norifumi; Irie, Mitsuteru
2018-03-01
Soil erosion can be reduced through the strategic selection and placement of best management practices (BMPs) in critical source areas (CSAs). In the present study, the Soil Water Assessment Tool (SWAT) model was used to identify CSAs and investigate the effectiveness of different BMPs in reducing sediment yield in the Joumine watershed, an agricultural river catchment located in northern Tunisia. A cost-benefit analysis (CBA) was used to evaluate the cost-effectiveness of different BMP scenarios. The objective of the present study was to determine the most cost-effective management scenario for controlling sediment yield. The model performance for the simulation of streamflow and sediment yield at the outlet of the Joumine watershed was good and satisfactory, respectively. The model indicated that most of the sediment was originated from the cultivated upland area. About 34% of the catchment area consisted of CSAs that were affected by high to very high soil erosion risk (sediment yield >10t/ha/year). Contour ridges were found to be the most effective individual BMP in terms of sediment yield reduction. At the watershed level, implementing contour ridges in the CSAs reduced sediment yield by 59%. Combinations of BMP scenarios were more cost-effective than the contour ridges alone. Combining buffer strips (5-m width) with other BMPs depending on land slope (> 20% slope: conversion to olive orchards; 10-20% slope: contour ridges; 5-10% slope: grass strip cropping) was the most effective approach in terms of sediment yield reduction and economic benefits. This approach reduced sediment yield by 61.84% with a benefit/cost ratio of 1.61. Compared with the cost of dredging, BMPs were more cost-effective for reducing sediment loads to the Joumine reservoir, located downstream of the catchment. Our findings may contribute to ensure the sustainability of future conservation programs in Tunisian regions. Copyright © 2017 Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Estes, E. R.; Hansel, C. M.; Orsi, W. D.; Anderson, C. H.; Murray, R. W.; Wankel, S. D.; Johnson, D.; Nordlund, D.; Spivack, A. J.; Sauvage, J.; McKinley, C. C.; Homola, K.; Present, T. M.; Pockalny, R. A.; D'Hondt, S.
2016-02-01
Pelagic marine sediments are often carbon-limited, with oxic sediments bearing exceedingly small concentrations of metabolizable organic carbon (OC) and anoxic sediments lacking electron acceptors to drive heterotrophy. This OC is typically considered recalcitrant and presumed to be of limited bioavailability as much of it is difficult to characterize molecularly. Here, we utilize a combination of spectrometry, spectroscopy, and fluorescent assays to characterize the OC content and composition of sediment cores from the western subtropical North Atlantic collected during R/V Knorr expedition 223 in November 2014. We find that OC concentrations decrease linearly over 15m burial depth from 0.15 to 0.075 mol OC/kg sediment, beyond which this lower OC level persists to depths approaching 30m. The ratio of organic carbon to nitrogen (C/N) varies but is consistently close to Redfield values of 6. Further, protein concentrations within the suboxic sediments are 1.75 to 4.90 μg protein/mg sediment, values in excess of predicted cell abundance in subsurface sediments. After an initial decrease in concentration between 0-3 meters below core top, protein content increases and stabilizes at 4 μg protein/mg sediment. RNA is detectable throughout the core and profiles (as μg cDNA amplified/g sediment) generally correlate with the shape of protein profiles. Combined, these results imply a small but active microbial community and the potential for these proteins to fuel heterotrophy at depth. Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy finds that amide and carboxyl C functionalities comprise 25% of total spectral area, with the remainder dominated by aromatic C and O-alkyl-C groups. These findings suggest that sedimentary OC contain identifiable components, including a substantial concentration of intact proteins that may fuel heterotrophic microbial communities.
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U-Th and 10Be constraints on sediment recycling in proglacial settings, Lago Buenos Aires, Patagonia
NASA Astrophysics Data System (ADS)
Cogez, Antoine; Herman, Frédéric; Pelt, Éric; Reuschlé, Thierry; Morvan, Gilles; Darvill, Christopher M.; Norton, Kevin P.; Christl, Marcus; Märki, Lena; Chabaux, François
2018-03-01
The estimation of sediment transfer times remains a challenge to our understanding of sediment budgets and the relationships between erosion and climate. Uranium (U) and thorium (Th) isotope disequilibria offer a means of more robustly constraining sediment transfer times. Here, we present new uranium and thorium disequilibrium data for a series of nested moraines around Lago Buenos Aires in Argentine Patagonia. The glacial chronology for the area is constrained using in situ cosmogenic 10Be analysis of glacial outwash. Sediment transfer times within the periglacial domain were estimated by comparing the deposition ages of moraines to the theoretical age of sediment production, i.e., the comminution age inferred from U disequilibrium data and recoil loss factor estimates. Our data show first that the classical comminution age approach must include weathering processes accounted for by measuring Th disequilibrium. Second, our combined data suggest that the pre-deposition history of the moraine sediments is not negligible, as evidenced by the large disequilibrium of the youngest moraines despite the equilibrium of the corresponding glacial flour. Monte Carlo simulations suggest that weathering was more intense before the deposition of the moraines and that the transfer time of the fine sediments to the moraines was on the order of 100-200 kyr. Long transfer times could result from a combination of long sediment residence times in the proglacial lake (recurrence time of a glacial cycle) and the remobilization of sediments from moraines deposited during previous glacial cycles. 10Be data suggest that some glacial cycles are absent from the preserved moraine record (seemingly every second cycle), supporting a model of reworking moraines and/or fluctuations in the extent of glacial advances. The chronological pattern is consistent with the U-Th disequilibrium data and the 100-200 kyr transfer time. This long transfer time raises the question of the proportion of freshly eroded sediments that escape (or not) the proglacial environments during glacial periods.
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Wang, Ren; Li, Da-peng; Huang, Yong; Liu, Yan-jian; Chen, Jun
2015-11-01
Synergistic effect of physical and Chironomus plumosus combination disturbance on the characteristics of the micro-environment and micro-interface was investigated by the Rhizon samplers and Unisense micro sensor system. The results showed that the oxygen penetration depth (OPD), total oxygen exchange (TOE), water content and total microbial activity increased under the combination disturbance and bioturbation and were kept at the higher level, compared with the control. These parameters increased with the physical intensity under combination disturbance. However, the content of Fe2+ decreased under the combination disturbance and bioturbation and the decrease was more obvious than that in the control. The changes of the Fe2+, the water content and the total microbial activity were large at 0-4 cm depth in the sediments. Therefore, the area might be the active area for the transformation of internal sedimentary phosphorus forms. The curve fitting was used for the OPD, TOE, the content of Fe2+, the water content and the total microbial activity with the physical intensity under combination disturbance. It was observed that the second-order polynomial equation was suitable for the curve fitting. In addition, jump type synergistic effect was presented in the above mentioned parameters under combination disturbance when the physical intensity was higher than 34 r x min(-1). The remodeling on the sediment micro-interface and micro-environment might be the main inducing mechanism for the transformation of internal phosphorus.
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Musumeci, Matias A.; Lozada, Mariana; Rial, Daniela V.; ...
2017-04-09
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putativemore » monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. As a result, this work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Musumeci, Matias A.; Lozada, Mariana; Rial, Daniela V.
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putativemore » monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. As a result, this work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.« less
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Musumeci, Matías A; Lozada, Mariana; Rial, Daniela V; Mac Cormack, Walter P; Jansson, Janet K; Sjöling, Sara; Carroll, JoLynn; Dionisi, Hebe M
2017-04-09
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.
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Musumeci, Matías A.; Lozada, Mariana; Rial, Daniela V.; Mac Cormack, Walter P.; Jansson, Janet K.; Sjöling, Sara; Carroll, JoLynn; Dionisi, Hebe M.
2017-01-01
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer–Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments. PMID:28397770
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Tianfu; Wang, Zhen; Li, Guoping
2015-10-15
A bottom-up approach combining soft template self-assembly with sol–gel process, was adopted to prepare the assembled Al/Fe{sub 2}O{sub 3} nanoenergetic materials, assembly-Al/Fe{sub 2}O{sub 3} sample. The other two unassembled Al/Fe{sub 2}O{sub 3}a nanoenergetic materials, sol–gel–Al/Fe{sub 2}O{sub 3} sample and mixing-Al/Fe{sub 2}O{sub 3} sample, were prepared by sol–gel method and physical mixing method respectively. The assembly process within the preparation of the assembly-Al/Fe{sub 2}O{sub 3} sample was analyzed through the changes in the average hydrodynamic diameters of the particles and the micelles in solution. SEM, EDS and TEM tests were performed to demonstrate a significant improvement regarding to dispersity and arrangementsmore » of the Al and Fe{sub 2}O{sub 3} particles in the assembled samples, compared to that of the unassembled Al/Fe{sub 2}O{sub 3} samples. DSC test was employed to characterize the reactivity of the samples. The heat release of the assembled Al/Fe{sub 2}O{sub 3} sample was 2088 J/g, about 400 and 990 J/g more than that of the sol–gel–Al/Fe{sub 2}O{sub 3} sample and mixing-Al/Fe{sub 2}O{sub 3} sample, respectively. - Graphical abstract: Modified aluminum (Al) nanoparticles with hydrophobic surface assembled into the Brij S10 micelle in Fe(III) sol, then the well dispersed system was transformed into Al/Fe{sub 2}O{sub 3} nanoenergetic materials with high reactivity. - Highlights: • An approach combining soft template self-assembly with sol–gel process was adopted. • The aggregation of Al nanoparticles in the final product was reduced significantly. • The reactivity of Al/Fe{sub 2}O{sub 3} nanoenergetic materials was improved to a large extent.« less
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Siebman, Coralie; Velev, Orlin D; Slaveykova, Vera I
2015-06-15
An alternative current (AC) dielectrophoretic lab-on-chip setup was evaluated as a rapid tool of capture and assembly of microalga Chlamydomonas reinhardtii in two-dimensional (2D) close-packed arrays. An electric field of 100 V·cm⁻¹, 100 Hz applied for 30 min was found optimal to collect and assemble the algae into single-layer structures of closely packed cells without inducing cellular oxidative stress. Combined with oxidative stress specific staining and fluorescence microscopy detection, the capability of using the 2D whole-cell assembly on-chip to follow the reactive oxygen species (ROS) production and oxidative stress during short-term exposure to several environmental contaminants, including mercury, methylmercury, copper, copper oxide nanoparticles (CuO-NPs), and diuron was explored. The results showed significant increase of the cellular ROS when C. reinhardtii was exposed to high concentrations of methylmercury, CuO-NPs, and 10⁻⁵ M Cu. Overall, this study demonstrates the potential of combining AC-dielectrophoretically assembled two-dimensional algal structures with cell metabolic analysis using fluorescence staining, as a rapid analytical tool for probing the effect of contaminants in highly impacted environment.
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NASA Astrophysics Data System (ADS)
Goode, J. R.; Candelaria, T.; Kramer, N. R.; Hill, A. F.
2016-12-01
As global energy demands increase, generating hydroelectric power by constructing dams and reservoirs on large river systems is increasingly seen as a renewable alternative to fossil fuels, especially in emerging economies. Many large-scale hydropower projects are located in steep mountainous terrain, where environmental factors have the potential to conspire against the sustainability and success of such projects. As reservoir storage capacity decreases when sediment builds up behind dams, high sediment yields can limit project life expectancy and overall hydropower viability. In addition, episodically delivered sediment from landslides can make quantifying sediment loads difficult. These factors, combined with remote access, limit the critical data needed to effectively evaluate development decisions. In the summer of 2015, we conducted a basic survey to characterize the geomorphology, hydrology and ecology of 620 km of the Rio Maranon, Peru - a major tributary to the Amazon River, which flows north from the semi-arid Peruvian Andes - prior to its dissection by several large hydropower dams. Here we present one component of this larger study: a first order analysis of potential sediment inputs to the Rio Maranon, Peru. To evaluate sediment delivery and storage in this system, we used high resolution Google Earth imagery to delineate landslides, combined with high resolution imagery from a DJI Phantom 3 Drone, flown at alluvial fan inputs to the river in the field. Because hillslope-derived sediment inputs from headwater tributaries are important to overall ecosystem health in large river systems, our study has the potential to contribute to the understanding the impacts of large Andean dams on sediment connectivity to the Amazon basin.
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Assembly of hard spheres in a cylinder: a computational and experimental study.
Fu, Lin; Bian, Ce; Shields, C Wyatt; Cruz, Daniela F; López, Gabriel P; Charbonneau, Patrick
2017-05-14
Hard spheres are an important benchmark of our understanding of natural and synthetic systems. In this work, colloidal experiments and Monte Carlo simulations examine the equilibrium and out-of-equilibrium assembly of hard spheres of diameter σ within cylinders of diameter σ≤D≤ 2.82σ. Although phase transitions formally do not exist in such systems, marked structural crossovers can nonetheless be observed. Over this range of D, we find in simulations that structural crossovers echo the structural changes in the sequence of densest packings. We also observe that the out-of-equilibrium self-assembly depends on the compression rate. Slow compression approximates equilibrium results, while fast compression can skip intermediate structures. Crossovers for which no continuous line-slip exists are found to be dynamically unfavorable, which is the main source of this difference. Results from colloidal sedimentation experiments at low diffusion rate are found to be consistent with the results of fast compressions, as long as appropriate boundary conditions are used.
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STORAGE/SEDIMENTATION FACILITIES FOR CONTROL OF STORM AND COMBINED SEWER OVERFLOW: DESIGN MANUAL
This manual describes applications of storage facilities in wet-weather flow management and presents step-by-step procedures for analysis and design of storage-treatment facilities. Retention, detention, and sedimentation storage information is classified and described. Internati...
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SEWER SEDIMENT AND CONTROL: A MANAGEMENT PRACTICES REFERENCES GUIDE
Sewer-solids sediment is one of major sources of pollutants in urban wet-weather flow (WWF) discharges that include combined-sewer overflow (CSO), separate sanitary-sewer overflow (SSO), and stormwater runoff. During low-flow, dry-weather periods, sanitary wastewater solids depo...
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Do predator-prey relationships on the river bed affect fine sediment ingress?
NASA Astrophysics Data System (ADS)
Mathers, Kate; Rice, Stephen; Wood, Paul
2016-04-01
Ecosystem engineers are organisms that alter their physical environment and thereby influence the flow of resources through ecosystems. In rivers, several ecosystem engineers are also important geomorphological agents that modify fluvial sediment dynamics. By altering channel morphology and bed material characteristics, such modifications can affect the availability of habitats for other organisms, with implications for ecosystem health and wider community composition. In this way geomorphological and ecological systems are intimately interconnected. This paper focuses on one element of this intricate abiotic-biotic coupling: the interaction between fine sediment ingress into the river bed and the predator-prey relationships of aquatic organisms living on and in the river bed. Signal crayfish (Pacifastacus leniusculus) have been shown to modify fine sediment fluxes in rivers, but their effect on fine sediment ingress into riverbeds remains unclear. Many macroinvertebrate taxa have adapted avoidance strategies to avoid predation by crayfish, with one example being the freshwater shrimp (Gammarus pulex) which relies on open interstitial spaces within subsurface sediments as a refuge from crayfish predation. Fine sedimentation that fills gravelly frameworks may preclude access to those spaces, therefore leaving freshwater shrimp susceptible to predation. Ex-situ experiments were conducted which sought to examine: i) if freshwater shrimps and signal crayfish, alone and in combination, influenced fine sediment infiltration rates; and ii) whether modifications to substratum composition, specifically the introduction of fine sediment, modified predator-prey interactions. The results demonstrate that crayfish are significant geomorphic agents and that fine sediment ingress rates were significantly enhanced in their presence compared to control conditions or the presence of only freshwater shrimps. The combination of both organisms (i.e. allowing the interaction between predator and prey) resulted in intermediate fine sediment infiltration rates. The results suggest that reductions in prey availability may enhance crayfish foraging behaviour and therefore their impact on fine sediment ingress into river beds. Consequently, as invading species become more established and prey resources are depleted, the implications of invasive crayfish on fine sediment dynamics may become more prominent. These experiments demonstrate the importance of abiotic-biotic coupling in fluvial systems for both geomorphological and ecological understanding.
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A new chicken genome assembly provides insight into avian genome structure
USDA-ARS?s Scientific Manuscript database
The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3) built from combined long single molecule sequencing t...
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Turbine blade vibration dampening
Cornelius, C.C.; Pytanowski, G.P.; Vendituoli, J.S.
1997-07-08
The present turbine wheel assembly increases component life and turbine engine longevity. The combination of the strap and the opening combined with the preestablished area of the outer surface of the opening and the preestablished area of the outer circumferential surface of the strap and the friction between the strap and the opening increases the life and longevity of the turbine wheel assembly. Furthermore, the mass ``M`` or combined mass ``CM`` of the strap or straps and the centrifugal force assist in controlling vibrations and damping characteristics. 5 figs.
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Turbine blade vibration dampening
Cornelius, Charles C.; Pytanowski, Gregory P.; Vendituoli, Jonathan S.
1997-07-08
The present turbine wheel assembly increases component life and turbine engine longevity. The combination of the strap and the opening combined with the preestablished area of the outer surface of the opening and the preestablished area of the outer circumferential surface of the strap and the friction between the strap and the opening increases the life and longevity of the turbine wheel assembly. Furthermore, the mass "M" or combined mass "CM" of the strap or straps and the centrifugal force assist in controlling vibrations and damping characteristics.
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Bed Surface Adjustments to Spatially Variable Flow in Low Relative Submergence Regimes
NASA Astrophysics Data System (ADS)
Monsalve, A.; Yager, E. M.
2017-11-01
In mountainous rivers, large relatively immobile grains partly control the local and reach-averaged flow hydraulics and sediment fluxes. When the flow depth is similar to the size of these grains (low relative submergence), heterogeneous flow structures and plunging flow cause spatial distributions of bed surface elevations, textures, and sedimentation rates. To explore how the bed surface responds to these flow variations we conducted a set of experiments in which we varied the relative submergence of staggered hemispheres (simulated large boulders) between runs. All experiments had the same average sediment transport capacity, upstream sediment supply, and initial bed thickness and grain size distribution. We combined our laboratory measurements with a 3-D flow model to obtain the detailed flow structure around the hemispheres. The local bed shear stress field displayed substantial variability and controlled the bed load transport rates and direction in which sediment moved. The divergence in bed shear stress caused by the hemispheres promoted size-selective bed load deposition, which formed patches of coarse sediment upstream of the hemisphere. Sediment deposition caused a decrease in local bed shear stress, which combined with the coarser grain size, enhanced the stability of this patch. The region downstream of the hemispheres was largely controlled by a recirculation zone and had little to no change in grain size, bed elevation, and bed shear stress. The formation, development, and stability of sediment patches in mountain streams is controlled by the bed shear stress divergence and magnitude and direction of the local bed shear stress field.
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Oestreicher, Jordan Sky; Lucotte, Marc; Moingt, Matthieu; Bélanger, Émilie; Rozon, Christine; Davidson, Robert; Mertens, Frédéric; Romaña, Christina A
2017-01-01
In the Tapajós River region of the Brazilian Amazon, mercury (Hg) is a prevalent contaminant in the aquatic ecosystem. Few studies have used comprehensive chronological analyses to examine the combined effects of environmental and anthropogenic factors on Hg accumulation in sediments. Total mercury (THg) content was measured in sediments from eight floodplain lakes and Pb 210 isotope analysis was used to develop a timeline of THg accumulation. Secondary data representing environmental and anthropogenic factors were analyzed using geo-spatial analyses. These include land-cover change, hydrometeorological time-series data, lake morphology, and watershed biophysical characteristics. The results indicate that THg accumulation and sedimentation rates have increased significantly at the surface of most sediment cores, sometimes doubling since the 1970s. Human-driven land-cover changes in the watershed correspond closely to these shifts. Tropical deforestation enhances erosion, thereby mobilizing the heavy metal that naturally occurs in soils. Environmental factors also contribute to increased THg content in lacustrine sediments. Climate shifts since the 1980s are further compounding erosion and THg accumulation in surface sediments. Furthermore, variations in topography, soil types, and the level of hydrological connectivity between lakes and the river explain observed variations in THg fluxes and sedimentation. Although connectivity naturally varies among sampled lakes, deforestation of sensitive floodplain vegetation has changed lake-river hydrology in several sites. In conclusion, the results point to a combination of anthropogenic and environmental factors as determinants of increased THg accumulation in tropical floodplain sediments in the Tapajós region.
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Methanation assembly using multiple reactors
Jahnke, Fred C.; Parab, Sanjay C.
2007-07-24
A methanation assembly for use with a water supply and a gas supply containing gas to be methanated in which a reactor assembly has a plurality of methanation reactors each for methanating gas input to the assembly and a gas delivery and cooling assembly adapted to deliver gas from the gas supply to each of said methanation reactors and to combine water from the water supply with the output of each methanation reactor being conveyed to a next methanation reactor and carry the mixture to such next methanation reactor.
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Zhang, Xiao-yong; Tang, Gui-ling; Xu, Xin-ya; Nong, Xu-hua; Qi, Shu-Hua
2014-01-01
The fungal diversity in deep-sea environments has recently gained an increasing amount attention. Our knowledge and understanding of the true fungal diversity and the role it plays in deep-sea environments, however, is still limited. We investigated the fungal community structure in five sediments from a depth of ∼4000 m in the East India Ocean using a combination of targeted environmental sequencing and traditional cultivation. This approach resulted in the recovery of a total of 45 fungal operational taxonomic units (OTUs) and 20 culturable fungal phylotypes. This finding indicates that there is a great amount of fungal diversity in the deep-sea sediments collected in the East Indian Ocean. Three fungal OTUs and one culturable phylotype demonstrated high divergence (89%–97%) from the existing sequences in the GenBank. Moreover, 44.4% fungal OTUs and 30% culturable fungal phylotypes are new reports for deep-sea sediments. These results suggest that the deep-sea sediments from the East India Ocean can serve as habitats for new fungal communities compared with other deep-sea environments. In addition, different fungal community could be detected when using targeted environmental sequencing compared with traditional cultivation in this study, which suggests that a combination of targeted environmental sequencing and traditional cultivation will generate a more diverse fungal community in deep-sea environments than using either targeted environmental sequencing or traditional cultivation alone. This study is the first to report new insights into the fungal communities in deep-sea sediments from the East Indian Ocean, which increases our knowledge and understanding of the fungal diversity in deep-sea environments. PMID:25272044
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Li, Haifeng; Li, Zhijian; Qu, Jianhang; Tian, Hailong; Yang, Xiaohong
2018-05-02
Simulation experiments were conducted using sediments collected from the Taihu Lake to determine the combined effects of submerged macrophytes Ceratophyllum demersum and phosphate-solubilizing bacteria (PSB) strain XMT-5 (Rhizobium sp.) on phosphorus (P) concentrations in overlying waters and sediments. After 30 days of experimental incubation, the total phosphorus (TP) and dissolved total phosphorus (DTP) concentrations of the overlying water subjected to AMB and AHMB treatments (both with the combined effects of PSB cells and submerged macrophytes) were generally lower than those of the AM (with individual effects of inoculated C. demersum) and AB (with individual effects of a smaller amount of inoculated PSB cells) control treatments but higher than that of the A (with no effects of inoculated PSB cells or C. demersum) and AHB (with individual effects of a larger amount of inoculated PSB) control treatments. The TP contents of the sediment in the AMB and AHMB treatments were significantly lower than those of the other control treatments. The TP contents of the C. demersum cocultured with the PSB strain XMT-5 cells in the AMB and AHMB treatments were all significantly higher than that of the AM treatment, indicating the enhancement of P uptake by submerged plants inoculated with PSB. The bacterial diversity structures of the rhizosphere sediment subjected to different treatments were also analyzed by the high-throughput sequencing method. According to the ACE and Chao 1 indices, the bacterial diversity in the AMB and AHMB treatments were the highest. Although many sources contributed to the decrease in the nutrient loads of the lake sediment, harvesting macrophytes inoculated with PSB cells prior to their senescence might constitute a significant in-lake measure for reducing internal P load.
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Marchant, A; Mougel, F; Almeida, C; Jacquin-Joly, E; Costa, J; Harry, M
2015-04-01
High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, <1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.
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Seasonal variability of suspended sediment transport in the Seine river catchment area (France)
NASA Astrophysics Data System (ADS)
Franke, Christine; Baati, Selma; Ayrault, Sophie; Bonte, Philippe; Evrard, Olivier; Kissel, Catherine
2010-05-01
This study consists in an innovative application of environmental physico-chemical techniques on fluvial sediments with the aim to trace the seasonal changes in suspended sediment transport of the complex Seine river catchment area in northern France. The aim of this project is to develop a detailed understanding for the discrimination of naturally triggered and anthropogenic induced processes and their temporal changes with weather conditions. With a focus on the heavy metal fraction, we determine the regional distribution of the suspended material and search for environmental fingerprints demonstrating the influence of fluvial transport mechanisms, changes in concentration related to discharge variations or different sediment sources, and in-situ alteration caused by variations in the geochemical conditions (oxy-redox, pH, Eh, etc.). To achieve these goals, we apply a combination of straightforward rock magnetic hysteresis measurements (performed using an AGM2900 at the LSCE) and advanced scanning electron microscopy analyses (SEM). This interdisciplinary approach allows refining the detailed analysis of sediment trap samples, originating from Tessier et al. (2003), as recently shown by Franke et al. (2009). In our preliminary results, we observe a general increase in magnetic concentrations from summer to winter conditions, coupled with a magneto-mineralogic change to rather reduced metallic mineral phases. However, each riversection of the Seine system shows its specific trend line depending on the regional initial input, weathering conditions, drainage area and potential pollution sources. A systematic analysis of the detailed results will allow highlighting the climatic/seasonal influence on the metallic particle assembly. Keywords: Seine river system, environmental magnetism, suspended particulate matter, anthropogenic and natural input, magnetic hysteresis, scanning electron microscopy (SEM),, heavy metal pollution, seasonal variability References: Franke, C., Kissel, C., Robin, E., Bonté, P. and Lagroix, F., 2009, Magnetic particle characterization in the Seine river system: Implications for the determination of natural versus anthropogenic input, Geochem. Geophys. Geosyst., doi:10.1029/2009GC002544. Tessier, L., Bonté, P., Mouchel, J.M., Lefevre, I., Sogon, S., Ayrault, S., Le Cloarec, M.F., 2003, Transport et characterisation des matieres en suspension dans le basin de la Seine : Identification des signatures naturelles et anthropiques, 14èmes Journées Scientifiques de l'Environnement : l'Eau, la Ville, la Vie, Créteil : France 2003. http://hal.archives-ouvertes.fr/docs/00/20/30/84/PDF/4-JSE-2003-Manuscrit-Tessier-HAL-2008-01-08.pdf
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Sediment Transport in the Lower Yampa River, Northwestern Colorado
Elliott, John G.; Kircher, James E.; Von Guerard, Paul
1984-01-01
Discharge measurements and sediment samples were taken at streamflow-gaging station 09260050 Yampa River at Deerlodge Park in 1982 and 1983 to determine the annual sediment supply to the Yampa Canyon in Dinosaur National Monument. Forty-three years of discharge records at two tributary sites were combined to determine the historic discharge of the Yampa River at Deerlodge Park. A mean annual hydrograph and flow-duration curve were derived from these data. Sediment-transport equations were derived for total sediment discharge, suspended-sediment discharge, bedload dischagre, and the discharge of sediment in several particle-sizes. Annual sediment discharge were determined by the flow-duration, sediment-rating-curve method and indicated annual total sediment discharge was approximately 2.0 million tons per year of which 0.8 million tons per year was sand-sized material. Bedload was almost entirely sand, and annual bedload discharge was 0.1 million tons per year. Development of water resources in the Yampa River basin could effect the geomorphic character of the Yampa River at Deerlodge Park and the Yampa Canyon. Several scenarios of altered streamflow frequency distribution, reduced streamflow volume, and reduced sediment supply are examined to estimate the effect on the sediment budget at Deerlodge Park. (USGS)
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Arvidson, R. E.; Acton, C.; Blaney, D.; Bowman, J.; Kim, S.; Klingelhofer, G.; Marshall, J.; Niebur, C.; Plescia, J.; Saunders, R.S.; Ulmer, C.T.
1998-01-01
Experiments with the Rocky 7 rover were performed in the Mojave Desert to better understand how to conduct rover-based, long-distance (kilometers) geological traverses on Mars. The rover was equipped with stereo imaging systems for remote sensing science and hazard avoidance and 57Fe Mo??ssbauer and nuclear magnetic resonance spectrometers for in situ determination of mineralogy of unprepared rock and soil surfaces. Laboratory data were also obtained using the spectrometers and an X ray diffraction (XRD)/XRF instrument for unprepared samples collected from the rover sites. Simulated orbital and descent image data assembled for the test sites were found to be critical for assessing the geologic setting, formulating hypotheses to be tested with rover observations, planning traverses, locating the rover, and providing a regional context for interpretation of rover-based observations. Analyses of remote sensing and in situ observations acquired by the rover confirmed inferences made from orbital and simulated descent images that the Sunshine Volcanic Field is composed of basalt flows. Rover data confirmed the idea that Lavic Lake is a recharge playa and that an alluvial fan composed of sediments with felsic compositions has prograded onto the playa. Rover-based discoveries include the inference that the basalt flows are mantled with aeolian sediment and covered with a dense pavement of varnished basalt cobbles. Results demonstrate that the combination of rover remote sensing and in situ analytical observations will significantly increase our understanding of Mars and provide key connecting links between orbital and descent data and analyses of returned samples. Copyright 1998 by the American Geophysical Union.
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Reference-guided de novo assembly approach improves genome reconstruction for related species.
Lischer, Heidi E L; Shimizu, Kentaro K
2017-11-10
The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.
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3D-Printing for Analytical Ultracentrifugation
Desai, Abhiksha; Krynitsky, Jonathan; Pohida, Thomas J.; Zhao, Huaying
2016-01-01
Analytical ultracentrifugation (AUC) is a classical technique of physical biochemistry providing information on size, shape, and interactions of macromolecules from the analysis of their migration in centrifugal fields while free in solution. A key mechanical element in AUC is the centerpiece, a component of the sample cell assembly that is mounted between the optical windows to allow imaging and to seal the sample solution column against high vacuum while exposed to gravitational forces in excess of 300,000 g. For sedimentation velocity it needs to be precisely sector-shaped to allow unimpeded radial macromolecular migration. During the history of AUC a great variety of centerpiece designs have been developed for different types of experiments. Here, we report that centerpieces can now be readily fabricated by 3D printing at low cost, from a variety of materials, and with customized designs. The new centerpieces can exhibit sufficient mechanical stability to withstand the gravitational forces at the highest rotor speeds and be sufficiently precise for sedimentation equilibrium and sedimentation velocity experiments. Sedimentation velocity experiments with bovine serum albumin as a reference molecule in 3D printed centerpieces with standard double-sector design result in sedimentation boundaries virtually indistinguishable from those in commercial double-sector epoxy centerpieces, with sedimentation coefficients well within the range of published values. The statistical error of the measurement is slightly above that obtained with commercial epoxy, but still below 1%. Facilitated by modern open-source design and fabrication paradigms, we believe 3D printed centerpieces and AUC accessories can spawn a variety of improvements in AUC experimental design, efficiency and resource allocation. PMID:27525659
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Core disruptive accident margin seal
Garin, John
1978-01-01
An apparatus for sealing the annulus defined between a substantially cylindrical rotatable first riser assembly and plug combination disposed in a substantially cylindrical second riser assembly and plug combination of a nuclear reactor system. The apparatus comprises a flexible metal member having a first side attached to one of the riser components and a second side extending toward the other riser component and an actuating mechanism attached to the flexible metal member while extending to an accessible location. When the actuating mechanism is not activated, the flexible metal member does not contact the other riser component thus allowing the free rotation of the riser assembly and plug combination. When desired, the actuating mechanism causes the second side of the flexible metal member to contact the other riser component thereby sealing the annulus between the components.
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Calculation of Suspended Sediment Transport by Combined Wave-Current Flows.
1994-11-01
Anderson, and Silberg (1985) presented a model that had an eddy viscosity and boundary layer thickness that varied in time. The reference concentration was...sediment model. This model, along with that of Fredsoe, Anderson, and Silberg (1985), are the only two models that account for both the sediment and the...ignores any correlation between the periodic components of the velocity and the concentration. Even in the model of Fredsoe, Anderson, and Silberg (1985
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Sewer solids separation by sedimentation--the problem of modeling, validation and transferability.
Kutzner, R; Brombach, H; Geiger, W F
2007-01-01
Sedimentation of sewer solids in tanks, ponds and similar devices is the most relevant process for the treatment of stormwater and combined sewer overflows in urban collecting systems. In the past a lot of research work was done to develop deterministic models for the description of this separation process. But these modern models are not commonly accepted in Germany until today. Water Authorities are sceptical with regard to model validation and transferability. Within this paper it is checked whether this scepticism is reasonable. A framework-proposal for the validation of mathematical models with zero or one dimensional spatial resolution for particle separation processes for stormwater and combined sewer overflow treatment is presented. This proposal was applied to publications of repute on sewer solids separation by sedimentation. The result was that none of the investigated models described in literature passed the validation entirely. There is an urgent need for future research in sewer solids sedimentation and remobilization!
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1969-01-01
In one of the initial assembly steps for the Saturn IB launch vehicle's S-IB (first) stage, workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, complete the lower shroud assembly. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized the eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.
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Protein-like Nanoparticles Based on Orthogonal Self-Assembly of Chimeric Peptides.
Jiang, Linhai; Xu, Dawei; Namitz, Kevin E; Cosgrove, Michael S; Lund, Reidar; Dong, He
2016-10-01
A novel two-component self-assembling chimeric peptide is designed where two orthogonal protein folding motifs are linked side by side with precisely defined position relative to one another. The self-assembly is driven by a combination of symmetry controlled molecular packing, intermolecular interactions, and geometric constraint to limit the assembly into compact dodecameric protein nanoparticles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Hill, B.R.; DeCarlo, E.H.; Fuller, C.C.; Wong, M.F.
1998-01-01
Reliable estimates of sediment-budget errors are important for interpreting sediment-budget results. Sediment-budget errors are commonly considered equal to sediment-budget imbalances, which may underestimate actual sediment-budget errors if they include compensating positive and negative errors. We modified the sediment 'fingerprinting' approach to qualitatively evaluate compensating errors in an annual (1991) fine (<63 ??m) sediment budget for the North Halawa Valley, a mountainous, forested drainage basin on the island of Oahu, Hawaii, during construction of a major highway. We measured concentrations of aeolian quartz and 137Cs in sediment sources and fluvial sediments, and combined concentrations of these aerosols with the sediment budget to construct aerosol budgets. Aerosol concentrations were independent of the sediment budget, hence aerosol budgets were less likely than sediment budgets to include compensating errors. Differences between sediment-budget and aerosol-budget imbalances therefore provide a measure of compensating errors in the sediment budget. The sediment-budget imbalance equalled 25% of the fluvial fine-sediment load. Aerosol-budget imbalances were equal to 19% of the fluvial 137Cs load and 34% of the fluval quartz load. The reasonably close agreement between sediment- and aerosol-budget imbalances indicates that compensating errors in the sediment budget were not large and that the sediment-budget imbalance as a reliable measure of sediment-budget error. We attribute at least one-third of the 1991 fluvial fine-sediment load to highway construction. Continued monitoring indicated that highway construction produced 90% of the fluvial fine-sediment load during 1992. Erosion of channel margins and attrition of coarse particles provided most of the fine sediment produced by natural processes. Hillslope processes contributed relatively minor amounts of sediment.
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Conditions affecting the release of phosphorus from surface lake sediments.
Christophoridis, Christophoros; Fytianos, Konstantinos
2006-01-01
Laboratory studies were conducted to determine the effect of pH and redox conditions, as well as the effect of Fe, Mn, Ca, Al, and organic matter, on the release of ortho-phosphates in lake sediments taken from Lakes Koronia and Volvi (Northern Greece). Results were evaluated in combination with experiments to determine P fractionation in the sediment. The study revealed the major effect of redox potential and pH on the release of P from lake sediments. Both lakes showed increased release rates under reductive conditions and high pH values. The fractionation experiments revealed increased mobility of the reductive P fraction as well as of the NaOH-P fraction, indicating participation of both fractions in the overall release of sediment-bound P, depending on the prevailing environmental conditions. The results were assessed in combination with the release patterns of Fe, Mn, Ca, Al, and organic matter, enabling the identification of more specific processes of P release for each lake. The basic release patterns included the redox induced reductive dissolution of P-bearing metal oxides and the competitive exchange of phosphate anions with OH- at high pH values. The formation of an oxidized surface microlayer under oxic conditions acted as a protective film, preventing further P release from the sediments of Lake Volvi, while sediments from Lake Koronia exhibited a continuous and increased tendency to release P under various physicochemical conditions, acting as a constant source of internal P loading.
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Lin, Yen-Heng; Ho, Kai-Siang; Yang, Chin-Tien; Wang, Jung-Hao; Lai, Chao-Sung
2014-06-02
The number and position of assembled nanowires cannot be controlled using most nanowire sensor assembling methods. In this paper, we demonstrate a high-yield, highly flexible platform for nanowire sensor assembly using a combination of optically induced dielectrophoresis (ODEP) and conventional dielectrophoresis (DEP). With the ODEP platform, optical images can be used as virtual electrodes to locally turn on a non-contact DEP force and manipulate a micron- or nano-scale substance suspended in fluid. Nanowires were first moved next to the previously deposited metal electrodes using optical images and, then, were attracted to and arranged in the gap between two electrodes through DEP forces generated by switching on alternating current signals to the metal electrodes. A single nanowire can be assembled within 24 seconds using this approach. In addition, the number of nanowires in a single nanowire sensor can be controlled, and the assembly of a single nanowire on each of the adjacent electrodes can also be achieved. The electrical properties of the assembled nanowires were characterized by IV curve measurement. Additionally, the contact resistance between the nanowires and electrodes and the stickiness between the nanowires and substrates were further investigated in this study.
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Cacchione, D.A.; Wiberg, P.L.; Lynch, J.; Irish, J.; Traykovski, P.
1999-01-01
Energetic waves, strong bottom currents, and relatively high rates of sediment discharge from the Eel River combined to produce large amounts of suspended-sediment transport on the inner continental shelf near the Eel River during the winter of 1995-1996. Bottom-boundary-layer (BBL) measurements at a depth of ~50 m using the GEOPROBE tripod showed that the strongest near-bottom flows (combined wave and current speeds of over 1 m/s) and highest sediment concentrations (exceeding 2 g/l at ~1.2 m above the bed) occurred during two storms, one in December 1995 and the other in February 1996. Discharge from the Eel River during these storms was estimated at between 2 and 4 x 103 m3/s. Suspended-sediment flux (SSF) was measured 1.2 m above the bed and calculated throughout the BBL, by applying the tripod data to a shelf sediment-transport model. These results showed initially northward along-shelf SSF during the storms, followed by abrupt and persistent southward reversals. Along-shelf flux was more pronounced during and after the December storm than in February. Across-shelf SSF over the entire measurement period was decidedly seaward. This seaward transport could be responsible for surficial deposits of recent sediment on the outer shelf and upper continental slope in this region. Sediment ripples and larger bedforms were observed in the very fine to fine sand at 50-m depth using a sector-scanning sonar mounted on the tripod. Ripple wavelengths estimated from the sonar images were about 9 cm, which compared favorably with photographs of the bottom taken with a camera mounted on the tripod. The ripple patterns were stable during periods of low combined wave-current bottom stresses, but changed significantly during high-stress events, such as the February storm. Two different sonic altimeters recorded changes in bed elevation of 10 to 20 cm during the periods of measurement. These changes are thought to have been caused principally by the migration of low-amplitude, long-wavelength sand waves into the measurement area.
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Human deforestation outweighs future climate change impacts of sedimentation on coral reefs
Maina, Joseph; de Moel, Hans; Zinke, Jens; Madin, Joshua; McClanahan, Tim; Vermaat, Jan E.
2013-01-01
Near-shore coral reef systems are experiencing increased sediment supply due to conversion of forests to other land uses. Counteracting increased sediment loads requires an understanding of the relationship between forest cover and sediment supply, and how this relationship might change in the future. Here we study this relationship by simulating river flow and sediment supply in four watersheds that are adjacent to Madagascar’s major coral reef ecosystems for a range of future climate change projections and land-use change scenarios. We show that by 2090, all four watersheds are predicted to experience temperature increases and/or precipitation declines that, when combined, result in decreases in river flow and sediment load. However, these climate change-driven declines are outweighed by the impact of deforestation. Consequently, our analyses suggest that regional land-use management is more important than mediating climate change for influencing sedimentation of Malagasy coral reefs. PMID:23736941
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A novel approach for assessments of erythrocyte sedimentation rate.
Pribush, A; Hatskelzon, L; Meyerstein, N
2011-06-01
Previous studies have shown that the dispersed phase of sedimenting blood undergoes dramatic structural changes: Discrete red blood cell (RBC) aggregates formed shortly after a settling tube is filled with blood are combined into a continuous network followed by its collapse via the formation of plasma channels, and finally, the collapsed network is dispersed into individual fragments. Based on this scheme of structural transformation, a novel approach for assessments of erythrocyte sedimentation is suggested. Information about erythrocyte sedimentation is extracted from time records of the blood conductivity measured after a dispersion of RBC network into individual fragments. It was found that the sedimentation velocity of RBC network fragments correlates positively with the intensity of attractive intercellular interactions, whereas no effect of hematocrit (Hct) was observed. Thus, unlike Westergren erythrocyte sedimentation rate, sedimentation data obtained by the proposed method do not require correction for Hct. © 2010 Blackwell Publishing Ltd.
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Human deforestation outweighs future climate change impacts of sedimentation on coral reefs.
Maina, Joseph; de Moel, Hans; Zinke, Jens; Madin, Joshua; McClanahan, Tim; Vermaat, Jan E
2013-01-01
Near-shore coral reef systems are experiencing increased sediment supply due to conversion of forests to other land uses. Counteracting increased sediment loads requires an understanding of the relationship between forest cover and sediment supply, and how this relationship might change in the future. Here we study this relationship by simulating river flow and sediment supply in four watersheds that are adjacent to Madagascar's major coral reef ecosystems for a range of future climate change projections and land-use change scenarios. We show that by 2090, all four watersheds are predicted to experience temperature increases and/or precipitation declines that, when combined, result in decreases in river flow and sediment load. However, these climate change-driven declines are outweighed by the impact of deforestation. Consequently, our analyses suggest that regional land-use management is more important than mediating climate change for influencing sedimentation of Malagasy coral reefs.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Arnott, R.W.C.
1993-05-01
Lower-shoreface to shallow-shelf strata of the Bootlegger Member of the Lower Cretaceous Blackleaf Formation are characterized by interbedded sandstone and mudstone. Sandstone beds are characterized by a peculiar planar lamination showing a subtle although perceptible undulation; spacing-to-height ratios of the undulation are generally 100 or more. Typically the undulation shows no evidence of lateral accretion but only vertical aggradation, and as a result most beds consist of a single laminaset. Aspects of quasi-planar-laminated beds indicate single-event storm sedimentation, and paleocurrent data indicate offshore sediment transport. By its sedimentary characteristics and its similarity with a bed configuration generated in an experimentalmore » wave duct, quasi-planar lamination is produced by high-energy combined flows. This style of stratification should be common in the shallow-marine stratigraphic record, and its recognition should aid in interpreting high-energy, combined-flow depositional events.« less
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NASA Technical Reports Server (NTRS)
Yue, G. K.; Deepak, A.
1980-01-01
The dense polydisperse aerosol particles in a quiet chamber may spontaneously go through different microphysical processes including gravitational sedimentation, thermal coagulation, and growth or evaporation. In an earlier paper, we presented the results of a parametric study of the combined and separate effects of thermal coagulation and sedimentation on the time dependence of extinction of four visible and IR laser beams traversing an aerosol medium. As a continuation of this series of studies, the separate and combined effects of growth or evaporation and gravitational sedimentation on the time dependence of extinction of the same four visible and IR laser beams traversing in artificial fogs will be reported in this paper. The method of numerically modeling the change of water droplet size distribution with time due to growth/evaporation and the cutoff of larger aerosols due to gravitational sedimentation is described in detail. Factors governing the relative importance of these two processes are discussed. Results of this study show that the relative humidity or ambient temperature is a crucial parameter in determining the optical depth of the water droplet and aerosol media undergoing microphysical processes.
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Acoustic Profiling of Bottom Sediments in Large Oil Storage Tanks
NASA Astrophysics Data System (ADS)
Svet, V. D.; Tsysar', S. A.
2018-01-01
Characteristic features of acoustic profiling of bottom sediments in large oil storage tanks are considered. Basic acoustic parameters of crude oil and bottom sediments are presented. It is shown that, because of the presence of both transition layers in crude oil and strong reverberation effects in oil tanks, the volume of bottom sediments that is calculated from an acoustic surface image is generally overestimated. To reduce the error, additional post-processing of acoustic profilometry data is proposed in combination with additional measurements of viscosity and tank density distributions in vertical at several points of the tank.
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NASA Astrophysics Data System (ADS)
Evrard, Olivier; Navratil, Oldrich; Ayrault, Sophie; Esteves, Michel; Legout, Cédric; Némery, Julien; Lefèvre, Irène; Bonté, Philippe
2013-04-01
Soil erosion and subsequent sediment supply to rivers are particularly massive and episodic in mountainous environments, such as in the Southern French Alps. Those processes typically lead to an increase in water turbidity and a rapid filling of reservoirs in downstream areas. This situation is particularly problematic in regions where reservoirs are used to provide clear water to hydroelectric power plants. Sediment source areas must first be delineated and sediment fluxes between hillslopes and the river system must be better understood to implement efficient sediment management. We therefore combined traditional monitoring techniques (i.e., installation of river gauges and sediment samplers in several subcatchments) and sediment fingerprinting using elemental geochemistry and fallout radionuclides as potential discriminant properties to quantify the supply of sediment provided by different lithological sources (i.e., black marls, marly limestones, conglomerates, Quaternary deposits) to the River Bléone (905 km²). Those analyses were conducted on different material types collected within the catchment (i.e. suspended and riverbed sediment), and at the catchment outlet (i.e. on a sequence of sections of a 3-m long sediment core). Sediment exports at the river catchment outlet (330±100 t km-2 yr-1) were mainly driven (80%) by the occurrence of widespread rainfall events (long duration, low intensities). In contrast, heavy, local and short duration storms generated high peak discharges and suspended sediment concentrations, but they were restricted to small upstream torrents. Our study (2007-2009) confirmed the important contribution of black marls (up to 70% at the flood scale) to sediment transported in rivers, although this substrate only occupies c. 10% of the total catchment surface. However, the contribution of other lithological sources varied at both intra- and inter-flood scales. Sediment exports generated by local convective storms were dominated by black marls/marly limestones. In contrast, widespread flood events that generate the bulk of annual sediment supply at the outlet were characterized by a more stable lithologic composition and by a larger contribution of limestones, Quaternary deposits and conglomerates, which corroborated the analysis of riverbed sediment. Finally, we found that black marls and marly limestone sources provided the main fraction of sediment analysed throughout the outlet core sequence (40 and 22 %, respectively, for the period 1962-2009). However, we also found evidence for the occurrence of major floods carrying large quantities of sediment originating from Quaternary deposits and conglomerates (25 and 16 %, respectively). The variability of sediment sources throughout the sequence may reflect the spatial variability of rainfall within the catchment, which in turn reflects its origin. This study emphasizes the importance of using archival data to validate the results of sediment fingerprinting studies conducted during short contemporary monitoring programmes.
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USDA-ARS?s Scientific Manuscript database
PacBio long-read sequencing technology is increasingly popular in genome sequence assembly and transcriptome cataloguing. Recently, a new-generation pig reference genome was assembled based on long reads from this technology. To finely annotate this genome assembly, transcriptomes of nine tissues fr...
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The Self-Assembly Properties of a Benzene-1,3,5-tricarboxamide Derivative
ERIC Educational Resources Information Center
Stals, Patrick J. M.; Haveman, Jan F.; Palmans, Anja R. A.; Schenning, Albertus P. H. J.
2009-01-01
A series of experiments involving the synthesis and characterization of a benzene-1,3,5-tricarboxamide derivative and its self-assembly properties are reported. These laboratory experiments combine organic synthesis, self-assembly, and physical characterization and are designed for upper-level undergraduate students to introduce the topic of…
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Szecsody, James E.; Comfort, Steve; Fredrickson, Herbert L.
2007-08-07
This project was initiated by SERDP to quantify processes and determine the effectiveness of abiotic/biotic mineralization of energetics (RDX, HMX, TNT) in aquifer sediments by combinations of biostimulation (carbon, trace nutrient additions) and chemical reduction of sediment to create a reducing environment. Initially it was hypothesized that a balance of chemical reduction of sediment and biostimulation would increase the RDX, HMX, and TNT mineralization rate significantly (by a combination of abiotic and biotic processes) so that this abiotic/biotic treatment may be a more efficient for remediation than biotic treatment alone in some cases. Because both abiotic and biotic processes aremore » involved in energetic mineralization in sediments, it was further hypothesized that consideration for both abiotic reduction and microbial growth was need to optimize the sediment system for the most rapid mineralization rate. Results show that there are separate optimal abiotic/biostimulation aquifer sediment treatments for RDX/HMX and for TNT. Optimal sediment treatment for RDX and HMX (which have chemical similarities and similar degradation pathways) is mainly chemical reduction of sediment, which increased the RDX/HMX mineralization rate 100 to150 times (relative to untreated sediment), with additional carbon or trace nutrient addition, which increased the RDX/HMX mineralization rate an additional 3 to 4 times. In contrast, the optimal aquifer sediment treatment for TNT involves mainly biostimulation (glucose addition), which stimulates a TNT/glucose cometabolic degradation pathway (6.8 times more rapid than untreated sediment), degrading TNT to amino-intermediates that irreversibly sorb (i.e., end product is not CO2). The TNT mass migration risk is minimized by these transformation reactions, as the triaminotoluene and 2,4- and 2,6-diaminonitrotoluene products that irreversibly sorb are no longer mobile in the subsurface environment. These transformation rates are increased 13 times further by chemical reduction of sediment. Dithionite reduction alone is not an effective treatment for TNT (intermediates that irreversibly sorb are not produced), even though the TNT degradation rate (to 2- or 4-aminodinitrotoluene) increases.« less
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Tidal river sediments in the Washington, D.C. area. 1. Distribution and sources of trace metals
DOE Office of Scientific and Technical Information (OSTI.GOV)
Velinsky, D.J.; Wade, T.L.; Schlekat, C.E.
1994-06-01
Thirty-three bottom sediments were collected from the Potomac and Anacostia rivers, Tidal Basin, and Washington Ship Channel in June 1991 to define the extent of trace metal contamination and to elucidate source areas of sediment contaminants. In addition, twenty-three sediment samples were collected directly in front of and within major storm and combined sewers that discharge directly to these areas. Trace metals (e.g., Cu, Crk Cd, Hg, Pb, and Zn) exhibited a wide range in values in the study area. Sediment concentrations of Pb ranged from 32.0{mu}g Pb g {sup -1} to 3,630 {mu}g Pb g{sup -1}, Cd from 0.24more » {mu}g Cd g{sup -1} to 4.1 {mu}g Cd g{sup -1}, and Hg from 0.13 {mu}g g{sup -1} to 9.2 {mu}g Hg g{sup -1}, with generally higher concentrations in either outfall or sewer sediments compared to river bottom-sediments. In the Anacostia River measurements indicate that numerous storm and combined sewers are major sources of trace metals. Similar results were observed in both the Tidal Basin and Washington Ship Channel. Cadmium and Pb concentrations are higher in specific sewers and outfalls, whereas the distribution of other metals suggests a more diffuse source to the rivers and basins of the area. Cadmium and Pb also exhibited the greatest enrichment throughout the study area, with peak values in the Anacostia River, near the Washington Navy Yard. Enrichment factors decrease in the order: Cd>Pb>Zn>Hg>Cu>Cr. Between 70% and 96% of sediment-bound Pb and Cd was released from a N{sub 2}-purged 1N HCI leach. On average, {le}40% of total sedimentary Cu was liberated, possibly due to the partial attack of organic components of the sediment. Sediments of the tidal freshwater portion of the Potomac estuary reflect moderate to highly contaminated area with substantial enrichments of sedimentary Pb, Cd, and Zn. The sediment phase containing these metals indicates potential mobility of the sediment-bound metals during either storm events or dredging. 39 refs., 5 figs., 6 tabs.« less
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Fine-grained suspended sediment source identification for the Kharaa River basin, northern Mongolia
NASA Astrophysics Data System (ADS)
Rode, Michael; Theuring, Philipp; Collins, Adrian L.
2015-04-01
Fine sediment inputs into river systems can be a major source of nutrients and heavy metals and have a strong impact on the water quality and ecosystem functions of rivers and lakes, including those in semiarid regions. However, little is known to date about the spatial distribution of sediment sources in most large scale river basins in Central Asia. Accordingly, a sediment source fingerprinting technique was used to assess the spatial sources of fine-grained (<10 microns) sediment in the 15 000 km2 Kharaa River basin in northern Mongolia. Five field sampling campaigns in late summer 2009, and spring and late summer in both 2010 and 2011, were conducted directly after high water flows, to collect an overall total of 900 sediment samples. The work used a statistical approach for sediment source discrimination with geochemical composite fingerprints based on a new Genetic Algorithm (GA)-driven Discriminant Function Analysis, the Kruskal-Wallis H-test and Principal Component Analysis. The composite fingerprints were subsequently used for numerical mass balance modelling with uncertainty analysis. The contributions of the individual sub-catchment spatial sediment sources varied from 6.4% (the headwater sub-catchment of Sugnugur Gol) to 36.2% (the Kharaa II sub-catchment in the middle reaches of the study basin) with the pattern generally showing higher contributions from the sub-catchments in the middle, rather than the upstream, portions of the study area. The importance of riverbank erosion was shown to increase from upstream to midstream tributaries. The source tracing procedure provides results in reasonable accordance with previous findings in the study region and demonstrates the general applicability and associated uncertainties of an approach for fine-grained sediment source investigation in large scale semi-arid catchments. The combined application of source fingerprinting and catchment modelling approaches can be used to assess whether tracing estimates are credible and in combination such approaches provide a basis for making sediment source apportionment more compelling to catchment stakeholders and managers.
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NASA Astrophysics Data System (ADS)
O'Carroll, Jack P. J.; Kennedy, Robert; Ren, Lei; Nash, Stephen; Hartnett, Michael; Brown, Colin
2017-10-01
The INFOMAR (Integrated Mapping For the Sustainable Development of Ireland's Marine Resource) initiative has acoustically mapped and classified a significant proportion of Ireland's Exclusive Economic Zone (EEZ), and is likely to be an important tool in Ireland's efforts to meet the criteria of the MSFD. In this study, open source and relic data were used in combination with new grab survey data to model EUNIS level 4 biotope distributions in Galway Bay, Ireland. The correct prediction rates of two artificial neural networks (ANNs) were compared to assess the effectiveness of acoustic sediment classifications versus sediments that were visually classified by an expert in the field as predictor variables. To test for autocorrelation between predictor variables the RELATE routine with Spearman rank correlation method was used. Optimal models were derived by iteratively removing predictor variables and comparing the correct prediction rates of each model. The models with the highest correct prediction rates were chosen as optimal. The optimal models each used a combination of salinity (binary; 0 = polyhaline and 1 = euhaline), proximity to reef (binary; 0 = within 50 m and 1 = outside 50 m), depth (continuous; metres) and a sediment descriptor (acoustic or observed) as predictor variables. As the status of benthic habitats is required to be assessed under the MSFD the Ecological Status (ES) of the subtidal sediments of Galway Bay was also assessed using the Infaunal Quality Index. The ANN that used observed sediment classes as predictor variables could correctly predict the distribution of biotopes 67% of the time, compared to 63% for the ANN using acoustic sediment classes. Acoustic sediment ANN predictions were affected by local sediment heterogeneity, and the lack of a mixed sediment class. The all-round poor performance of ANNs is likely to be a result of the temporally variable and sparsely distributed data within the study area.
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Kirchner, Gerald
2011-05-01
For aquatic sediments, the use of (210)Pb originating from the decay of atmospheric (222)Rn is a well-established methodology to estimate sediment ages and sedimentation rates. Traditionally, the measurement of (210)Pb in soils and sediments involved laborious and time-consuming radiochemical separation procedures. Due to the recent development of advanced planar ('n-type') semi-conductors with high efficiencies in the low-energy range which enable the gamma-spectrometric analysis of the 46.5 keV decay line of (210)Pb, sediment dating using this radionuclide has gained renewed interest. In this contribution, potentials and limitations of the (210)Pb methodology and of the models used for estimating sediment ages and sedimentation rates are discussed and illustrated by examples of freshwater and marine sediments. Comparison with the use of (137)Cs shows that the information which may be gained by these two tracers is complementary. As a consequence, both radionuclides should be used in combination for dating of recent sediments. It is shown that for various sedimentation regimes additional information from other sources (e.g. sediment lithology) may be needed to establish a reliable chronology. A strategy for sediment dating using (210)Pb is recommended. Copyright © 2010 Elsevier Ltd. All rights reserved.
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Geomorphic considerations for erosion prediction
Osterkamp, W.R.; Toy, T.J.
1997-01-01
Current soil-erosion prediction technology addresses processes of rainsplash, overland-flow sediment transport, and rill erosion in small watersheds. The effects of factors determining sediment yield from larger-scale drainage basins, in which sediment movement is controlled by the combined small-scale processes and a complex set of channel and other basin-scale sediment-delivery processes, such as soil creep, bioturbation, and accelerated erosion due to denudation of vegetation, have been poorly evaluated. General suggestions are provided for the development of erosion-prediction technology at the geomorphic or drainage-basin scale based on the separation of sediment-yield data for channel and geomorphic processes from those of field-scale soil loss. An emerging technology must consider: (1) the effects on sediment yield of climate, geology and soils, topography, biotic interactions with other soil processes, and land-use practices; (2) all processes of sediment delivery to a channel system; and (3) the general tendency in most drainage basins for progressively greater sediment storage in the downstream direction.
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Saher, Noor Us; Siddiqui, Asmat Saleem
2016-04-15
Heavy metals concentrations (Fe, Cu, Zn, Ni, Cr, Co, Pb, and Cd) were scrutinized during two monitoring years (2001 and 2011) in the coastal sediment of Pakistan. The status of metal contamination in coastal sediment was interpreted using sediment quality guidelines, and single and combined metal pollution indices. Ni, Cr, and Cd were recognized for their significant (p<0.05) intensification in the sediment during the last decade. Sediment quality guidelines recognized the frequent adverse biological effect of Ni and the occasional adverse biological effect of Cu, Cr, Pb and Cd. Single metal pollution indices (Igeo, EF, CF, and ER) revealed that sediment pollution is predominantly caused by Pb and Cd. Low to moderate contamination was appraised along the coast by multi-metal pollution indices (CD and PERI). Correlation study specifies that heavy metals were presented diverse affiliations and carriers for distribution in the sediment during the last decade. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Field performance of self-siphon sediment cleansing set for sediment removal in deep CSO chamber.
Zhou, Yongchao; Zhang, Yiping; Tang, Ping
2013-01-01
This paper presents a study of the self-siphon sediment cleansing set (SSCS), a system designed to remove sediment from the deep combined sewer overflow (CSO) chamber during dry-weather periods. In order to get a better understanding of the sediment removal effectiveness and operational conditions of the SSCS system, we carried out a full-scale field study and comparison analysis on the sediment depth changes in the deep CSO chambers under the conditions with and without the SSCS. The field investigation results demonstrated that the SSCS drains the dry-weather flow that accumulated for 50-57 min from the sewer channel to the intercepting system in about 10 min. It is estimated that the bed shear stress in the CSO chamber and sewer channel is improved almost 25 times on average. The SSCS acts to remove the near bed solids with high pollution load efficiently. Moreover, it cleans up not only the new sediment layer but also part of the previously accumulated sediment.
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DEVELOPMENT AND DEMONSTRATION OF A BIDIRECTIONAL ADVECTIVE FLUX METER FOR SEDIMENT-WATER INTERFACE
A bidirectional advective flux meter for measuring water transport across the sediment-water interface has been successfully developed and field tested. The flow sensor employs a heat-pulse technique combined with a flow collection funnel for the flow measurement. Because the dir...
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NASA Astrophysics Data System (ADS)
Dasher, D. H.; Lomax, T. J.; Bethe, A.; Jewett, S.; Hoberg, M.
2016-02-01
A regional probabilistic survey of 20 randomly selected stations, where water and sediments were sampled, was conducted over an area of Simpson Lagoon and Gwydyr Bay in the Beaufort Sea adjacent Prudhoe Bay, Alaska, in 2014. Sampling parameters included water column for temperature, salinity, dissolved oxygen, chlorophyll a, nutrients and sediments for macroinvertebrates, chemistry, i.e., trace metals and hydrocarbons, and grain size. The 2014 probabilistic survey design allows for inferences to be made of environmental status, for instance the spatial or aerial distribution of sediment trace metals within the design area sampled. Historically, since the 1970's a number of monitoring studies have been conducted in this estuary area using a targeted rather than regional probabilistic design. Targeted non-random designs were utilized to assess specific points of interest and cannot be used to make inferences to distributions of environmental parameters. Due to differences in the environmental monitoring objectives between probabilistic and targeted designs there has been limited assessment see if benefits exist to combining the two approaches. This study evaluates if a combined approach using the 2014 probabilistic survey sediment trace metal and macroinvertebrate results and historical targeted monitoring data can provide a new perspective on better understanding the environmental status of these estuaries.
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Substantial export of suspended sediment to the global oceans from glacial erosion in Greenland
NASA Astrophysics Data System (ADS)
Overeem, I.; Hudson, B. D.; Syvitski, J. P. M.; Mikkelsen, A. B.; Hasholt, B.; van den Broeke, M. R.; Noël, B. P. Y.; Morlighem, M.
2017-11-01
Limited measurements along Greenland's remote coastline hamper quantification of the sediment and associated nutrients draining the Greenland ice sheet, despite the potential influence of river-transported suspended sediment on phytoplankton blooms and carbon sequestration. Here we calibrate satellite imagery to estimate suspended sediment concentration for 160 proglacial rivers across Greenland. Combining these suspended sediment reconstructions with numerical calculations of meltwater runoff, we quantify the amount and spatial pattern of sediment export from the ice sheet. We find that, although runoff from Greenland represents only 1.1% of the Earth's freshwater flux, the Greenland ice sheet produces approximately 8% of the modern fluvial export of suspended sediment to the global ocean. Sediment loads are highly variable between rivers, consistent with observed differences in ice dynamics and thus with control by glacial erosion. Rivers that originate from deeply incised, fast-moving glacial tongues form distinct sediment-export hotspots: just 15% of Greenland's rivers transport 80% of the total sediment load of the ice sheet. We conclude that future acceleration of melt and ice sheet flow may increase sediment delivery from Greenland to its fjords and the nearby ocean.
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NASA Astrophysics Data System (ADS)
Abd el-aal, Abd el-aziz Khairy
2018-05-01
In this contribution, new relationship between the fundamental site frequency and the thickness of soft sediments is obtained for many sites in Egypt. The Horizontal-to-Vertical Spectral Ratio ("H/V") technique (known as Nakamura technique) can be used as a robust tool to determine the thickness of soft sediments layers overlaying bedrock from observations and measurements of seismic ambient noise data. In Egypt, numerous seismic ambient noise measurements have been conducted in several areas to determine the dynamic properties of soft soil for engineering purposes. At each site in each studied area, the fundamental site frequency was accurately estimated from the main peak in the spectral ratio between the horizontal and vertical component. Consequently, an extensive database of microtremor measurements, well logging data, and shallow seismic refraction data have been configured and assembled for the studied areas. New formula between fundamental site frequency (f 0 ) and thickness of soft sediments (h) is established. The new formula has been validated and compared with other formulas of earlier scientists, and the results indicate that the calculated depth and geometry of the bedrock surface using new formula are in a good agreement with well logs data and previously published seismic refraction surveys in the investigated sites.
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Maximizing coupling-efficiency of high-power diode lasers utilizing hybrid assembly technology
NASA Astrophysics Data System (ADS)
Zontar, D.; Dogan, M.; Fulghum, S.; Müller, T.; Haag, S.; Brecher, C.
2015-03-01
In this paper, we present hybrid assembly technology to maximize coupling efficiency for spatially combined laser systems. High quality components, such as center-turned focusing units, as well as suitable assembly strategies are necessary to obtain highest possible output ratios. Alignment strategies are challenging tasks due to their complexity and sensitivity. Especially in low-volume production fully automated systems are economically at a disadvantage, as operator experience is often expensive. However reproducibility and quality of automatically assembled systems can be superior. Therefore automated and manual assembly techniques are combined to obtain high coupling efficiency while preserving maximum flexibility. The paper will describe necessary equipment and software to enable hybrid assembly processes. Micromanipulator technology with high step-resolution and six degrees of freedom provide a large number of possible evaluation points. Automated algorithms are necess ary to speed-up data gathering and alignment to efficiently utilize available granularity for manual assembly processes. Furthermore, an engineering environment is presented to enable rapid prototyping of automation tasks with simultaneous data ev aluation. Integration with simulation environments, e.g. Zemax, allows the verification of assembly strategies in advance. Data driven decision making ensures constant high quality, documents the assembly process and is a basis for further improvement. The hybrid assembly technology has been applied on several applications for efficiencies above 80% and will be discussed in this paper. High level coupling efficiency has been achieved with minimized assembly as a result of semi-automated alignment. This paper will focus on hybrid automation for optimizing and attaching turning mirrors and collimation lenses.
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Complex Effects of Ecosystem Engineer Loss on Benthic Ecosystem Response to Detrital Macroalgae.
Rossi, Francesca; Gribsholt, Britta; Gazeau, Frederic; Di Santo, Valentina; Middelburg, Jack J
2013-01-01
Ecosystem engineers change abiotic conditions, community assembly and ecosystem functioning. Consequently, their loss may modify thresholds of ecosystem response to disturbance and undermine ecosystem stability. This study investigates how loss of the bioturbating lugworm Arenicola marina modifies the response to macroalgal detrital enrichment of sediment biogeochemical properties, microphytobenthos and macrofauna assemblages. A field manipulative experiment was done on an intertidal sandflat (Oosterschelde estuary, The Netherlands). Lugworms were deliberately excluded from 1× m sediment plots and different amounts of detrital Ulva (0, 200 or 600 g Wet Weight) were added twice. Sediment biogeochemistry changes were evaluated through benthic respiration, sediment organic carbon content and porewater inorganic carbon as well as detrital macroalgae remaining in the sediment one month after enrichment. Microalgal biomass and macrofauna composition were measured at the same time. Macroalgal carbon mineralization and transfer to the benthic consumers were also investigated during decomposition at low enrichment level (200 g WW). The interaction between lugworm exclusion and detrital enrichment did not modify sediment organic carbon or benthic respiration. Weak but significant changes were instead found for porewater inorganic carbon and microalgal biomass. Lugworm exclusion caused an increase of porewater carbon and a decrease of microalgal biomass, while detrital enrichment drove these values back to values typical of lugworm-dominated sediments. Lugworm exclusion also decreased the amount of macroalgae remaining into the sediment and accelerated detrital carbon mineralization and CO2 release to the water column. Eventually, the interaction between lugworm exclusion and detrital enrichment affected macrofauna abundance and diversity, which collapsed at high level of enrichment only when the lugworms were present. This study reveals that in nature the role of this ecosystem engineer may be variable and sometimes have no or even negative effects on stability, conversely to what it should be expected based on current research knowledge.
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NASA Astrophysics Data System (ADS)
Walsh, Rory; Higton, Sam; Marshall, Jake; Bidin, Kawi; Blake, William; Nainar, Anand
2015-04-01
This paper reports some methodological issues and early results of a project investigating the erosional impacts of land use changes (multiple selective logging and progressive, partial conversion to oil palm) over the last 25-40 years in the 600km2 Brantian river catchment in Sabah, Borneo. A combined sediment fingerprinting and radioisotope dating approach is being applied to sediment cores taken in stream hierarchical fashion across the intermediate catchment scale. Changes in sediment sources and sedimentation rates over time can be captured by changes in the relative importance of geochemical elements with depth in downstream sediment cores, which in turn can be linked to parallel changes in upstream cores by the application of unmixing models and statistical techniques. Radioisotope analysis of the sediment cores allows these changes to be dated and sedimentation rates to be estimated. Work in the neighbouring Segama catchment had successfully demonstrated the potential of such an approach in a rainforest environment (Walsh et al. 2011). The paper first describes steps taken to address methodological issues. The approach relies on taking continuous sediment cores which have aggraded progressively over time and remain relatively undisturbed and uncontaminated. This issue has been tackled (1) through careful core sampling site selection with a focus on lateral bench sites and (2) deployment of techniques such as repeat-measurement erosion bridge transects to assess the contemporary nature of sedimentation to validate (or reject) candidate sites. The issue of sediment storage and uncertainties over lag times has been minimised by focussing on sets of above- and below-confluence sites in the intermediate zone of the catchment, thus minimising sediment transit times between upstream contributing and downstream destination core sites. This focus on the intermediate zone was also driven by difficulties in finding suitable core sites in the mountainous headwaters area due to the prevalence of steep, incised channels without even narrow floodplains. Preliminary results are reported from (1) a field visit to investigate potential sampling sites in July 2014 and (2) initial analysis of a sediment core at a promising lateral bench site. Marked down-profile geochemistry changes of the core indicate a history of phases of high deposition and lateral growth of the channel caused by mobilisation of sediment linked to logging and clearance upstream. Recent channel bed degradation suggests the system has been adjusting a decline in sediment supply with forest recovery since logging in 2005, but a renewed sedimentation phase heralded by > 10 cm deposition at the site in a flood in July 2014 appears to have started linked to partial forest clearance for oil palm. These preliminary results support the ability of a combined fingerprinting and dating approach to reflect the spatial history of land-use change in a catchment undergoing disturbance. Walsh R. P. D. , Bidin K., Blake W.H., Chappell N.A., Clarke M.A., Douglas I., Ghazali R., Sayer A.M., Suhaimi J., Tych W. & Annammala K.V. (2011) Long-term responses of rainforest erosional systems at different spatial scales to selective logging and climatic change. Philosophical Transactions of the Royal Society B, 366, 3340-3353.
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NASA Astrophysics Data System (ADS)
Jorge, Guillermo A.; Llera, María; Bekeris, Victoria
2017-12-01
We study the propulsion of superparamagnetic particles dispersed in a viscous fluid upon the application of an elliptically polarized rotating magnetic field. Reducing the fluid surface tension the particles sediment due to density mismatch and rotate close to the low recipient confining plate. We study the net translational motion arising from the hydrodynamic coupling with the plate and find that, above a cross over magnetic field, magnetically assembled doublets move faster than single particles. In turn, particles are driven in complex highly controlled trajectories by rotating the plane containing the magnetic field vector. The effect of the field rotation on long self assembled chains is discussed and the alternating breakup and reformation of the particle chains is described.
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2014-04-01
sedimentation according to the Stokes Law through pipettes (Plumb, 1981) or hydrometer (ASTM, 1988). Various optical techniques, electro-resistance (Coulter...used by the contracting laboratory (ASTM, 1998) is a combined mechanical sieving and hydrometer method. The sieves are used to quantify particle sizes...in the sand range (> 63 µm) and larger, and a sedimentation- hydrometer technique is used to quantify the silt and clay size ranges (< 63 µm
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NASA Astrophysics Data System (ADS)
Nitschke, Matthew R.; Davy, Simon K.; Ward, Selina
2016-03-01
Of all reef-building coral species, 80-85 % initially draw their intracellular symbionts (dinoflagellates of the genus Symbiodinium) from the environment. Although Symbiodinium cells are crucial for the growth of corals and the formation of coral reefs, little is known about how corals first encounter free-living Symbiodinium cells. We report how the supply of free-living Symbiodinium cells to the benthos by adult corals can increase the rate of horizontal symbiont acquisition for conspecific recruits. Three species of newly settled aposymbiotic (i.e., symbiont-free) corals were maintained in an open aquarium system containing: sterilized sediment and adult coral fragments combined; adult coral fragments alone; sterilized sediment alone; or seawater at Heron Island, Great Barrier Reef, Australia. In all instances, the combination of an adult coral and sediment resulted in the highest symbiont acquisition rates by juvenile corals (up to five-fold greater than seawater alone). Juvenile corals exposed to individual treatments of adult coral or sediment produced an intermediate acquisition response (<52 % of recruits), and symbiont acquisition from unfiltered seawater was comparatively low (<20 % of recruits). Additionally, benthic free-living Symbiodinium cells reached their highest densities in the adult coral + sediment treatment (up to 1.2 × 104 cells mL-1). Our results suggest that corals seed microhabitats with free-living Symbiodinium cells suitable for many coral species during the process of coral recruitment.
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Exploring Geochemical Markers of the Anthropocene in River Sediments: Southern New England
NASA Astrophysics Data System (ADS)
Tran, J.
2015-12-01
The sedimentary record of New England is complex. From glacial till to colonial land use to the industrial revolution, any sediment preserved is intertwined and muddled by humans. Recent studies support the idea that any anthropogenic markers in the sediment record are site specific. Southern New England is marked by a myriad of practices including farming, charcoal kilns, hatting, mill dams, and iron furnaces. While specific markers of the anthropocene have been identified, little work has been done to correlate and quantify these noted markers across multiple basins. Specifically, a combination of x-ray fluorescence (XRF), x-ray diffraction (XRD), and grain size analysis were done on sediment cores taken within Southern New England across various watersheds. We present a combination of geochemical analysis and detrital zircon geochronology in order identify and account for basin differences. This in turn results in a more comprehensive trans-basin understanding of the anthropocene in this region. We observe strong evidence that supports the idea of geochemical markers anthropocene which include an increase in Mercury and Lead content in the sediments. Additionally, in basins where mill dams are present we observe sediment records consistent with flood events and dam degradation. While still fairly novel and understudied, our results provide insight to the much often question topic of the anthropocene in relation to this particular region and the potential pitfalls of doing large scale anthropogenic dating.
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Inactive end cell assembly for fuel cells for improved electrolyte management and electrical contact
Yuh, Chao-Yi [New Milford, CT; Farooque, Mohammad [Danbury, CT; Johnsen, Richard [New Fairfield, CT
2007-04-10
An assembly for storing electrolyte in a carbonate fuel cell is provided. The combination of a soft, compliant and resilient cathode current collector and an inactive anode part including a foam anode in each assembly mitigates electrical contact loss during operation of the fuel cell stack. In addition, an electrode reservoir in the positive end assembly and an electrode sink in the negative end assembly are provided, by which ribbed and flat cathode members inhibit electrolyte migration in the fuel cell stack.
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Poerschmann, Juergen; Koschorreck, Matthias; Górecki, Tadeusz
2017-02-01
Natural neutralization of acidic mining lakes is often limited by organic matter. The knowledge of the sources and degradability of organic matter is crucial for understanding alkalinity generation in these lakes. Sediments collected at different depths (surface sediment layer from 0 to 1 cm and deep sediment layer from 4 to 5cm) from an acidic mining lake were studied in order to characterize sedimentary organic matter based on neutral signature markers. Samples were exhaustively extracted, subjected to pre-chromatographic derivatizations and analyzed by GC/MS. Herein, molecular distributions of diagnostic alkanes/alkenes, terpenes/terpenoids, polycyclic aromatic hydrocarbons, aliphatic alcohols and ketones, sterols, and hopanes/hopanoids were addressed. Characterization of the contribution of natural vs. anthropogenic sources to the sedimentary organic matter in these extreme environments was then possible based on these distributions. With the exception of polycyclic aromatic hydrocarbons, combined concentrations across all marker classes proved higher in the surface sediment layer as compared to those in the deep sediment layer. Alkane and aliphatic alcohol distributions pointed to predominantly allochthonous over autochthonous contribution to sedimentary organic matter. Sterol patterns were dominated by phytosterols of terrestrial plants including stigmasterol and β-sitosterol. Hopanoid markers with the ββ-biohopanoid "biological" configuration were more abundant in the surface sediment layer, which pointed to higher bacterial activity. The pattern of polycyclic aromatic hydrocarbons pointed to prevailing anthropogenic input. Pyrolytic makers were likely to due to atmospheric deposition from a nearby former coal combustion facility. The combined analysis of the array of biomarkers provided new insights into the sources and transformations of organic matter in lake sediments. Copyright © 2016 Elsevier B.V. All rights reserved.
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2014-01-01
The study of high-affinity protein interactions with equilibrium dissociation constants (KD) in the picomolar range is of significant interest in many fields, but the characterization of stoichiometry and free energy of such high-affinity binding can be far from trivial. Analytical ultracentrifugation has long been considered a gold standard in the study of protein interactions but is typically applied to systems with micromolar KD. Here we present a new approach for the study of high-affinity interactions using fluorescence detected sedimentation velocity analytical ultracentrifugation (FDS-SV). Taking full advantage of the large data sets in FDS-SV by direct boundary modeling with sedimentation coefficient distributions c(s), we demonstrate detection and hydrodynamic resolution of protein complexes at low picomolar concentrations. We show how this permits the characterization of the antibody–antigen interactions with low picomolar binding constants, 2 orders of magnitude lower than previously achieved. The strongly size-dependent separation and quantitation by concentration, size, and shape of free and complex species in free solution by FDS-SV has significant potential for studying high-affinity multistep and multicomponent protein assemblies. PMID:24552356
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Ryan, K E; Walsh, J P; Corbett, D R; Winter, A
2008-06-01
Increased sediment flux to the coastal ocean due to coastal development is considered a major threat to the viability of coral reefs. A change in the nature of sediment supply and storage has been identified in a variety of coastal settings, particularly in response to European colonization, but sedimentation around reefs has received less attention. This research examines the sedimentary record adjacent to a coastal village that has experienced considerable land-use change over the last few decades. Sediment cores were analyzed to characterize composition and sediment accumulation rates. Sedimentation rates decreased seaward across the shelf from 0.85 cm y(-1) in a nearshore bay to 0.19 cm y(-1) in a fore-reef setting. Data reflected a significant (up to 2x) increase over the last approximately 80 years in terrestrial sediment accumulating in the back-reef setting, suggesting greater terrestrial sediment flux to the area. Reef health has declined, and increased turbidity is believed to be an important impact, particularly when combined with additional stressors.
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Human and Environmental Impacts on River Sediment Microbial Communities
Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; ...
2014-05-19
Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUsmore » do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.« less
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Kennedy, Gregory; Kappel, William M.
2000-01-01
Military-type mat??riel was recovered from the bottom of Lake Ontario near Rochester, N.Y., during bottom-trawl, fish-stock surveys at depths of 75 to 180 feet each year from 1978 through 1996. The recovered mat??riel included many shell-detonator nose cones (2 inches in diameter by about 3.5 inches long); several electronic components; one corroded box of detonators; a corrugated container of mercury-filled capsules; and corroded batteries. Most of the recovered mat??riel has been identified as defective components of shell detonators (proximity-fuze assemblies) that were jettisoned in the lake to protect them from discovery during World War II. Side-scan SONAR, metal-detector, and ROV (remotely-operated-vehicle) surveys found no evidence of any large piles of mat??riel containing potentially hazardous, toxic, or polluting materials within the 17-square-mile study site. Many scattered magnetic anomalies were detected in this area, but chemical analysis of bottom sediment and of zebra- and quagga-mussel (Dreissena spp.) tissue indicate that the concentrations of mercury and other heavy metals are within the previously documented ranges for Lake Ontario sediment. The failure of ROV videos and of SCUBA-diver surveys and probes of the lake bottom to locate any debris indicates that most, if not all, of the debris is scattered and buried under a layer of fine-grained sediment and, possibly, mussels.
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NASA Astrophysics Data System (ADS)
Mazumder, S.; Tep, Blecy; Pangtey, K. K. S.; Das, K. K.; Mitra, D. S.
2017-08-01
The Gondwanaland assembly rifted dominantly during Late Carboniferous-Early Permian forming several intracratonic rift basins. These rifts were subsequently filled with a thick sequence of continental clastic sediments with minor marine intercalations in early phase. In western part of India, these sediments are recorded in enclaves of Bikaner-Nagaur and Jaisalmer basins in Rajasthan. Facies correlatives of these sediments are observed in a number of basins that were earlier thought to be associated with the western part of India. The present work is a GIS based approach to reconnect those basins to their position during rifting and reconstruct the tectono-sedimentary environment at that time range. The study indicates a rift system spanning from Arabian plate in the north and extending to southern part of Africa that passes through Indus basin, western part of India and Madagascar, and existed from Late Carboniferous to Early Jurassic. Extensions related to the opening of Neo-Tethys led to the formation of a number of cross trends in the rift systems that acted as barriers to marine transgressions from the north as well as disrupted the earlier continuous longitudinal drainage systems. The axis of this rift system is envisaged to pass through present day offshore Kutch and Saurashtra and implies a thick deposit of Late Carboniferous to Early Jurassic sediments in these areas. Based on analogy with other basins associated with this rift system, these sediments may be targeted for hydrocarbon exploration.
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NASA Astrophysics Data System (ADS)
Harrison, B. K.; Bailey, J. V.
2013-12-01
Sediment horizons represent a significant - but not permanent - barrier to microbial transport. Cells commonly attach to mineral surfaces in unconsolidated sediments. However, by taxis, growth, or passive migration under advecting fluids, some portion of the microbial community may transgress sedimentary boundaries. Few studies have attempted to constrain such transport of community signatures in the marine subsurface and its potential impact on biogeography. Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula recovered sediments over a greater than 1km interval representing a gradual decrease of terrestrial influence, from tidal to continental shelf depositional settings. This sequence represents a key opportunity to link subsurface microbial communities to lithological variability and investigate the permanence of community signatures characteristic of distinct depositional regimes. The phylogenetic connectivity between marine and terrestrially-influenced deposits may demonstrate to what degree sediments offer a substantial barrier to cell transport in the subsurface. Previous work has demonstrated that the Actinobacterial phylum is broadly distributed in marine sediments (Maldonado et al., 2005), present and active in the deep subsurface (Orsi et al., 2013), and that marine and terrestrial lineages may potentially be distinguished by 16S rRNA gene sequencing (e.g. Prieto-Davó et al., 2013). We report on Actinobacteria-specific 16S rRNA gene diversity recovered between 1370 and 2642 mbsf with high-throughput sequencing using the Illumina MiSeq platform, as well as selective assembly and analysis of environmental clone libraries.
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Multiple anthropogenic stressors exert complex, interactive effects on a coral reef community
NASA Astrophysics Data System (ADS)
Muthukrishnan, Ranjan; Fong, Peggy
2014-12-01
Multiple natural and anthropogenic stressors impact coral reefs across the globe leading to declines of coral populations, but the relative importance of different stressors and the ways they interact remain poorly understood. Because coral reefs exist in environments commonly impacted by multiple stressors simultaneously, understanding their interactions is of particular importance. To evaluate the role of multiple stressors we experimentally manipulated three stressors (herbivore abundance, nutrient supply, and sediment loading) in plots on a natural reef in the Gulf of Panamá in the Eastern Tropical Pacific. Monitoring of the benthic community (coral, macroalgae, algal turf, and crustose coralline algae) showed complex responses with all three stressors impacting the community, but at different times, in different combinations, and with varying effects on different community members. Reduction of top-down control in combination with sediment addition had the strongest effect on the community, and led to approximately three times greater algal biomass. Coral cover was reduced in all experimental units with a negative effect of nutrients over time and a synergistic interaction between herbivore exclosures and sediment addition. In contrast, nutrient and sediment additions interacted antagonistically in their impacts on crustose coralline algae and turf algae so that in combination the treatments limited each other's effects. Interactions between stressors and temporal variability indicated that, while each stressor had the potential to impact community structure, their combinations and the broader environmental conditions under which they acted strongly influenced their specific effects. Thus, it is critical to evaluate the effects of stressors on community dynamics not only independently but also under different combinations or environmental conditions to understand how those effects will be played out in more realistic scenarios.
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Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology
Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal
2015-01-01
Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein–protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies. PMID:25970732
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PERIPHYTON AND SEDIMENT BIOASSESSMENT AS INDICATORS OF THE EFFECT OF A COASTAL PULP MILL WASTEWATER
A two year study was conducted near Port St. Joe, Florida, in a coastal transportation canal and bay receiving combined municipal and pulp mill wastewater. The objective of the study was to determine the effectiveness of periphyton analysis techniques and sediment toxicity as ind...
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GATE AND VACUUM FLUSHING OF SEWER SEDIMENT: LABORATORY TESTING
The objective of this study was to test the performance of a traditional gate-flushing device and a newly-designed vacuum-flushing device in removing sediment from combined sewers and CSO storage tanks. A laboratory hydraulic flume was used to simulate a reach of sewer or storag...
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The Gold Standard for determining freely dissolved concentrations (Cfree) of hydrophobic organic compounds in sediment interstitial water would be in situ deployment combined with equilibrium sampling, which is generally difficult to achieve. In the present study, ex situ equilib...
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SEWER SEDIMENT GATE AND VACUUM FLUSHING TANKS: LABORATORY FLUME STUDIES
The objective of this study was to test the performance of a traditional gate-flushing device and a newly designed vacuum-flushing device in removing sediments from combined sewers and CSO storage tanks. A laboratory hydraulic flune was used to simulate a reach of sewer or storag...
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Sediment transport through self-adjusting, bedrock-walled waterfall plunge pools
NASA Astrophysics Data System (ADS)
Scheingross, Joel S.; Lamb, Michael P.
2016-05-01
Many waterfalls have deep plunge pools that are often partially or fully filled with sediment. Sediment fill may control plunge-pool bedrock erosion rates, partially determine habitat availability for aquatic organisms, and affect sediment routing and debris flow initiation. Currently, there exists no mechanistic model to describe sediment transport through waterfall plunge pools. Here we develop an analytical model to predict steady-state plunge-pool depth and sediment-transport capacity by combining existing jet theory with sediment transport mechanics. Our model predicts plunge-pool sediment-transport capacity increases with increasing river discharge, flow velocity, and waterfall drop height and decreases with increasing plunge-pool depth, radius, and grain size. We tested the model using flume experiments under varying waterfall and plunge-pool geometries, flow hydraulics, and sediment size. The model and experiments show that through morphodynamic feedbacks, plunge pools aggrade to reach shallower equilibrium pool depths in response to increases in imposed sediment supply. Our theory for steady-state pool depth matches the experiments with an R2 value of 0.8, with discrepancies likely due to model simplifications of the hydraulics and sediment transport. Analysis of 75 waterfalls suggests that the water depths in natural plunge pools are strongly influenced by upstream sediment supply, and our model provides a mass-conserving framework to predict sediment and water storage in waterfall plunge pools for sediment routing, habitat assessment, and bedrock erosion modeling.
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NASA Astrophysics Data System (ADS)
Jordan, Hannah; Hamilton, Ken; Lawley, Russell; Price, Simon James
2016-01-01
Reconstruction of artificial or anthropogenic topographies, sediment thicknesses and volumes provides a mechanism for quantifying anthropogenic changes to sedimentary systems in the context of the proposed Anthropocene epoch. We present a methodology for determining the volumetric contribution of anthropogenic deposits to the geological and geomorphological record and apply it to the Great Yarmouth area of Norfolk, UK. 115 boreholes, drilled to a maximum depth of 6 m below ground level, were used to determine the thickness and distribution of seven geo-archaeological units comprising natural and anthropogenic deposits in the central Great Yarmouth area. This was supplemented by additional depth information derived from 467 existing ground investigation boreholes and published 1:50 000 scale geological maps. The top and base of each geo-archaeological unit were modelled from elevations recorded in the borehole data. Grids were produced using a natural neighbour analysis with a 25 m cell size using MapInfo 8.0 Vertical Mapper 3.1 to produce palaeotopographical surfaces. Maximum, minimum and average elevations for each geo-archaeological unit generally increase with decreasing age with the exception of the Early-Medieval palaeotopographical surface which locally occurs at higher elevations than that of the younger Late-Medieval unit. The total sediment volume for the combined Modern, Post-Medieval, Late-Medieval and Early-Medieval geo-archaeological units is 10.91 × 105 m3. The total sediment volume for the Aeolian, River Terrace and Marine geo-archaeological units combined is 65.58 × 105 m3. Anthropogenic sedimentation rates were calculated to increase from 590 m3/yr during the Early-Medieval period, 1500 m3/yr during the Post-Medieval period and 2300 m3/yr during the Modern period. It is estimated that the combined anthropogenic geo-archaeological units contribute approximately 15% of the total volume of sediments that would have been traditionally considered natural Holocene deposits in the Great Yarmouth area. The results indicate that an approach combining geological and archaeological deposit modelling can be used to quantify anthropogenic landscape impact and its associated sediment flux.
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NASA Astrophysics Data System (ADS)
Ramos-Scharron, Carlos; Gray, Sarah; Sears, Whitney
2014-05-01
Erosion from unpaved road networks represents a critical source of stress affecting the coral reef systems of the U.S. Virgin Islands in the Northeastern Caribbean. Combined community- and government-driven efforts to reduce sediment contributions from unpaved roads in the island of St. John have consisted in improving road drainage design, paving selected road segments, and constructing sediment retention structures. Here we describe empirical evidence attesting to the efficacy of these mitigation efforts. Road drainage improvements reduced sediment production rates to about a third of pre-treatment levels. Road-segment scale erosion rates following paving ranged from 5-30% of pre-treatment levels, depending on road slope and road grading frequency. A 616-m3 sediment retention pond proved to contain 86 Mg of sediment annually and about 94% of the runoff generated from a 12 ha sub-catchment with an unpaved road density of 19 km km-2. Watershed-scale modeling evaluations suggested that the combination of these three treatments within the 13-km2 Coral Bay watershed resulted in the reduction of annual sediment delivery rates from 445 Mg yr-1 to 327 Mg yr-1. Cost-effectiveness analyses suggest that road drainage improvements and construction of the detention pond provided the greatest reductions in sediment delivery per total amount of funds spent. Even though paving is a proven erosion control method, the high costs involved made it a relatively cost-inefficient method. Marine sedimentation of terrigenous sediment (land-derived) was regularly monitored (every 26 days) at 15 near-shore and reef sites from 2008 to 2013 below the treated and undeveloped watersheds. Sediment composition (% terrigenous) determined by loss on ignition was multiplied by the total sediment accumulation rate in tube sediment traps to obtain terrigenous sediment accumulation rates (in mg cm-2 d-1). Mean terrigenous sediment accumulation rates were over 24 (near-shore) and 6 (reef) times greater below developed compared to undeveloped watersheds. Comparisons of marine terrigenous accumulation rates between undeveloped and developed areas were consistent with those based on modeled sediment yields. At all near-shore sites below mitigated watersheds, mean post-mitigation marine terrigenous sediment accumulation rates were reduced by up to 70% of mean pre-mitigation values. Nevertheless, further analysis is required to evaluate whether the observed post-mitigation reduction is strictly related to watershed restoration. At the developed coral reef sites, acute terrigenous sediment accumulation rates during major storms equaled or exceeded coral-stressing levels (>50 mg cm-2d-1). Results from this research are being employed in the design of mitigation strategies within our study areas as well as in other parts of the Caribbean where roads are considered a major threat to coral reefs.
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The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa
Dirks, Paul HGM; Roberts, Eric M; Hilbert-Wolf, Hannah; Kramers, Jan D; Hawks, John; Dosseto, Anthony; Duval, Mathieu; Elliott, Marina; Evans, Mary; Grün, Rainer; Hellstrom, John; Herries, Andy IR; Joannes-Boyau, Renaud; Makhubela, Tebogo V; Placzek, Christa J; Robbins, Jessie; Spandler, Carl; Wiersma, Jelle; Woodhead, Jon; Berger, Lee R
2017-01-01
New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of 222Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology. DOI: http://dx.doi.org/10.7554/eLife.24231.001 PMID:28483040
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Dinwoodie, Thomas L.
2002-12-17
A stabilized PV system comprises an array of photovoltaic (PV) assemblies mounted to a support surface. Each PV assembly comprises a PV module and a support assembly securing the PV module to a position overlying the support surface. The array of modules is circumscribed by a continuous, belt-like perimeter assembly. Cross strapping, extending above, below or through the array, or some combination of above, below and through the array, secures a first position along the perimeter assembly to at least a second position along the perimeter assembly thereby stabilizing the array against wind uplift forces. The first and second positions may be on opposite sides on the array.
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NASA Astrophysics Data System (ADS)
Eichhorn, Luise; Pirrung, Michael; Zolitschka, Bernd; Büchel, Georg
2017-09-01
Differentiating between regularly seasonal, irregular and event-based clastic sedimentation is difficult if sedimentation structures resemble and dating methods are imprecise. In this study - clastic light and dark laminae from lava-dammed Paleolake Alf in the Late Pleistocene in the Quaternary West Eifel Volcanic Field are analyzed to clarify how they formed and if they are of annual origin and comparable to assumed periglacial varves from neighboring Lake Holzmaar. Therefore, a multiproxy approach is applied combining sediment thin section analysis which focuses on composition and structure with 14C dates. The results are compared to recently-formed annually-laminated clastic sediments of, e.g., the High Canadian Arctic. Observed sedimentation structures reveal sediment delivery by over- and interflows and deposition from suspension forming two characteristic microfacies: Type I graded laminae and Type II laminae with graded sublayers. Additionally, erosional bases and event deposits indicate episodic underflows. Thus, lamination is potentially seasonal but is significantly veiled by extreme runoff causing erosion and resuspension processes or a mixed water body preventing sediment delivery into the lake basin. However, sedimentation processes between watershed and lake could be reconstructed by comparing recent and paleosediment structures.
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Toxicity of lead-contaminated sediment to mute swans
Day, D.D.; Beyer, W.N.; Hoffman, D.J.; Morton, Alexandra; Sileo, L.; Audet, D.J.; Ottinger, M.A.
2003-01-01
Most ecotoxicological risk assessments of wildlife emphasize contaminant exposure through ingestion of food and water. However, the role of incidental ingestion of sediment-bound contaminants has not been adequately appreciated in these assessments. This study evaluates the toxicological consequences of contamination of sediments with metals from hard-rock mining and smelting activities. Lead-contaminated sediments collected from the Coeur d'Alene River Basin in Idaho were combined with either a commercial avian maintenance diet or ground rice and fed to captive mute swans (Cygnus olor) for 6 weeks. Experimental treatments consisted of maintenance or rice diets containing 0, 12 (no rice group), or 24% highly contaminated (3,950 ug/g lead) sediment or 24% reference (9.7 ug/g lead) sediment. Although none of the swans died, the group fed a rice diet containing 24% lead-contaminated sediment were the most severely affected, experiencing a 24% decrease in mean body weight, including three birds that became emaciated. All birds in this treatment group had nephrosis; abnormally dark, viscous bile; and significant (p < 0.05) reductions in hematocrit and hemoglobin concentrations compared to their pretreatment levels. This group also had the greatest mean concentrations of lead in blood (3.2 ug/g), brain (2.2 ug/g), and liver (8.5 ug/g). These birds had significant (alpha = 0.05) increases in mean plasma alanine aminotransferase activity, cholesterol, and uric acid concentrations and decreased plasma triglyceride concentrations compared to all other treatment groups. After 14 days of exposure, mean protoporphyrin concentrations increased substantially, and mean delta-aminolevulinic acid dehydratase activity decreased by more than 95% in all groups fed diets containing highly contaminated sediments. All swans fed diets that contained 24% lead-contaminated sediment had renal acid-fast intranuclear inclusion bodies, which are diagnostic of lead poisoning in waterfowl. Body weight and hematocrit and hemoglobin concentrations in swans on control (no sediment) and reference (uncontaminated) sediment diets remained unchanged. These data provide evidence that mute swans consuming environmentally relevant concentrations of Coeur d'Alene River Basin sediment developed severe sublethal lead poisoning. Furthermore, toxic effects were more pronounced when the birds were fed lead contaminated sediment combined with rice, which closely resembles the diet of swans in the wild.
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NASA Astrophysics Data System (ADS)
Mackens, Sonja; Klitzsch, Norbert; Grützner, Christoph; Klinger, Riccardo
2017-09-01
Detailed information on shallow sediment distribution in basins is required to achieve solutions for problems in Quaternary geology, geomorphology, neotectonics, (geo)archaeology, and climatology. Usually, detailed information is obtained by studying outcrops and shallow drillings. Unfortunately, such data are often sparsely distributed and thus cannot characterise entire basins in detail. Therefore, they are frequently combined with remote sensing methods to overcome this limitation. Remote sensing can cover entire basins but provides information of the land surface only. Geophysical methods can close the gap between detailed sequences of the shallow sediment inventory from drillings at a few spots and continuous surface information from remote sensing. However, their interpretation in terms of sediment types is often challenging, especially if permafrost conditions complicate their interpretation. Here we present an approach for the joint interpretation of the geophysical methods ground penetrating radar (GPR) and capacitive coupled resistivity (CCR), drill core, and remote sensing data. The methods GPR and CCR were chosen because they allow relatively fast surveying and provide complementary information. We apply the approach to the middle Orkhon Valley in central Mongolia where fluvial, alluvial, and aeolian processes led to complex sediment architecture. The GPR and CCR data, measured on profiles with a total length of about 60 km, indicate the presence of two distinct layers over the complete surveying area: (i) a thawed layer at the surface, and (ii) a frozen layer below. In a first interpretation step, we establish a geophysical classification by considering the geophysical signatures of both layers. We use sedimentological information from core logs to relate the geophysical classes to sediment types. This analysis reveals internal structures of Orkhon River sediments, such as channels and floodplain sediments. We also distinguish alluvial fan deposits and aeolian sediments by their distinct geophysical signature. With this procedure we map aeolian sediments, debris flow sediments, floodplains, and channel sediments along the measured profiles in the entire basin. We show that the joint interpretation of drillings and geophysical profile measurements matches the information from remote sensing data, i.e., the sediment architecture of vast areas can be characterised by combining these techniques. The method presented here proves powerful for characterising large areas with minimal effort and can be applied to similar settings.
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NASA Astrophysics Data System (ADS)
Fox, P. M.; Nico, P. S.; Hao, Z.; Gilbert, B.; Tfaily, M. M.; Devadoss, J.
2015-12-01
Sediment-associated natural organic matter (NOM) is an extremely complex assemblage of organic molecules with a wide range of sizes, functional groups, and structures, which is intricately associated with mineral particles. The chemical nature of NOM may control its' reactivity towards metals, minerals, enzymes, and bacteria. Organic carbon concentrations in subsurface sediments are typically much lower than in surface soils, posing a distinct challenge for characterization. In this study, we investigated NOM associated with shallow alluvial aquifer sediments in a floodplain of the Colorado River. Total organic carbon (TOC) contents in these subsurface sediments are typically around 0.1%, but can range from 0.03% up to approximately 1.5%. Even at the typical TOC values of 0.1%, the mass of sediment-associated OC is approximately 5000 times higher than the mass of dissolved OC, representing a large pool of carbon that may potentially be mobilized or degraded under changing environmental conditions. Sediment-associated OC is much older than both the depositional age of the alluvial sediments and dissolved OC in the groundwater, indicating that the vast majority of NOM was sequestered by the sediment long before it was deposited in the floodplain. We have characterized the sediment-bound NOM from two locations within the floodplain with differing physical and geochemical properties. One location has relatively low organic carbon (<0.2%) and is considered suboxic [dissolved oxygen is low or absent, but no dissolved Fe(II) observed], while the other is a naturally reducing zone with higher organic carbon (0.2-1.5%) and Fe(II)-reducing conditions. An extraction scheme was developed using a combination of sequential extraction [water and sodium pyrophosphate (pH 10)] and purification in order to isolate different fractions of sediment-associated NOM. Analysis of these different NOM fractions was then carried out by FTIR and ESI-FTICR-MS to allow for comparison of NOM structure and composition both across sites and across fractions for a single location. Using this combination of analytical techniques we can probe the variation in NOM chemical composition and mineral association across different biogeochemical regimes and assess the potential reactivity of various NOM pools.
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Combined Flow Abstraction and Climate Change Impacts on an Aggrading Alpine River
NASA Astrophysics Data System (ADS)
Bakker, M.; Costa, A.; Silva, T. A.; Stutenbecker, L.; Girardclos, S.; Loizeau, J.-L.; Molnar, P.; Schlunegger, F.; Lane, S. N.
2018-01-01
Recent climatic warming and associated glacial retreat may have a large impact on sediment release and transfer in Alpine river basins. Concurrently, the sediment transport capacity of many European Alpine streams is affected by hydropower exploitation, notably where flow is abstracted but the sediment supply downstream is maintained. Here, we investigate the combined effects of climate change and flow abstraction on morphodynamics and sediment transfer in the Borgne River, Switzerland. From photogrammetrically derived historical Digital Elevation Models (DEMs), we find considerable net aggradation of the braided river bed (up to 5 m) since the onset of flow abstraction in 1963. Reaches responded through bed level steepening which was strongest in the upper most reach. Widespread aggradation however did not commence until the onset of glacier retreat in the late 1980s and the dry and warm years of the early 1990s. Upstream flow intake data shows that this aggradation coincided with an increase in sediment supply, although aggradation accounts for no more than 25% of supplied material. The remainder was transferred through the studied reaches. Estimations of bed load transport capacity indicate that flow abstraction reduces transport capacity by 1-2 orders of magnitude. While residual transport rates vary with morphological evolution, they are in the same order of magnitude as the sediment supply rates, which is why significant transport remains. However, the reduction in transport capacity makes the system more sensitive to short-term (annual) changes in climate-driven hydrological variability and climate-induced changes in intake management and sediment delivery rates.
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Recent Deforestation Causes Rapid Increase in River Sediment Load in the Northern Andes
NASA Astrophysics Data System (ADS)
Restrepo, J. D.; Kettner, A.; Syvitski, J. P.
2016-12-01
Human induced soil erosion reduces soil productivity; compromises freshwater ecosystem services, and drives geomorphic and ecological change in rivers and their floodplains. The Andes of Colombia have witnessed severe changes in land-cover and forest loss during the last three decades with the period 2000 and 2010 being the highest on record. We address the following: (1) what are the cumulative impacts of tropical forest loss on soil erosion? and (2) what effects has deforestation had on sediment production, availability, and the transport capacity of Andean rivers? Models and observations are combined to estimate the amount of sediment liberated from the landscape by deforestation within a major Andean basin, the Magdalena. We use a scaling model BQART that combines natural and human forces, like basin area, relief, temperature, runoff, lithology, and sediment trapping and soil erosion induced by humans. Model adjustments in terms of land cover change were used to establish the anthropogenic-deforestation factor for each of the sub-basins. Deforestation patterns across 1980-2010 were obtained from satellite imagery. Models were employed to simulate scenarios with and without human impacts. We estimate that, 9% of the sediment load in the Magdalena River basin is due to deforestation; 482 Mt of sediments was produced due to forest clearance over the last three decades. Erosion rates within the Magdalena drainage basin have increased 33% between 1972 and 2010; increasing the river's sediment load by 44 Mt/y. Much of the river catchment (79%) is under severe erosional conditions due in part to the clearance of more than 70% natural forest between 1980 and 2010.
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Wetland Sedimentation from Hurricanes Katrina and Rita
NASA Astrophysics Data System (ADS)
Turner, R. Eugene; Baustian, Joseph J.; Swenson, Erick M.; Spicer, Jennifer S.
2006-10-01
More than 131 × 106 metric tons (MT) of inorganic sediments accumulated in coastal wetlands when Hurricanes Katrina and Rita crossed the Louisiana coast in 2005, plus another 281 × 106 MT when accumulation was prorated for open water area. The annualized combined amount of inorganic sediments per hurricane equals (i) 12% of the Mississippi River's suspended load, (ii) 5.5 times the inorganic load delivered by overbank flooding before flood protection levees were constructed, and (iii) 227 times the amount introduced by a river diversion built for wetland restoration. The accumulation from hurricanes is sufficient to account for all the inorganic sediments in healthy saltmarsh wetlands.
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Using R to unravel animal-sediment interactions.
NASA Astrophysics Data System (ADS)
Soetaert, Karline
2017-04-01
Marine sediments are often characterized by seabed features ranging from small sand ripples to large sandbanks. These sediments also form the living space of many marine organisms, impacting the sediment dynamics and the geochemical cycles. In a number of projects in the Northsea, we have started to investigate these interactions, combining field sampling with laboratory experiments and modelling. R is used to interpret the various data sets and to model the effects of biology and geomorphology on the geochemistry. I will discuss these new developments in R, based on my previous R-work (packages FME, ReacTran, deSolve, rootSolve, plot3D, marelac).
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Ruthenium red-induced bundling of bacterial cell division protein, FtsZ.
Santra, Manas Kumar; Beuria, Tushar K; Banerjee, Abhijit; Panda, Dulal
2004-06-18
The assembly of FtsZ plays a major role in bacterial cell division, and it is thought that the assembly dynamics of FtsZ is a finely regulated process. Here, we show that ruthenium red is able to modulate FtsZ assembly in vitro. In contrast to the inhibitory effects of ruthenium red on microtubule polymerization, we found that a substoichiometric concentration of ruthenium red strongly increased the light-scattering signal of FtsZ assembly. Further, sedimentable polymer mass was increased by 1.5- and 2-fold in the presence of 2 and 10 microm ruthenium red, respectively. In addition, ruthenium red strongly reduced the GTPase activity and prevented dilution-induced disassembly of FtsZ polymers. Electron microscopic analysis showed that 4-10 microm of ruthenium red produced thick bundles of FtsZ polymers. The significant increase in the light-scattering signal and pelletable polymer mass in the presence of ruthenium red seemed to be due to the bundling of FtsZ protofilaments into larger polymers rather than the actual increase in the level of polymeric FtsZ. Furthermore, ruthenium red was found to copolymerize with FtsZ, and the copolymerization of substoichiometric amounts of ruthenium red with FtsZ polymers promoted cooperative assembly of FtsZ that produced large bundles. Calcium inhibited the binding of ruthenium red to FtsZ. However, a concentration of calcium 1000-fold higher than that of ruthenium red was required to produce similar effects on FtsZ assembly. Ruthenium red strongly modulated FtsZ polymerization, suggesting the presence of an important regulatory site on FtsZ and suggesting that a natural ligand, which mimics the action of ruthenium red, may regulate the assembly of FtsZ in bacteria.
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He, Zhen; Jiang, Hui-Jun; Wu, Long-Long; Liu, Jian-Wei; Wang, Geng; Wang, Xiao; Wang, Jin-Long; Hou, Zhong-Huai; Chen, Gang; Yu, Shu-Hong
2018-07-02
Although many assembly strategies have been used to successfully construct well-aligned nanowire (NW) assemblies, the understanding of their assembly kinetics has remained elusive, which restricts the development of NW-based device and circuit fabrication. Now a versatile strategy that combines interfacial assembly and synchrotron-based grazing-incidence small-angle X-ray scattering (GISAXS) is presented to track the assembly evolution of the NWs in real time. During the interface assembly process, the randomly dispersed NWs gradually aggregate to form small ordered NW-blocks and finally are constructed into well-defined NW monolayer driven by the conformation entropy. The NW assembly mechanism can be well revealed by the thermodynamic analysis and large-scale molecular dynamics theoretical evaluation. These findings point to new opportunities for understanding NW assembly kinetics and manipulating NW assembled structures by bottom-up strategy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Feedbacks between community assembly and habitat selection shape variation in local colonization
Kraus, J.M.; Vonesh, J.R.
2010-01-01
1. Non-consumptive effects of predators are increasingly recognized as important drivers of community assembly and structure. Specifically, habitat selection responses to top predators during colonization and oviposition can lead to large differences in aquatic community structure, composition and diversity. 2. These differences among communities due to predators may develop as communities assemble, potentially altering the relative quality of predator vs. predator-free habitats through time. If so, community assembly would be expected to modify the subsequent behavioural responses of colonists to habitats containing top predators. Here, we test this hypothesis by manipulating community assembly and the presence of fish in experimental ponds and measuring their independent and combined effects on patterns of colonization by insects and amphibians. 3. Assembly modified habitat selection of dytscid beetles and hylid frogs by decreasing or even reversing avoidance of pools containing blue-spotted sunfish (Enneacanthus gloriosus). However, not all habitat selection responses to fish depended on assembly history. Hydrophilid beetles and mosquitoes avoided fish while chironomids were attracted to fish pools, regardless of assembly history. 4. Our results show that community assembly causes taxa-dependent feedbacks that can modify avoidance of habitats containing a top predator. Thus, non-consumptive effects of a top predator on community structure change as communities assemble and effects of competitors and other predators combine with the direct effects of top predators to shape colonization. 5. This work reinforces the importance of habitat selection for community assembly in aquatic systems, while illustrating the range of factors that may influence colonization rates and resulting community structure. Directly manipulating communities both during colonization and post-colonization is critical for elucidating how sequential processes interact to shape communities.
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1981-08-01
assembling stores at Presque Isle (present site of Erie , Pa.) and building fortifications along the Allegheny. The French also formu- lated plans to...Steubenville-Weirton North Carolina Asheville Pennsylvania Erie Johnstown Pittsburgh D36 State(s) SMSA Tennessee Knoxville Nashville-Davidson...result of lumbering, farming, and mining activi- ties. The Beaver River drainage, situated in northeastern Ohio and northwestern Pennsylvania , covers 3130
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Physical phenomena and the microgravity response
NASA Technical Reports Server (NTRS)
Todd, Paul
1989-01-01
The living biological cell is not a sack of Newtonian fluid containing systems of chemical reactions at equilibrium. It is a kinetically driven system, not a thermodynamically driven system. While the cell as a whole might be considered isothermal, at the scale of individual macromolecular events there is heat generated, and presumably sharp thermal gradients exist at the submicron level. Basic physical phenomena to be considered when exploring the cell's response to inertial acceleration include particle sedimentation, solutal convection, motility electrokinetics, cytoskeletal work, and hydrostatic pressure. Protein crystal growth experiments, for example, illustrate the profound effects of convection currents on macromolecular assembly. Reaction kinetics in the cell vary all the way from diffusion-limited to life-time limited. Transport processes vary from free diffusion, to facilitated and active transmembrane transport, to contractile-protein-driven motility, to crystalline immobilization. At least four physical states of matter exist in the cell: aqueous, non-aqueous, immiscible-aqueous, and solid. Levels of order vary from crystalline to free solution. The relative volumes of these states profoundly influence the cell's response to inertial acceleration. Such subcellular phenomena as stretch-receptor activation, microtubule re-assembly, synaptic junction formation, chemotactic receptor activation, and statolith sedimentation were studied recently with respect to both their basic mechanisms and their responsiveness to inertial acceleration. From such studies a widespread role of cytoskeletal organization is becoming apparent.
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Effects of temperature and oxygen concentration in sediment toxicity testing.
Airas, Sari; Leppänen, Matti; Kukkonen, Jussi V K
2008-07-01
Joint effects of temperature and oxygen concentrations for the results of sediment toxicity tests were studied at 10 and 20 degrees C with 40% and 80% dissolved oxygen (DO) saturation. Growth, feeding rate, and reproduction of Lumbriculus variegatus (Oligochaete) and growth, emergence, and survival of Chironomus riparius (Diptera) were tested in a polluted and in a reference sediment. Both the feeding of L. variegatus and the emergence of C. riparius were significantly retarded at low temperature. Additionally, differences in the sex ratio of the emerged adults of C. riparius were observed. The oxygen concentration alone did not have any significant effect on the endpoints, but significant combined effects of polluted sediment and low DO were observed on the biomass of L. variegatus. The standard sediment toxicity tests might offer only limited data for risk assessment of contaminated sediments at sites where the actual conditions largely differ from the laboratory conditions.
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NASA Astrophysics Data System (ADS)
Sawyer, Derek E.; Reece, Robert S.; Gulick, Sean P. S.; Lenz, Brandi L.
2017-08-01
The southern Alaskan offshore margin is prone to submarine landslides and tsunami hazards due to seismically active plate boundaries and extreme sedimentation rates from glacially enhanced mountain erosion. We examine the submarine landslide potential with new shear strength measurements acquired by Integrated Ocean Drilling Program Expedition 341 on the continental slope and Surveyor Fan. These data reveal lower than expected sediment strength. Contrary to other active margins where seismic strengthening enhances slope stability, the high-sedimentation margin offshore southern Alaska behaves like a passive margin from a shear strength perspective. We interpret that seismic strengthening occurs but is offset by high sedimentation rates and overpressure. This conclusion is supported by shear strength outside of the fan that follow an active margin trend. More broadly, seismically active margins with wet-based glaciers are susceptible to submarine landslide hazards because of the combination of high sedimentation rates and earthquake shaking.
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Ruhl, C.A.; Schoellhamer, D.H.; Stumpf, R.P.; Lindsay, C.L.
2001-01-01
Analysis of suspended-sediment concentration data in San Francisco Bay is complicated by spatial and temporal variability. In situ optical backscatterance sensors provide continuous suspended-sediment concentration data, but inaccessibility, vandalism, and cost limit the number of potential monitoring stations. Satellite imagery reveals the spatial distribution of surficial-suspended sediment concentrations in the Bay; however, temporal resolution is poor. Analysis of the in situ sensor data in conjunction with the satellite reflectance data shows the effects of physical processes on both the spatial and temporal distribution of suspended sediment in San Francisco Bay. Plumes can be created by large freshwater flows. Zones of high suspended-sediment concentrations in shallow subembayments are associated with wind-wave resuspension and the spring-neap cycle. Filaments of clear and turbid water are caused by different transport processes in deep channels, as opposed to adjacent shallow water.
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[Research of urban eutrophic water repair by water/sediment biological bases].
Zhou, Hui-Hua; Song, Xiao-Guang; Wu, Ge; Xie, Xin-Yuan
2013-10-01
A micro power turbine water aeration system with a water biological base and a sediment biological base was independently developed, aimed at urban water eutrophication. The results showed that the average removal rates of COD, NH+4 -N, TP by the water biological base were 82. 33% , 98. 00% and 54. 73% , respectively; The sediment reduction rate achieved by the sediment biological base could reach 20% within 5 days, and aeration in the overlying water could relieve the nutrient releasing caused by the degradation of organic matter; The effect of nutrient removal and organic matter reduction in sediment by the combined ecological restoration technology was perfect in pilot scale. The average removal rates of COD, NH+4 -N, TP were 52. 0%, 33. 6% and 23.4%, respectively, and the organic content in sediment was reduced from 38. 20% to 12.20% .
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Juracek, K.E.
2008-01-01
A combination of sediment-thickness measurement and bottom-sediment coring was used to investigate sediment storage and severity of contamination in Empire Lake (Kansas), a shallow reservoir affected by historical Pb and Zn mining. Cd, Pb, and Zn concentrations in the contaminated bottom sediment typically exceeded baseline concentrations by at least an order of magnitude. Moreover, the concentrations of Cd, Pb, and Zn typically far exceeded probable-effects guidelines, which represent the concentrations above which toxic biological effects usually or frequently occur. Despite a pre-1954 decrease in sediment concentrations likely related to the end of major mining activity upstream by about 1920, concentrations have remained relatively stable and persistently greater than the probable-effects guidelines for at least the last 50 years. Cesium-137 evidence from sediment cores indicated that most of the bottom sediment in the reservoir was deposited prior to 1954. Thus, the ability of the reservoir to store the contaminated sediment has declined over time. Because of the limited storage capacity, Empire Lake likely is a net source of contaminated sediment during high-inflow periods. The contaminated sediment that passes through, or originates from, Empire Lake will be deposited in downstream environments likely as far as Grand Lake O' the Cherokees (Oklahoma). ?? 2007 Springer-Verlag.
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NASA Astrophysics Data System (ADS)
Sawyer, D.; Reece, R.; Gulick, S. P. S.; Lenz, B. L.
2017-12-01
The southern Alaskan offshore margin is prone to submarine landslides and tsunami hazards due to seismically active plate boundaries and extreme sedimentation rates from glacially enhanced mountain erosion. We examine the submarine landslide potential with new shear strength measurements acquired by Integrated Ocean Drilling Program Expedition 341 on the continental slope and Surveyor Fan. These data reveal lower than expected sediment strength. Contrary to other active margins where seismic strengthening enhances slope stability, the high-sedimentation margin offshore southern Alaska behaves like a passive margin from a shear strength perspective. We interpret that seismic strengthening occurs but is offset by high sedimentation rates and overpressure within the slope and Surveyor Fan. This conclusion is supported because shear strength follows an expected active margin profile outside of the fan, where background sedimentation rates occur. More broadly, seismically active margins with wet-based glaciers are susceptible to submarine landslide hazards because of the combination of high sedimentation rates and earthquake shaking
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Complex response of a midcontinent north America drainage system to late Wisconsinan sedimentation
Bettis, E. Arthur; Autin, W.J.
1997-01-01
The geomorphic evolution of Mud Creek basin in eastern Iowa, U.S.A. serves to illustrate how geomorphic influences such as sediment supply, valley gradient, climate, and vegetation are recorded in the alluvial stratigraphic record. Sediment supply to the fluvial system increased significantly during the late Wisconsinan through a combination of periglacial erosion and loess accumulation. Subsequent evolution of the Holocene alluvial stratigraphic record reflects long-term routing of the late Wisconsinan sediment through the drainage basin in a series of cut-and-fill cycles whose timing was influenced by hydrologic response to change in climate and vegetation. When viewed in a regional context, the alluvial stratigraphic record appears to reflect a long-term complex response of the fluvial system to increased sediment supply during the late Wisconsinan. Hydrologic and sediment-supply changes accompanying the spread of Euroamerican agriculture to the basin in the 180Os dramatically upset trends in sedimentation and channel behavior established during the Holocene. Copyright ?? 1997, SEPM (Society for Sedimentary Geology).
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Conn, Kathleen E.; Black, Robert W.; Vanderpool-Kimura, Ann M.; Foreman, James R.; Peterson, Norman T.; Senter, Craig A.; Sissel, Stephen K.
2015-12-23
Median chemical concentrations in suspended-sediment samples were greater than median chemical concentrations in fine bed sediment (less than 62.5 µm) samples, which were greater than median chemical concentrations in paired bulk bed sediment (less than 2 mm) samples. Suspended-sediment concentration, sediment particle-size distribution, and general water-quality parameters were measured concurrent with the chemistry sampling. From this discrete data, combined with the continuous streamflow record, estimates of instantaneous sediment and chemical loads from the Green River to the Lower Duwamish Waterway were calculated. For most compounds, loads were higher during storms than during baseline conditions because of high streamflow and high chemical concentrations. The highest loads occurred during dam releases (periods when stored runoff from a prior storm is released from the Howard Hanson Dam into the upper Green River) because of the high river streamflow and high suspended-sediment concentration, even when chemical concentrations were lower than concentrations measured during storm events.
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Offshore sediments record the history of onshore iron ore mining in Goa State, India.
Sebastian, Tyson; Nath, B Nagender; Naik, Sangeeta; Borole, D V; Pierre, Salou; Yazing, Armoury Kazip
2017-01-30
Environmental magnetic and geochemical analyses combined with 210 Pb dating were carried out on a sediment core off Goa from Arabian Sea to reconstruct the sedimentation history of last three and a half centuries and to investigate the impact of onshore iron ore mining on the offshore sedimentation. A drastic increase in sedimentation rate and mineral magnetic concentration parameters divides the core into two units (1 & 2) at a depth of 41cm (1982CE). The high magnetic susceptibility values in Unit 1 sediments are coeval with increased iron ore production on land and illustrate the role of terrestrial mining on the increased offshore sedimentation. The early diagenetic signals were observed in Unit 2 of the core with low concentration parameters, coarse magnetic grain size and magnetically hard mineralogy. The geochemical data of the core also record the Little Ice Age (LIA) climatic events of Dalton and Maunder solar minima. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Sedimentation and chronology of heavy metal pollution in Oslo harbor, Norway.
Lepland, Aivo; Andersen, Thorbjørn J; Lepland, Aave; Arp, Hans Peter H; Alve, Elisabeth; Breedveld, Gijs D; Rindby, Anders
2010-09-01
Stratigraphic profiles of Cu, Cd and Hg in ten sediment cores from the Oslo harbor, Norway, combined with results of radiometric dating demonstrate that pollution by these metals peaked between 1940 and 1970. Dating results indicate that Hg discharges peaked between 1940 and 1950, Cd reached maximum ca. 1955-1960, and Cu has the highest concentration in sediment interval corresponding to ca. 1970. Geochemical profiles and maxima of Cu, Cd and Hg concentrations can be used as chronostratigraphic markers for sediment cores from the Oslo harbor. Acoustic backscatter and sediment core data indicate that propeller wash affects the seabed in the Oslo harbor. The propeller-induced turbulence causes erosion, and in places exposes and remobilizes contaminated sediments that accumulated in the harbor during previous decades. Such re-exposure of contaminated sediments could be detrimental to local ecosystems and offset remediation efforts, warranting further impact studies and potential mitigation strategies to prevent redistribution. Copyright 2010 Elsevier Ltd. All rights reserved.
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NASA Technical Reports Server (NTRS)
Pirie, D. M.; Steller, D. D. (Principal Investigator)
1973-01-01
The author has identified the following significant results. Large scale sediment plumes from intermittent streams and rivers form detectable seasonal patterns on ERTS-1 imagery. The ocean current systems, as plotted from three California coast ERTS mosaics, were identified. Offshore patterns of sediment in areas such as the Santa Barbara Channel are traceable. These patterns extend offshore to heretofore unanticipated ranges as shown on the ERTS-1 imagery. Flying spot scanner enhancements of NASA tapes resulted in details of subtle and often invisible (to the eye) nearshore features. The suspended sediments off San Francisco and in Monterey Bay are emphasized in detail. These are areas of extremely changeable offshore sediment transport patterns. Computer generated contouring of radiance levels resulted in maps that can be used in determining surface and nearsurface suspended sediment distribution. Tentative calibrations of ERTS-1 spectral brightness against sediment load have been made using shipboard measurements. Information from the combined enhancement and interpretation techniques is applicable to operational coastal engineering programs.
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Integrated approach to monitor water dynamics with drones
NASA Astrophysics Data System (ADS)
Raymaekers, Dries; De Keukelaere, Liesbeth; Knaeps, Els; Strackx, Gert; Decrop, Boudewijn; Bollen, Mark
2017-04-01
Remote sensing has been used for more than 20 years to estimate water quality in the open ocean and study the evolution of vegetation on land. More recently big improvements have been made to extend these practices to coastal and inland waters, opening new monitoring opportunities, eg. monitoring the impact of dredging activities on the aquatic environment. While satellite sensors can provide complete coverage and historical information of the study area, they are limited in their temporal revisit time and spatial resolution. Therefore, deployment of drones can create an added value and in combination with satellite information increase insights in the dynamics and actors of coastal and aquatic systems. Drones have the advantages of monitoring at high spatial detail (cm scale), with high frequency and are flexible. One of the important water quality parameters is the suspended sediment concentration. However, retrieving sediment concentrations from unmanned systems is a challenging task. The sediment dynamics in the port of Breskens, the Netherlands, were investigated by combining information retrieved from different data sources: satellite, drone and in-situ data were collected, analysed and inserted in sediment models. As such, historical (satellite), near-real time (drone) and predictive (sediment models) information, integrated in a spatial data infrastructure, allow to perform data analysis and can support decision makers.
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Vegetation Loss Decreases Salt Marsh Denitrification Capacity: Implications for Marsh Erosion.
Hinshaw, Sarra E; Tatariw, Corianne; Flournoy, Nikaela; Kleinhuizen, Alice; Taylor, Caitlin; Sobecky, Patricia A; Mortazavi, Behzad
2017-08-01
Salt marshes play a key role in removing excess anthropogenic nitrogen (N) loads to nearshore marine ecosystems through sediment microbial processes such as denitrification. However, in the Gulf of Mexico, the loss of marsh vegetation because of human-driven disturbances such as sea level rise and oil spills can potentially reduce marsh capacity for N removal. To investigate the effect of vegetation loss on ecosystem N removal, we contrasted denitrification capacity in marsh and subtidal sediments impacted by the Deepwater Horizon oil spill using a combination of 29 N 2 and 30 N 2 production (isotope pairing), denitrification potential measurements (acetylene block), and quantitative polymerase chain reaction (qPCR) of functional genes in the denitrification pathway. We found that, on average, denitrification capacity was 4 times higher in vegetated sediments because of a combination of enhanced nitrification and higher organic carbon availability. The abundance of nirS-type denitrifers indicated that marsh vegetation regulates the activity, rather than the abundance, of denitrifier communities. We estimated that marsh sediments remove an average of 3.6 t N km -2 y -1 compared to 0.9 t N km -2 y -1 in unvegetated sediments. Overall, our findings indicate that marsh loss results in a substantial loss of N removal capacity in coastal ecosystems.
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Volpi Ghirardini, A; Arizzi Novelli, A; Tagliapietra, D
2005-09-01
The capacity of two toxicity bioassays (fertilization and embryo toxicity tests) to discriminate sediment toxicity using the sea urchin Paracentrotus lividus was tested in five stations with different levels of pollution in the Lagoon of Venice. Two stations were located in estuarine sites, two in the industrial zone, and one in a site at the top of our quality gradient (reference). Elutriate was chosen as sediment matrix to assess the potential effects of bioavailable pollutants in the water column as a consequence of sediment resuspension (dredging and dumping, fishing gear, etc.). An experimental design based on Quality Assurance/Quality Control procedures (QA/QC) was adopted in order to set the methodological basis for an effective use of these bioassays in monitoring programs. Results revealed both higher embriotoxicity than spermiotoxicity in all stations and the efficacy of combined use of both toxicity bioassays in discriminating differing pollution/bioavailability between stations and periods. The good representativeness of the integrated sampling scheme and the standardization of all experimental phases yielded high precision of results. Clear Toxicity Fingerprints were evidenced for the investigated sites through the combined use of both bioassays. A good fit between ecotoxicological data and chemical contamination levels was found, except for unnatural sediment texture.
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Legacy Sediments in U.S. River Environments: Atrazine and Aggradation to Zinc and Zoobenthos
NASA Astrophysics Data System (ADS)
Wohl, E.
2014-12-01
Legacy sediments are those that are altered by human activities. Alterations include (i) human-caused aggradation (and subsequent erosion), such as sediment accumulating upstream from relict or contemporary dams, (ii) human-caused lack of continuing deposition that results in changing moisture and nutrient levels within existing sediments, such as on floodplains that no longer receive lateral or vertical accretion deposits because of levees, bank stabilization, and other channel engineering, and (iii) human-generated contaminants such as PCBs and pesticides that adsorb to fine sediment. Existing estimates of human alterations of river systems suggest that legacy sediments are ubiquitous. Only an estimated 2% of river miles in the United States are not affected by flow regulation that alters sediment transport, for example, and less than half of major river basins around the world are minimally altered by flow regulation. Combined with extensive but poorly documented reduction in floodplain sedimentation, as well as sediment contamination by diverse synthetic compounds, excess nutrients, and heavy metals, these national and global estimates suggest that legacy sediments now likely constitute a very abundant type of fluvial sediment. Because legacy sediments can alter river form and function for decades to centuries after the cessation of the human activity that created the legacy sediments, river management and restoration must be informed by accurate knowledge of the distribution and characteristics of legacy sediments. Geomorphologists can contribute understanding of sediment dynamics, including: the magnitude, frequency, and duration of flows that mobilize sediments with adsorbed contaminants; sites where erosion and deposition are most likely to occur under specified flow and sediment supply; residence time of sediments; and the influence of surface and subsurface water fluxes on sediment stability and geochemistry.
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A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin; ...
2015-01-31
We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible tomore » construct a mapping population.« less
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A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin
We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible tomore » construct a mapping population.« less
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Damper mechanism for nuclear reactor control elements
Taft, William Elwood
1976-01-01
A damper mechanism which provides a nuclear reactor control element decelerating function at the end of the scram stroke. The total damping function is produced by the combination of two assemblies, which operate in sequence. First, a tapered dashram assembly decelerates the control element to a lower velocity, after which a spring hydraulic damper assembly takes over to complete the final damping.
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1969-01-01
Workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, hoist the thrust structure assembly for the Saturn IB S-IB (first) stage. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.
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Velocity field measurements in tailings dam failure experiments using a combined PIV-PTV approach
USDA-ARS?s Scientific Manuscript database
Tailings dams are built to impound mining waste, also called tailings, which consists of a mixture of fine-sized sediments and water contaminated with some hazardous chemicals used for extracting the ore by leaching. Non-Newtonian flow of sediment-water mixture resulting from a failure of tailings d...
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Ammonia is suspected of causing some of the toxicity observed in marine sediment toxicity tests because it is sometimes found at elevated concentrations in marine interstitial waters. In marine waters, ammonia exists as un-ionized ammonia (NH3) and ammonium (NH4+) which combine ...
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Long-term kinematics and sediment flux of an active earthflow, Eel River, California
B. H. Mackey; J. J. Roering; J. A. McKean
2009-01-01
Although earthflows are the dominant erosion mechanism in many mountainous landscapes, estimates of long-term earthflow-driven sediment flux remain elusive because landslide displacement data are typically limited to contemporary time periods. Combining high-resolution topography from airborne LiDAR (light detection and ranging), total station surveying, orthorectified...
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Results from the field testing of some innovative sampling methods developed to evaluate risk management strategies for polychlorinated biphenyl (PCB) contaminated sediments are presented. Semipermeable membrane devices (SPMDs) were combined with novel deployment methods to quan...
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Carter, Joshua D; LaBean, Thomas H
2011-03-22
An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.
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Majima, Yutaka; Hackenberger, Guillaume; Azuma, Yasuo; Kano, Shinya; Matsuzaki, Kosuke; Susaki, Tomofumi; Sakamoto, Masanori; Teranishi, Toshiharu
2017-01-01
Abstract Single-electron transistors (SETs) are sub-10-nm scale electronic devices based on conductive Coulomb islands sandwiched between double-barrier tunneling barriers. Chemically assembled SETs with alkanethiol-protected Au nanoparticles show highly stable Coulomb diamonds and two-input logic operations. The combination of bottom-up and top-down processes used to form the passivation layer is vital for realizing multi-gate chemically assembled SET circuits, as this combination enables us to connect conventional complementary metal oxide semiconductor (CMOS) technologies via planar processes. Here, three-input gate exclusive-OR (XOR) logic operations are demonstrated in passivated chemically assembled SETs. The passivation layer is a hybrid bilayer of self-assembled monolayers (SAMs) and pulsed laser deposited (PLD) aluminum oxide (AlOx), and top-gate electrodes were prepared on the hybrid passivation layers. Top and two-side-gated SETs showed clear Coulomb oscillation and diamonds for each of the three available gates, and three-input gate XOR logic operation was clearly demonstrated. These results show the potential of chemically assembled SETs to work as logic devices with multi-gate inputs using organic and inorganic hybrid passivation layers. PMID:28634499
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Majima, Yutaka; Hackenberger, Guillaume; Azuma, Yasuo; Kano, Shinya; Matsuzaki, Kosuke; Susaki, Tomofumi; Sakamoto, Masanori; Teranishi, Toshiharu
2017-01-01
Single-electron transistors (SETs) are sub-10-nm scale electronic devices based on conductive Coulomb islands sandwiched between double-barrier tunneling barriers. Chemically assembled SETs with alkanethiol-protected Au nanoparticles show highly stable Coulomb diamonds and two-input logic operations. The combination of bottom-up and top-down processes used to form the passivation layer is vital for realizing multi-gate chemically assembled SET circuits, as this combination enables us to connect conventional complementary metal oxide semiconductor (CMOS) technologies via planar processes. Here, three-input gate exclusive-OR (XOR) logic operations are demonstrated in passivated chemically assembled SETs. The passivation layer is a hybrid bilayer of self-assembled monolayers (SAMs) and pulsed laser deposited (PLD) aluminum oxide (AlO[Formula: see text]), and top-gate electrodes were prepared on the hybrid passivation layers. Top and two-side-gated SETs showed clear Coulomb oscillation and diamonds for each of the three available gates, and three-input gate XOR logic operation was clearly demonstrated. These results show the potential of chemically assembled SETs to work as logic devices with multi-gate inputs using organic and inorganic hybrid passivation layers.
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PA700, the regulatory complex of the 26S proteasome, interferes with alpha-synuclein assembly.
Ghee, Medeva; Melki, Ronald; Michot, Nadine; Mallet, Jacques
2005-08-01
Parkinson's disease is characterized by the loss of dopaminergic neurons in the nigrostriatal pathway accompanied by the presence of intracellular cytoplasmic inclusions, termed Lewy bodies. Fibrillized alpha-synuclein forms the major component of Lewy bodies. We reported a specific interaction between rat alpha-synuclein and tat binding protein 1, a subunit of PA700, the regulatory complex of the 26S proteasome. It has been demonstrated that PA700 prevents the aggregation of misfolded, nonubiquinated substrates. In this study, we examine the effect of PA700 on the aggregation of wild-type and A53T mutant alpha-synuclein. PA700 inhibits both wild-type and A53T alpha-synuclein fibril formation as measured by Thioflavin T fluorescence. Using size exclusion chromatography, we present evidence for a stable PA700-alpha-synuclein complex. Sedimentation analyses reveal that PA700 sequesters alpha-synuclein in an assembly incompetent form. Analysis of the morphology of wild-type and A53T alpha-synuclein aggregates during the course of fibrillization by electron microscopy demonstrate the formation of amyloid-like fibrils. Secondary structure analyses of wild-type and A53T alpha-synuclein assembled in the presence of PA700 revealed a decrease in the overall amount of assembled alpha-synuclein with no significant change in protein conformation. Thus, PA700 acts on alpha-synuclein assembly and not on the structure of fibrils. We hypothesize that PA700 sequesters alpha-synuclein oligomeric species that are the precursors of the fibrillar form of the protein, thus preventing its assembly into fibrils.
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Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities
NASA Astrophysics Data System (ADS)
Bowles, Marshall W.; Mogollón, José M.; Kasten, Sabine; Zabel, Matthias; Hinrichs, Kai-Uwe
2014-05-01
Sulfate reduction is a globally important redox process in marine sediments, yet global rates are poorly quantified. We developed an artificial neural network trained with 199 sulfate profiles, constrained with geomorphological and geochemical maps to estimate global sulfate-reduction rate distributions. Globally, 11.3 teramoles of sulfate are reduced yearly (~15% of previous estimates), accounting for the oxidation of 12 to 29% of the organic carbon flux to the sea floor. Combined with global cell distributions in marine sediments, these results indicate a strong contrast in sub-sea-floor prokaryote habitats: In continental margins, global cell numbers in sulfate-depleted sediment exceed those in the overlying sulfate-bearing sediment by one order of magnitude, whereas in the abyss, most life occurs in oxic and/or sulfate-reducing sediments.
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Sedimentation in small reservoirs on the San Rafael Swell, Utah
King, Norman Julius; Mace, Mervyn M.
1953-01-01
Movement of sediment from upland areas and eventually into main drainages and rivers is by no means through continuous transportation of material from the source to the delta. Instead it consists of a series of intermittent erosional and depositional phases that present a pulsating movement. Hence, sediment carried off upland areas may be deposited in lower reaches or along main drainages if an existing combination of factors tend to effect deposition. During this period actual sediment movement out of the basin may be relatively small. Following any change in existing conditions, however, these unconsolidated alluvial fills may be subjected to rapid removal; thus, for a limited time, abnormally high sediment production rates occur until the deposits are either removed or another cycle of deposition is started.
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Chen, Xinsheng; Liao, Yulin; Xie, Yonghong; Wu, Chao; Li, Feng; Deng, Zhengmiao; Li, Xu
2017-01-01
Sediment accretion (burial) and nutrient enrichment occur concurrently in lacustrine wetlands, but the role of these two aspects of sedimentation on macrophyte performance has rarely been examined. Here, we investigated the concurrent effects of sediment accretion and nutrient enrichment on the growth and propagation of Phalaris arundinacea L. using a factorial sediment burial by nutrient addition experimental design. Regardless of burial depth, nutrient addition increased biomass accumulation, shoot mass ratio, the number of rhizomes, and the length of ramets and rhizomes. While burial had little effect on plant growth and propagation, it had an interactive effect with nutrient addition on belowground growth and ramet production. These results indicate that P. arundinacea is tolerant to burial, which allows it to grow in habitats with high sedimentation rates. However, the enhanced growth and propagation of P. arundinacea following sedimentation were primarily related to nutrient enrichment. This suggests that nutrient enrichment of sediments, which occurs in many lacustrine wetlands, increases the risk of invasion by P. arundinacea. PMID:28054590
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Assembly and diploid architecture of an individual human genome via single-molecule technologies
Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali
2015-01-01
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404
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Assembly and diploid architecture of an individual human genome via single-molecule technologies.
Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali
2015-08-01
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
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Cerveau, Nicolas; Jackson, Daniel J
2016-12-09
Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be closer to biological reality than any of the three individual assembly packages we investigated. This approach (freely available as a simple perl script) will be of use to researchers working with species for which there is little or no reference data against which the assembly of a transcriptome can be performed.
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Neutron spectra as a function of angle at two meters from the Little Boy assembly
DOE Office of Scientific and Technical Information (OSTI.GOV)
Griffith, R.V.; Huntzinger, C.J.; Thorngate, J.H.
1984-07-02
Measurements of neutron spectra produced by the Los Alamos National Laboratory (LANL) Little Boy replica assembly (Comet) were made with a combined multisphere and liquid scintillator system, that has been widely used at the Lawrence Livermore National Laboratory. The combined system was used for measurements at the side (90/sup 0/) and nose (0/sup 0/) of the assembly; additional measurements were made at 45/sup 0/ using only the liquid scintillator. Data were obtained at two meters from the center of the reactive region of the assembly, with good agreement between the multisphere and scintillator results. Comparison with liquid scintillator measurements performedmore » by experimenters from the Canadian Defence Research Establishment, Ottawa (DREO) and calculations from LANL depended on the specific angle, obtaining the best agreement at 90/sup 0/. 32 references, 11 figures, 4 tables.« less
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Surface erosion at disturbed alpine sites: effects of vegetation cover and plant diversity
NASA Astrophysics Data System (ADS)
Martin, C.; Pohl, M.; Alewell, C.; Körner, C.; Buttler, A.; Rixen, C.
2009-04-01
The relationship between plant diversity and soil stability in disturbed alpine terrain is poorly studied. In this paper, we investigated the influence of plant cover and diversity on water run-off and sediment yield on ski slopes. Rainfall simulations were conducted on a micro-scale (25 x 25 cm) to be able to replicate plots with different degrees of vegetation cover. We selected plots with 10%, 30% and 60% of vegetation cover containing different combinations of plant diversities: (i) grass, (ii) herb, (iii) moss/ lichen, and all combinations of these plant groups. Each combination was replicated five times with an applied rain intensity of 375 ml min-1 for about 5 minutes. As could be expected, percent vegetation cover had a large effect on surface erosion: sediment yield decreased with increasing vegetation cover. However, within the plots with 60% cover, sediment yield was lower at higher plant diversity and functional group diversity. The findings of this study support the view that beside the re-establishment of a closed vegetation cover, plant diversity is a relevant factor to reduce surface erosion at disturbed sites in alpine ecosystems.
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NASA Astrophysics Data System (ADS)
Clary, W. A.; Worthington, L. L.; Scuderi, L. A.; Daigle, H.; Swartz, J. M.
2017-12-01
The Pamplona zone fold and thrust belt is the offshore expression of convergence and shallow subduction of the Yakutat microplate beneath North America in the northeastern Alaska subduction zone. The combination of convergent tectonics and glaciomarine sedimentary processes create patterns of deformation and deposition resulting in a shallow sedimentary sequence with varying compaction, fluid pressure, and fault activity. We propose that velocity variations observed in our tomographic analysis represent long-lived fluid overpressure due to loading by ice sheets and sediments. Regions with bathymetric and stratigraphic evidence of recent ice sheets and associated sedimentation should be collocated with evidence of overpressure (seismic low velocity zones) in the shallow sediments. Here, we compare a velocity model with shelf seismic stratigraphic facies and modern seafloor morphology. To document glacially derived morphology we use high resolution bathymetry to identify channel and gully networks on the western Yakutat shelf-slope then analyze cross-channel shape indices across the study area. We use channel shape index measurements as a proxy of recent ice-proximal sedimentation based on previously published results that proposed a close correlation. Profiles taken at many locations were fitted with a power function and assigned a shape - U-shape channels likely formed proximal to recent ice advances. Detailed velocity models were created by a combination of streamer tomography and pre-stack depth migration velocities with seismic data including: a 2008 R/V Langseth dataset from the St. Elias Erosion and Tectonics Project (STEEP); and a 2004 high-resolution R/V Ewing dataset. Velocity-porosity-permeability relationships developed using IODP Expedition 341 drilling data inform interpretation and physical properties analyses of the shallow sediments. Initial results from a 35 km profile extending SE seaward of the Bering glacier and subparallel to the Bering trough suggest a spatial relationship between the extent of U-shaped profiles and low-velocity shallow sediments. Towards the SE end of the model we observe a large overlap of U-shaped indices, and a shallow low-velocity zone in the mapped extent of the last glacial maximum suggestive of overpressure due to loading by ice sheet activity.
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NASA Astrophysics Data System (ADS)
Box, Walter; Keestra, Saskia; Nyman, Petter; Langhans, Christoph; Sheridan, Gary
2015-04-01
South-eastern Australia is generally regarded as one of the world's most fire-prone environments because of its high temperatures, low rainfall and flammable native Eucalyptus forests. Modifications to the landscape by fire can lead to significant changes to erosion rates and hydrological processes. Debris flows in particular have been recognised as a process which increases in frequency as a result of fire. This study used a debris flow event in the east Upper Ovens occurred on the 28th of February 2013 as a case study for analysing sediment transport processes and connectivity of sediment sources and sinks. Source areas were identified using a 15 cm resolution areal imagery and a logistic regression model was made based on fire severity, aridity index and slope to predict locations of source areas. Deposits were measured by making cross-sections using a combination of a differential GPS and a total station. In total 77 cross-sections were made in a 14.1 km2 sub-catchment and distributed based on channel gradient and width. A more detailed estimation was obtained by making more cross-sections where the volume per area is higher. Particle size distribution between sources and sink areas were obtained by combination of field assessment, photography imagery analyses and sieve and laser diffraction. Sediment was locally eroded, transported and deposited depending on factors such as longitude gradient, stream power and the composition of bed and bank material. The role of headwaters as sediment sinks changed dramatically as a result of the extreme erosion event in the wildfire affected areas. Disconnected headwaters became connected to low order streams due to debris flow processes in the contributing catchment. However this redistribution of sediment from headwaters to the drainage network was confined to upper reaches of the Ovens. Below this upper part of the catchment the event resulted in redistribution of sediment already existing in the channel through a combination of debris flows and hyperconcentrated flows. These results indicate that there is a stepwise outflow of sediment influencing long-term erosion rates and landform development.
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Suspended-sediment sources in an urban watershed, Northeast Branch Anacostia River, Maryland
Devereux, Olivia H.; Prestegaard, Karen L.; Needelman, Brian A.; Gellis, Allen C.
2010-01-01
Fine sediment sources were characterized by chemical composition in an urban watershed, the Northeast Branch Anacostia River, which drains to the Chesapeake Bay. Concentrations of 63 elements and two radionuclides were measured in possible land-based sediment sources and suspended sediment collected from the water column at the watershed outlet during storm events. These tracer concentrations were used to determine the relative quantity of suspended sediment contributed by each source. Although this is an urbanized watershed, there was not a distinct urban signature that can be evaluated except for the contributions from road surfaces. We identified the sources of fine sediment by both physiographic province (Piedmont and Coastal Plain) and source locale (streambanks, upland and street residue) by using different sets of elemental tracers. The Piedmont contributed the majority of the fine sediment for seven of the eight measured storms. The streambanks contributed the greatest quantity of fine sediment when evaluated by source locale. Street residue contributed 13% of the total suspended sediment on average and was the source most concentrated in anthropogenically enriched elements. Combining results from the source locale and physiographic province analyses, most fine sediment in the Northeast Branch watershed is derived from streambanks that contain sediment eroded from the Piedmont physiographic province of the watershed. Sediment fingerprinting analyses are most useful when longer term evaluations of sediment erosion and storage are also available from streambank-erosion measurements, sediment budget and other methods.
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Sommerville, John; Brumwell, Craig L; Politz, Joan C Ritland; Pederson, Thoru
2005-03-15
The signal recognition particle (SRP) is a ribonucleoprotein machine that controls the translation and intracellular sorting of membrane and secreted proteins. The SRP contains a core RNA subunit with which six proteins are assembled. Recent work in both yeast and mammalian cells has identified the nucleolus as a possible initial site of SRP assembly. In the present study, SRP RNA and protein components were identified in the extrachromosomal, amplified nucleoli of Xenopus laevis oocytes. Fluorescent SRP RNA microinjected into the oocyte nucleus became specifically localized in the nucleoli, and endogenous SRP RNA was also detected in oocyte nucleoli by RNA in situ hybridization. An initial step in the assembly of SRP involves the binding of the SRP19 protein to SRP RNA. When green fluorescent protein (GFP)-tagged SRP19 protein was injected into the oocyte cytoplasm it was imported into the nucleus and became concentrated in the amplified nucleoli. After visiting the amplified nucleoli, GFP-tagged SRP19 protein was detected in the cytoplasm in a ribonucleoprotein complex, having a sedimentation coefficient characteristic of the SRP. These results suggest that the amplified nucleoli of Xenopus oocytes produce maternal stores not only of ribosomes, the classical product of nucleoli, but also of SRP, presumably as a global developmental strategy for stockpiling translational machinery for early embryogenesis.
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NASA Astrophysics Data System (ADS)
Colombi, P.; Alessandri, I.; Bergese, P.; Federici, S.; Depero, L. E.
2009-08-01
In this paper, self-assembled polystyrene nanospheres are proposed as a shape characterizer sample for SPM tips. Ordered arrays or 2D islands of polystyrene spheres may be prepared either by sedimentation or by crystallization of the colloidal spheres' suspension. The self-assembling mechanism guarantees high reproducibility; thus the characterizer sample can be 'freshly' prepared at each use, avoiding the problem of time and use deterioration and reducing the problem of sample structure fidelity that occurs when lithographic structures are employed. The spheres could also be deposited on the sample itself in order to speed up the characterization process in applications requiring frequent tip characterizations. We present numerical calculations of geometrical convoluted profiles on the proposed structures showing that, for a variety of different tip shapes, at the border between a couple of touching spheres the tip flanks do not come into contact with the spheres. Due to this behaviour, touching spheres are an optimum characterizer sample for SPM tip curvature radius characterization, enabling a straightforward procedure for calculating the curvature radius from the amplitude of tip oscillation along profiles connecting spheres' centres. The new procedure for the characterization of SPM probes was assessed exploiting different kinds of self-assembled structures and comparing results to those obtained by spiked structures and SEM observations.
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Knuesel, Robert J.; Jacobs, Heiko O.
2010-01-01
This paper introduces a method for self-assembling and electrically connecting small (20–60 micrometer) semiconductor chiplets at predetermined locations on flexible substrates with high speed (62500 chips/45 s), accuracy (0.9 micrometer, 0.14°), and yield (> 98%). The process takes place at the triple interface between silicone oil, water, and a penetrating solder-patterned substrate. The assembly is driven by a stepwise reduction of interfacial free energy where chips are first collected and preoriented at an oil-water interface before they assemble on a solder-patterned substrate that is pulled through the interface. Patterned transfer occurs in a progressing linear front as the liquid layers recede. The process eliminates the dependency on gravity and sedimentation of prior methods, thereby extending the minimal chip size to the sub-100 micrometer scale. It provides a new route for the field of printable electronics to enable the integration of microscopic high performance inorganic semiconductors on foreign substrates with the freedom to choose target location, pitch, and integration density. As an example we demonstrate a fault-tolerant segmented flexible monocrystalline silicon solar cell, reducing the amount of Si that is used when compared to conventional rigid cells. PMID:20080682
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Bravo, Andrea G; Bouchet, Sylvain; Guédron, Stéphane; Amouroux, David; Dominik, Janusz; Zopfi, Jakob
2015-09-01
Sewage treatment plants (STPs) are important point sources of mercury (Hg) to the environment. STPs are also significant sources of iron when hydrated ferric oxide (HFO) is used as a dephosphatation agent during water purification. In this study, we combined geochemical and microbiological characterization with Hg speciation and sediment amendments to evaluate the impact of STP's effluents on monomethylmercury (MMHg) production. The highest in-situ Hg methylation was found close to the discharge pipe in subsurface sediments enriched with Hg, organic matter, and iron. There, ferruginous conditions were prevailing with high concentrations of dissolved Fe(2+) and virtually no free sulfide in the porewater. Sediment incubations demonstrated that the high MMHg production close to the discharge was controlled by low demethylation yields. Inhibition of dissimilatory sulfate reduction with molybdate led to increased iron reduction rates and Hg-methylation, suggesting that sulfate-reducing bacteria (SRB) may not have been the main Hg methylators under these conditions. However, Hg methylation in sediments amended with amorphous Fe(III)-oxides was only slightly higher than control conditions. Thus, in addition to iron-reducing bacteria, other non-SRB most likely contributed to Hg methylation. Overall, this study highlights that sediments impacted by STP discharges can become local hot-spots for Hg methylation due to the combined inputs of i) Hg, ii) organic matter, which fuels bacterial activities and iii) iron, which keeps porewater sulfide concentration low and hence Hg bioavailable. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Shifting Gravel and the Acoustic Detection Range of Killer Whale Calls
NASA Astrophysics Data System (ADS)
Bassett, C.; Thomson, J. M.; Polagye, B. L.; Wood, J.
2012-12-01
In environments suitable for tidal energy development, strong currents result in large bed stresses that mobilize sediments, producing sediment-generated noise. Sediment-generated noise caused by mobilization events can exceed noise levels attributed to other ambient noise sources at frequencies related to the diameters of the mobilized grains. At a site in Admiralty Inlet, Puget Sound, Washington, one year of ambient noise data (0.02 - 30 kHz) and current velocity data are combined. Peak currents at the site exceed 3.5 m/s. During slack currents, vessel traffic is the dominant noise source. When currents exceed 0.85 m/s noise level increases between 2 kHz and 30 kHz are correlated with near-bed currents and bed stress estimates. Acoustic spectrum levels during strong currents exceed quiescent slack tide conditions by 20 dB or more between 2 and 30 kHz. These frequencies are consistent with sound generated by the mobilization of gravel and pebbles. To investigate the implications of sediment-generated noise for post-installation passive acoustic monitoring of a planned tidal energy project, ambient noise conditions during slack currents and strong currents are combined with the characteristics of Southern Resident killer whale (Orcinus orca) vocalizations and sound propagation modeling. The reduction in detection range is estimated for common vocalizations under different ambient noise conditions. The importance of sediment-generated noise for passive acoustic monitoring at tidal energy sites for different marine mammal functional hearing groups and other sediment compositions are considered.
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Zienowicz, Agata; Bamm, Vladimir V; Vassall, Kenrick A; Harauz, George
2015-05-22
The 18.5-kDa splice isoform of myelin basic protein (MBP) predominates in the adult brain, adhering the cytoplasmic leaflets of the oligodendrocyte membrane together, but also assembling the cytoskeleton at leading edges of membrane processes. Here, we characterized MBP's role as a microtubule-assembly protein (MAP). Using light scattering and sedimentation assays we found that pseudo-phosphorylation of Ser54 (murine 18.5-kDa sequence) significantly enhanced the rate but not the final degree of polymerization. This residue lies within a short KPGSG motif identical to one in tau, a ubiquitous MAP important in neuronal microtubule assembly. Using polypeptide constructs, each comprising one of three major amphipathic α-helical molecular recognition fragments of 18.5-kDa MBP, we identified the N-terminal α1-peptide as sufficient to cause microtubule polymerization, the rate of which was significantly enhanced in the presence of dodecylphosphocholine (DPC) micelles to mimic a lipidic environment. Copyright © 2015 Elsevier Inc. All rights reserved.
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What a drag: Quantifying the global impact of chronic bottom trawling on continental shelf sediment
Oberle, Ferdinand K.J.; Storlazzi, Curt; Hanebuth, Till J.J.
2016-01-01
Continental shelves worldwide are subject to intense bottom trawling that causes sediment to be resuspended. The widely used traditional concepts of modern sedimentary transport systems on the shelf rely only on estimates for naturally driven sediment resuspension such as through storm waves, bottom currents, and gravity-driven flows but they overlook a critical anthropogenic factor. The strong influence of bottom trawling on a source-to-sink sediment budget is explored on the NW Iberian shelf. Use of Automated Information System vessel tracking data provides for a high-resolution vessel track reconstruction and the accurate calculation of the spatial distribution of bottom trawling intensity and associated resuspended sediment load. The mean bottom trawling-induced resuspended sediment mass for the NW Iberian shelf is 13.50 Mt yr− 1, which leads to a six-fold increase in off-shelf sediment transport when compared to natural resuspension mechanisms. The source-to-sink budget analysis provides evidence that bottom trawling causes a rapid erosion of the fine sediment on human time scales. Combining global soft sediment distribution data of the shelves with worldwide bottom trawling intensity estimates we show that the bottom trawling-induced resuspended sediment mass amounts to approximately the same mass of all sediment entering the shelves through rivers. Spatial delineations between natural and anthropogenic sediment resuspension areas are presented to aid in marine management questions.
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NASA Astrophysics Data System (ADS)
Ziebis, W.; Patel, A.; Krupke, A.; Ferdelman, T. G.
2012-12-01
The vast majority of scientific drilling expeditions have focused on continental margins where oxygen is depleted within the surface (1 m) layer of the sediment and buried organic carbon sustains anaerobic microbial communities. IODP expeditions 329 (South Pacific Gyre) and 336 (Mid-Atlantic Ridge - North Pond) took place in oligotrophic open ocean regions, which constitute 48% of the world ocean. These expeditions have revealed that unlike continental margins the seafloor underneath oligotrophic ocean gyres is oxic. Within the South Pacific Gyre (SPG) dissolved oxygen persists throughout the sediment cover and reaches the basement even at the sites with thickest sediment cover (62 and 75 mbsf). North Pond is a sedimented pond (< 300 m sediment cover) located on the flank of the Mid-Atlantic Ridge underlying the oligotrophic central Atlantic. Here, oxygen diffuses upward from the basaltic aquifer underlying the sediment package in addition to deep oxygen penetration from the overlying water. Oxygen is the main electron acceptor available for sub-seafloor microbial activity in these vast oligotrophic open ocean regions. Microbial cells are present and active in the organic poor sediments, albeit numbers are near or below the detection limit (<103 cm-3 sediment) in the extremely organic-poor sediment of the SPG (below 2 -15 m sediment depth, depending on the location). However, we have very limited knowledge on the microbial community compositions and metabolic activities. Even the dominance of bacteria or archaea remains largely elusive. It has been suggested that while archaea dominate in the anoxic sediments of continental margins bacteria might be more abundant in the oxic seafloor underlying oligotrophic ocean gyres where aerobic respiration prevails. Experiments were conducted with sediment samples from the SPG and North Pond to explore the pattern of microbial diversity and metabolic activity using a suite of radio and stable isotopes in combination with single cell analyses. Our goal was to track the uptake and turnover of metabolically important elements (C, N, P) and to compare metabolic activities (heterotrophy / autotrophy) between sites and with depth. Labeling of cells using fluorescent oligonucleotide probes (HISH and CARD-FISH) in combination with nanoSIMS has thus far revealed a clear dominance of bacteria in SPG sub-seafloor sediments, which showed a high uptake of nitrogen (ammonium). Current experiments using cell extractions and cell encapsulations followed by incubations with radiotracers will further reveal carbon turnover pathways of specific microorganisms.
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Watching Nanoscale Self-Assembly Kinetics of Gold Prisms in Liquids
NASA Astrophysics Data System (ADS)
Kim, Juyeong; Ou, Zihao; Jones, Matthew R.; Chen, Qian
We use liquid-phase transmission electron microscopy to watch self-assembly of gold triangular prisms into polymer-like structures. The in situ dynamics monitoring enabled by liquid-phase transmission electron microscopy, single nanoparticle tracking, and the marked conceptual similarity between molecular reactions and nanoparticle self-assembly combined elucidate the following mechanistic understanding: a step-growth polymerization based assembly statistics, kinetic pathways sampling particle curvature dependent energy minima and their interconversions, and directed assembly into polymorphs (linear or cyclic chains) through in situ modulation of the prism bonding geometry. Our study bridges the constituent kinetics on the molecular and nanoparticle length scales, which enriches the design rules in directed self-assembly of anisotropic nanoparticles.
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Suspended sediments of the modern Amazon and Orinoco rivers
Meade, R.H.
1994-01-01
The Amazon and Orinoco Rivers are massive transcontinental conveyance systems for suspended sediment. They derive about 90% of their sediment from the Andes that support their western headwaters, transport it for thousands of kilometers across the breadth of the continent and deposit it in the coastal zones of the Atlantic. At their points of maximum suspended-sediment discharge, the Amazon transports an average of 1100-1300 ?? 106 tons per year and the Orinoco transports about 150 ?? 106 tons per year. Relations of sediment discharge to water discharge are complicated by unusual patterns of seasonal storage and remobilization, increased storage and reduced transport of sediment in the middle Orinoco during periods of peak water discharge, and storage of suspended sediment in the lower Amazon during rising discharge and resuspension during falling discharge. Spatial distributions of suspended sediment in cross-sections of both rivers are typically heterogeneous, not only in the vertical sense but also in the lateral. The cross-channel mixing of tributary inputs into the mainstem waters is a slow process that requires several hundred kilometers of downriver transport to complete. Considerable fine-grained sediment is exchanged between rivers and floodplains by the combination of overbank deposition and bank erosion. ?? 1994.
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Machine learning assembly landscapes from particle tracking data.
Long, Andrew W; Zhang, Jie; Granick, Steve; Ferguson, Andrew L
2015-11-07
Bottom-up self-assembly offers a powerful route for the fabrication of novel structural and functional materials. Rational engineering of self-assembling systems requires understanding of the accessible aggregation states and the structural assembly pathways. In this work, we apply nonlinear machine learning to experimental particle tracking data to infer low-dimensional assembly landscapes mapping the morphology, stability, and assembly pathways of accessible aggregates as a function of experimental conditions. To the best of our knowledge, this represents the first time that collective order parameters and assembly landscapes have been inferred directly from experimental data. We apply this technique to the nonequilibrium self-assembly of metallodielectric Janus colloids in an oscillating electric field, and quantify the impact of field strength, oscillation frequency, and salt concentration on the dominant assembly pathways and terminal aggregates. This combined computational and experimental framework furnishes new understanding of self-assembling systems, and quantitatively informs rational engineering of experimental conditions to drive assembly along desired aggregation pathways.
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NASA Technical Reports Server (NTRS)
Eigenbrode, J. L.; McAdam, A.; Franz, H.; Freissinet, C.; Bower, H.; Floyd, M.; Conrad, P.; Mahaffy, P.; Feldman, J.; Hurowitz, J.;
2013-01-01
Polytetrafluoroethylene (PTFE or trade name: Teflon by Dupont Co.) has been detected in rocks drilled during terrestrial testing of the Mars Science Laboratory (MSL) drilling hardware. The PTFE in sediments is a wear product of the seals used in the Drill Bit Assemblies (DBAs). It is expected that the drill assembly on the MSL flight model will also shed Teflon particles into drilled samples. One of the primary goals of the Sample Analysis at Mars (SAM) instrument suite on MSL is to test for the presence of martian organics in samples. Complications introduced by the potential presence of PTFE in drilled samples to the SAM evolved gas analysis (EGA or pyrolysisquadrupole mass spectrometry, pyr-QMS) and pyrolysis- gas chromatography mass spectrometry (Pyr- GCMS) experiments was investigated.
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NASA Technical Reports Server (NTRS)
Moeller, Christopher C.; Gunshor, Mathew M.; Menzel, W. Paul; Huh, Oscar K.; Walker, Nan D.; Rouse, Lawrence J.; Frey, Herbert V. (Technical Monitor)
2001-01-01
The University of Wisconsin and Louisiana State University have teamed to study the forcing of winter season cold frontal wind systems on sediment distribution patterns and geomorphology in the Louisiana coastal zone. Wind systems associated with cold fronts have been shown to modify coastal circulation and resuspend sediments along the microtidal Louisiana coast. The assessment includes quantifying the influence of cumulative winter season atmospheric forcing (through surface wind observations) from year to year in response to short term climate variability, such as El Nino events. A correlation between winter cyclone frequency and the strength of El Nino events has been suggested. The atmospheric forcing data are being correlated to geomorphic measurements along western Louisiana's prograding muddy coast. Remote sensing data is being used to map and track sediment distribution patterns for various wind conditions. Transferring a suspended sediment concentration (SSC) algorithm to EOS MODIS observations will enable estimates of SSC in case 2 waters over the global domain. Progress in Year 1 of this study has included data collection and analysis of wind observations for atmospheric forcing characterization, a field activity (TX-2001) to collect in situ water samples with co-incident remote sensing measurements from the NASA ER-2 based MODIS Airborne Simulator (MAS) and the EOS Terra based MODerate resolution Imaging Spectroradiometer (MODIS) instruments, aerial photography and of sediment burial pipe field measurements along the prograding muddy Chenier Plain coast of western Louisiana for documenting coastal change in that dynamic region, and routine collection of MODIS 250 in resolution data for monitoring coastal sediment patterns. The data sets are being used in a process to transfer an SSC estimation algorithm to the MODIS platform. Work is underway on assessing coastal transport for the winter 2000-01 season. Water level data for use in a Geomorphic Impact Index, which relates wind energy, water level conditions, and geomorphic change along the microtidal western Louisiana coastline is being assembled.
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NASA Astrophysics Data System (ADS)
Pinho, J.; Costa, N.; Venâncio, S.; Martins, M.; Vieira, J.; Granja, H.
2016-12-01
The NW coast of Iberian Peninsula is mainly formed by rocky cliffs northern of the river Minho mouth and by narrow sandy beaches south of this river. These beaches are mainly in a sedimentary deficit status resulting from the north-south longitudinal drift driven by the dominant wave climate that acts from the NW direction. In this scenario understand and quantify river sediment inputs to the coast is crucial in order to follow a sustainable management policy to mitigate erosion impacts both in the natural and social environments. This work will present results from research conducted at rive Lima Estuary, one of the rivers flowing to the NW Iberian coast, based on both numerical modeling and field data acquisition. A hydrological model of the river basin and a detailed morphodynamic model of the estuary were implemented. Instrumentation of the estuary that is being conducted comprises traditional sensor pressures and new ones that are being designed and assembled to be installed at different measurement stations within the estuary. Modelling results for flood events showed that the river is capable of remove all the sediments that are deposited in the narrow estuarine canal located near the river mouth. Some of these sediments are immediately deposited downstream, within the interior of the harbor. Here, there is a strong possibility of silting of the river mouth and the central area of the harbor. Since the river flows during extreme events are controlled by an upstream reservoir, the capacity of the river to transport sediments to the coast was lowered during the last decades, which, moreover, requires dredging works over the years to maintain navigation depth requirements. Dredging sediments should be correctly deposited at the coast in order to properly feed the longitudinal drift, otherwise they will be out of the system, which aggravate the installed erosion tendency.
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Challenges and advances in the field of self-assembled membranes.
van Rijn, Patrick; Tutus, Murat; Kathrein, Christine; Zhu, Leilei; Wessling, Matthias; Schwaneberg, Ulrich; Böker, Alexander
2013-08-21
Self-assembled membranes are of vital importance in biological systems e.g. cellular and organelle membranes, however, more focus is being put on synthetic self-assembled membranes not only as an alternative for lipid membranes but also as an alternative for lithographic methods. More investigations move towards self-assembly processes because of the low-cost preparations, structural self-regulation and the ease of creating composite materials and tunable properties. The fabrication of new smart membrane materials via self-assembly is of interest for delivery vessels, size selective separation and purification, controlled-release materials, sensors and catalysts, scaffolds for tissue engineering, low dielectric constant materials for microelectronic devices, antireflective coatings and proton exchange membranes for polymer electrolyte membrane fuel cells. Polymers and nanoparticles offer the most straightforward approaches to create membrane structures. However, alternative approaches using small molecules or composite materials offer novel ultra-thin membranes or multi-functional membranes, respectively. Especially, the composite material membranes are regarded as highly promising since they offer the possibility to combine properties of different systems. The advantages of polymers which provide elastic and flexible yet stable matrices can be combined with nanoparticles being either inorganic, organic or even protein-based which offers pore-size control, catalytic activity or permeation regulation. It is therefore believed that at the interface of different disciplines with each offering different materials or approaches, the most novel and interesting membrane structures are going to be produced. The combinations and approaches presented in this review offer non-conventional self-assembled membrane materials which exhibit a high potential to advance membrane science and find more practical applications.
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Export Time of Earthquake-Derived Landslides in Active Mountain Ranges
NASA Astrophysics Data System (ADS)
Croissant, T.; Lague, D.; Steer, P.; Davy, P.
2016-12-01
In active mountain ranges, large earthquakes (Mw > 5-6) trigger numerous landslides that impact river dynamics. These landslides bring local and sudden sediment deposits which are eroded and transported along the river network, causing downstream changes in river geometry, transport capacity and erosion efficiency. The progressive removal of landslide materials has implications for downstream hazards management and for landscape dynamics at the timescale of the seismic cycle. Although the export time of suspended sediments from landslides triggered by large-magnitude earthquakes has been extensively studied, the processes and time scales associated to bedload transport remains poorly studied. Here, we study the sediment export of large landslides with the 2D morphodynamic model, Eros. This model combines: (i) an hydrodynamic model, (ii) a sediment transport and deposition model and (iii) a lateral erosion model. Eros is particularly well suited for this issue as it accounts for the complex retro-actions between sediment transport and fluvial geometry for rivers submitted to external forcings such as abrupt sediment supply increase. Using a simplified synthetic topography we systematically study the influence of pulse volume (Vs) and channel transport capacity (QT) on the export time of landslides. The range of simulated river behavior includes landslide vertical incision, its subsequent removal by lateral erosion and the river morphology modifications induced by downstream sediment propagation. The morphodynamic adaptation of the river increases its transport capacity along the channel and tends to accelerate the landslide evacuation. Our results highlight two regimes: (i) the export time is linearly related to Vs/QT when the sediment pulse introduced in the river does not affect significantly the river hydrodynamic (low Vs/QT) and (ii) the export time is a non-linear function of Vs/QT when the pulse undergoes significant morphodynamic modifications during its evacuation (high Vs/QT). By combining our newly derived export time functions with the frequency-magnitude of earthquake intensity and the induced sediment production, we investigate the sediment export of several plausible earthquake scenarii in different mountain ranges (New Zealand, Taiwan, Nepal).
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Marvin-DiPasquale, Mark; Lutz, Michelle A; Brigham, Mark E.; Krabbenhoft, David P.; Aiken, George R.; Orem, William H.; Hall, Britt D.
2009-01-01
Mercury speciation, controls on methylmercury (MeHg) production, and bed sediment−pore water partitioning of total Hg (THg) and MeHg were examined in bed sediment from eight geochemically diverse streams where atmospheric deposition was the predominant Hg input. Across all streams, sediment THg concentrations were best described as a combined function of sediment percent fines (%fines; particles < 63 μm) and organic content. MeHg concentrations were best described as a combined function of organic content and the activity of the Hg(II)-methylating microbial community and were comparable to MeHg concentrations in streams with Hg inputs from industrial and mining sources. Whole sediment tin-reducible inorganic reactive Hg (Hg(II)R) was used as a proxy measure for the Hg(II) pool available for microbial methylation. In conjunction with radiotracer-derived rate constants of 203Hg(II) methylation, Hg(II)R was used to calculate MeHg production potential rates and to explain the spatial variability in MeHg concentration. The %Hg(II)R (of THg) was low (2.1 ± 5.7%) and was inversely related to both microbial sulfate reduction rates and sediment total reduced sulfur concentration. While sediment THg concentrations were higher in urban streams, %MeHg and %Hg(II)R were higher in nonurban streams. Sediment pore water distribution coefficients (log Kd’s) for both THg and MeHg were inversely related to the log-transformed ratio of pore water dissolved organic carbon (DOC) to bed sediment %fines. The stream with the highest drainage basin wetland density also had the highest pore water DOC concentration and the lowest log Kd’s for both THg and MeHg. No significant relationship existed between overlying water MeHg concentrations and those in bed sediment or pore water, suggesting upstream sources of MeHg production may be more important than local streambed production as a driver of water column MeHg concentration in drainage basins that receive Hg inputs primarily from atmospheric sources.
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Combined Climate and Flow Abstraction Impacts on an Aggrading Alpine River
NASA Astrophysics Data System (ADS)
Bakker, M.; Costa, A.; Silva, T. A.; Stutenbecker, L.; Girardclos, S.; Loizeau, J. L.; Molnar, P.; Schlunegger, F.; Lane, S. N.
2017-12-01
Recent climatic warming and associated glacial retreat may have a large impact on sediment release and transfer in Alpine river basins. In parallel, the sediment transport capacity of many European Alpine streams is affected by hydropower exploitation, notably where flow is abstracted but the sediment supply to the headwaters is maintained at flow intakes. Here, we investigate the combined effects of climate change and flow abstraction on morphodynamics and sediment transfer in one such Alpine stream, the Borgne River, Switzerland. A unique dataset forms the basis for determining sediment deposition and transfer: (1) a set of high resolution Digital Elevation Models (DEMs) of braided river reaches is derived through applying Structure from Motion (SfM) photogrammetry to archival aerial photographs available for the period 1959-2014; (2) flow intake management data is used for the reconstruction of (up- and downstream) discharge and sediment supply since 1977. Subsequently we use bedload transport capacity calculations and climate data to assess their relative impact on the system evolution over the last 25 years. From the historical DEMs we find considerable aggradation of the river bed (up to 5 meters) since the onset of flow abstraction in 1963. Rapid and widespread aggradation however did not commence until the onset of glacier retreat in the late 1980s and the dry and notably warm years of the early 1990s. This aggradation coincided with an increase in sediment supply, although it accounts for only c. 25% of supplied material, the remainder was transferred through the studied reaches. Flow abstraction reduces transport capacity by an order of magnitude but the residual transport rates are close to sediment supply rates, which is why significant transport remains. However, the reduction in transport capacity due to direct human impacts in basin hydrology (flow abstraction) makes the system much more sensitive to changes in climate-driven hydrological variability and climate induced changes in intake management and sediment supply rates. This was exemplified by an increasingly strong climate (winter precipitation and summer temperature) influence on the delivery of glacially derived sediment.
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Zhao, Huaying; Ghirlando, Rodolfo; Alfonso, Carlos; Arisaka, Fumio; Attali, Ilan; Bain, David L; Bakhtina, Marina M; Becker, Donald F; Bedwell, Gregory J; Bekdemir, Ahmet; Besong, Tabot M D; Birck, Catherine; Brautigam, Chad A; Brennerman, William; Byron, Olwyn; Bzowska, Agnieszka; Chaires, Jonathan B; Chaton, Catherine T; Cölfen, Helmut; Connaghan, Keith D; Crowley, Kimberly A; Curth, Ute; Daviter, Tina; Dean, William L; Díez, Ana I; Ebel, Christine; Eckert, Debra M; Eisele, Leslie E; Eisenstein, Edward; England, Patrick; Escalante, Carlos; Fagan, Jeffrey A; Fairman, Robert; Finn, Ron M; Fischle, Wolfgang; de la Torre, José García; Gor, Jayesh; Gustafsson, Henning; Hall, Damien; Harding, Stephen E; Cifre, José G Hernández; Herr, Andrew B; Howell, Elizabeth E; Isaac, Richard S; Jao, Shu-Chuan; Jose, Davis; Kim, Soon-Jong; Kokona, Bashkim; Kornblatt, Jack A; Kosek, Dalibor; Krayukhina, Elena; Krzizike, Daniel; Kusznir, Eric A; Kwon, Hyewon; Larson, Adam; Laue, Thomas M; Le Roy, Aline; Leech, Andrew P; Lilie, Hauke; Luger, Karolin; Luque-Ortega, Juan R; Ma, Jia; May, Carrie A; Maynard, Ernest L; Modrak-Wojcik, Anna; Mok, Yee-Foong; Mücke, Norbert; Nagel-Steger, Luitgard; Narlikar, Geeta J; Noda, Masanori; Nourse, Amanda; Obsil, Tomas; Park, Chad K; Park, Jin-Ku; Pawelek, Peter D; Perdue, Erby E; Perkins, Stephen J; Perugini, Matthew A; Peterson, Craig L; Peverelli, Martin G; Piszczek, Grzegorz; Prag, Gali; Prevelige, Peter E; Raynal, Bertrand D E; Rezabkova, Lenka; Richter, Klaus; Ringel, Alison E; Rosenberg, Rose; Rowe, Arthur J; Rufer, Arne C; Scott, David J; Seravalli, Javier G; Solovyova, Alexandra S; Song, Renjie; Staunton, David; Stoddard, Caitlin; Stott, Katherine; Strauss, Holger M; Streicher, Werner W; Sumida, John P; Swygert, Sarah G; Szczepanowski, Roman H; Tessmer, Ingrid; Toth, Ronald T; Tripathy, Ashutosh; Uchiyama, Susumu; Uebel, Stephan F W; Unzai, Satoru; Gruber, Anna Vitlin; von Hippel, Peter H; Wandrey, Christine; Wang, Szu-Huan; Weitzel, Steven E; Wielgus-Kutrowska, Beata; Wolberger, Cynthia; Wolff, Martin; Wright, Edward; Wu, Yu-Sung; Wubben, Jacinta M; Schuck, Peter
2015-01-01
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.
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NASA Astrophysics Data System (ADS)
Pereira, M. F.; Ribeiro, C.; Vilallonga, F.; Chichorro, M.; Drost, K.; Silva, J. B.; Albardeiro, L.; Hofmann, M.; Linnemann, U.
2014-07-01
This study combines geochemical and geochronological data in order to decipher the provenance of Carboniferous turbidites from the South Portuguese Zone (SW Iberia). Major and trace elements of 25 samples of graywackes and mudstones from the Mértola (Visean), Mira (Serpukhovian), and Brejeira (Moscovian) Formations were analyzed, and 363 U-Pb ages were obtained on detrital zircons from five samples of graywackes from the Mira and Brejeira Formations using LA-ICPMS. The results indicate that turbiditic sedimentation during the Carboniferous was marked by variability in the sources, involving the denudation of different crustal blocks and a break in synorogenic volcanism. The Visean is characterized by the accumulation of immature turbidites (Mértola Formation and the base of the Mira Formation) inherited from a terrane with intermediate to mafic source rocks. These source rocks were probably formed in relation to Devonian magmatic arcs poorly influenced by sedimentary recycling, as indicated by the almost total absence of pre-Devonian zircons typical of the Gondwana and/or Laurussia basements. The presence of Carboniferous grains in Visean turbidites indicates that volcanism was active at this time. Later, Serpukhovian to Moscovian turbiditic sedimentation (Mira and Brejeira Formations) included sedimentary detritus derived from felsic mature source rocks situated far from active magmatism. The abundance of Precambrian and Paleozoic zircons reveals strong recycling of the Gondwana and/or Laurussia basements. A peri-Gondwanan provenance is indicated by zircon populations with Neoproterozoic (Cadomian-Avalonian and Pan-African zircon-forming events), Paleoproterozoic, and Archean ages. The presence of late Ordovician and Silurian detrital zircons in Brejeira turbidites, which have no correspondence in the Gondwana basement of SW Iberia, indicates Laurussia as their most probable source.
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Zhao, Huaying; Ghirlando, Rodolfo; Alfonso, Carlos; Arisaka, Fumio; Attali, Ilan; Bain, David L.; Bakhtina, Marina M.; Becker, Donald F.; Bedwell, Gregory J.; Bekdemir, Ahmet; Besong, Tabot M. D.; Birck, Catherine; Brautigam, Chad A.; Brennerman, William; Byron, Olwyn; Bzowska, Agnieszka; Chaires, Jonathan B.; Chaton, Catherine T.; Cölfen, Helmut; Connaghan, Keith D.; Crowley, Kimberly A.; Curth, Ute; Daviter, Tina; Dean, William L.; Díez, Ana I.; Ebel, Christine; Eckert, Debra M.; Eisele, Leslie E.; Eisenstein, Edward; England, Patrick; Escalante, Carlos; Fagan, Jeffrey A.; Fairman, Robert; Finn, Ron M.; Fischle, Wolfgang; de la Torre, José García; Gor, Jayesh; Gustafsson, Henning; Hall, Damien; Harding, Stephen E.; Cifre, José G. Hernández; Herr, Andrew B.; Howell, Elizabeth E.; Isaac, Richard S.; Jao, Shu-Chuan; Jose, Davis; Kim, Soon-Jong; Kokona, Bashkim; Kornblatt, Jack A.; Kosek, Dalibor; Krayukhina, Elena; Krzizike, Daniel; Kusznir, Eric A.; Kwon, Hyewon; Larson, Adam; Laue, Thomas M.; Le Roy, Aline; Leech, Andrew P.; Lilie, Hauke; Luger, Karolin; Luque-Ortega, Juan R.; Ma, Jia; May, Carrie A.; Maynard, Ernest L.; Modrak-Wojcik, Anna; Mok, Yee-Foong; Mücke, Norbert; Nagel-Steger, Luitgard; Narlikar, Geeta J.; Noda, Masanori; Nourse, Amanda; Obsil, Tomas; Park, Chad K.; Park, Jin-Ku; Pawelek, Peter D.; Perdue, Erby E.; Perkins, Stephen J.; Perugini, Matthew A.; Peterson, Craig L.; Peverelli, Martin G.; Piszczek, Grzegorz; Prag, Gali; Prevelige, Peter E.; Raynal, Bertrand D. E.; Rezabkova, Lenka; Richter, Klaus; Ringel, Alison E.; Rosenberg, Rose; Rowe, Arthur J.; Rufer, Arne C.; Scott, David J.; Seravalli, Javier G.; Solovyova, Alexandra S.; Song, Renjie; Staunton, David; Stoddard, Caitlin; Stott, Katherine; Strauss, Holger M.; Streicher, Werner W.; Sumida, John P.; Swygert, Sarah G.; Szczepanowski, Roman H.; Tessmer, Ingrid; Toth, Ronald T.; Tripathy, Ashutosh; Uchiyama, Susumu; Uebel, Stephan F. W.; Unzai, Satoru; Gruber, Anna Vitlin; von Hippel, Peter H.; Wandrey, Christine; Wang, Szu-Huan; Weitzel, Steven E.; Wielgus-Kutrowska, Beata; Wolberger, Cynthia; Wolff, Martin; Wright, Edward; Wu, Yu-Sung; Wubben, Jacinta M.; Schuck, Peter
2015-01-01
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies. PMID:25997164
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NASA Astrophysics Data System (ADS)
Delile, H.; Mazzini, I.; Blichert-Toft, J.; Goiran, J. P.; Arnaud-Godet, F.; Salomon, F.; Albarède, F.
2014-03-01
From the 1st century AD and for the duration of the Roman Empire, the Portus complex was the main harbor of Rome. Its location on the Tiber delta next to the Tyrrhenian Sea produced rapid environmental changes that, together with historical vicissitudes, largely determined the fate of the harbor. We have assembled data on the mineralogy, sedimentology, geochemistry, and ostracod populations of a sediment core drilled in the access channel of the hexagonal basin of Trajan, with the expectation that such a combined data set will shed new light on how the connections of the inland Trajan basin with the Tiber river, the earlier Claudius harbor on the nearby shoreline, and the sea evolved through the centuries. The data define four distinct periods which geochemistry characterizes by different conditions of salinity and oxygenation. These in turn can be related to historical periods and events by means of 14C data. The early Imperial Period was dominated by input of well-oxygenated freshwater from the Tiber. During the Late Empire, harbor water became relatively more influenced by seawater and increasingly oxygen deficient, which attests to a decommissioning of the Canale Trasverso connecting the harbor to the Tiber. The strong anthropogenic signal, which is visible very clearly in geochemical parameters, attests to the human occupation of the harbor area up to the Early Middle Ages, when human activity was brought to an abrupt end. The simultaneous use in this study of multiple complementary tracers has allowed for the sedimentary sources of the different classes of particles in the harbor basin to be identified and assigned to either the freshwater supply from the Canale Trasverso or the seawater of the Claudius harbor.
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Targeting sediment management strategies using sediment quantification and fingerprinting methods
NASA Astrophysics Data System (ADS)
Sherriff, Sophie; Rowan, John; Fenton, Owen; Jordan, Phil; hUallacháin, Daire Ó.
2016-04-01
Cost-effective sediment management is required to reduce excessive delivery of fine sediment due to intensive land uses such as agriculture, resulting in the degradation of aquatic ecosystems. Prioritising measures to mitigate dominant sediment sources is, however, challenging, as sediment loss risk is spatially and temporally variable between and within catchments. Fluctuations in sediment supply from potential sources result from variations in land uses resulting in increased erodibility where ground cover is low (e.g., cultivated, poached and compacted soils), and physical catchment characteristics controlling hydrological connectivity and transport pathways (surface and/or sub-surface). Sediment fingerprinting is an evidence-based management tool to identify sources of in-stream sediments at the catchment scale. Potential sediment sources are related to a river sediment sample, comprising a mixture of source sediments, using natural physico-chemical characteristics (or 'tracers'), and contributions are statistically un-mixed. Suspended sediment data were collected over two years at the outlet of three intensive agricultural catchments (approximately 10 km2) in Ireland. Dominant catchment characteristics were grassland on poorly-drained soils, arable on well-drained soils and arable on moderately-drained soils. High-resolution (10-min) calibrated turbidity-based suspended sediment and discharge data were combined to quantify yield. In-stream sediment samples (for fingerprinting analysis) were collected at six to twelve week intervals, using time-integrated sediment samplers. Potential sources, including stream channel banks, ditches, arable and grassland field topsoils, damaged road verges and tracks were sampled, oven-dried (<40oC) and sieved (125 microns). Soil and sediment samples were analysed for mineral magnetics, geochemistry and radionuclide tracers, particle size distribution and soil organic carbon. Tracer data were corrected to account for particle size and organic matter selectivity processes. Contributions from potential sources type groups (channel - ditches and stream banks, roads - road verges and tracks, fields - grassland and arable topsoils) were statistically un-mixed using FR2000, an uncertainty-inclusive algorithm, and combined with sediment yield data. Results showed sediment contributions from channel, field and road groups were 70%, 25% and 5% in the poorly-drained catchment, 59%, 22% and 19% in the well-drained catchment, and 17%, 74% and 9% in the moderately-drained catchment. Higher channel contributions in the poorly-drained catchment were attributed to bank erosion accelerated by the rapid diversion of surface runoff into channels, facilitated by surface and sub-surface artificial drainage networks, and bank seepage from lateral pressure gradients due to confined groundwater. Despite the greatest proportion of arable soils in the well-drained catchment, this source was frequently hydrologically disconnected as well-drained soils largely infiltrated rainfall and prevented surface soil erosion. Periods of high and intense rainfall were associated with greater proportions of field losses in the well-drained catchment likely due to infiltration exceeding the saturated hydraulic conductivity of soils and establishment of surface hydrological connectivity. Losses from field topsoils dominated in the moderately-drained catchment as antecedent soil wetness maintained surface flow pathways and coincided with low groundcover on arable soils. For cost-effective management of sediment pressures to aquatic ecosystems, catchment specific variations in sediment sources must be considered.
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Gigadalton-scale shape-programmable DNA assemblies
NASA Astrophysics Data System (ADS)
Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik
2017-12-01
Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.
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Gigadalton-scale shape-programmable DNA assemblies.
Wagenbauer, Klaus F; Sigl, Christian; Dietz, Hendrik
2017-12-06
Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.
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The combination of direct and paired link graphs can boost repetitive genome assembly
Shi, Wenyu; Ji, Peifeng
2017-01-01
Abstract Currently, most paired link based scaffolding algorithms intrinsically mask the sequences between two linked contigs and bypass their direct link information embedded in the original de Bruijn assembly graph. Such disadvantage substantially complicates the scaffolding process and leads to the inability of resolving repetitive contig assembly. Here we present a novel algorithm, inGAP-sf, for effectively generating high-quality and continuous scaffolds. inGAP-sf achieves this by using a new strategy based on the combination of direct link and paired link graphs, in which direct link is used to increase graph connectivity and to decrease graph complexity and paired link is employed to supervise the traversing process on the direct link graph. Such advantage greatly facilitates the assembly of short-repeat enriched regions. Moreover, a new comprehensive decision model is developed to eliminate the noise routes accompanying with the introduced direct link. Through extensive evaluations on both simulated and real datasets, we demonstrated that inGAP-sf outperforms most of the genome scaffolding algorithms by generating more accurate and continuous assembly, especially for short repetitive regions. PMID:27924003
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Interactive effects of three pervasive marine stressors in a post-disturbance coral reef
NASA Astrophysics Data System (ADS)
Gil, Michael A.; Goldenberg, Silvan U.; Ly Thai Bach, Anne; Mills, Suzanne C.; Claudet, Joachim
2016-12-01
Ecosystems are commonly affected by natural, episodic disturbances that can abruptly and drastically alter communities. Although it has been shown that resilient ecosystems can eventually recover to pre-disturbed states, the extent to which communities in early stages of recovery could be affected by multiple anthropogenic stressors is poorly understood. Pervasive and rising anthropogenic stressors in coastal marine systems that could interactively affect the recovery of these systems following natural disturbances include high sedimentation, nutrient enrichment, and overfishing. Using a 6-month field experiment, we examined the effects of all combinations of these three stressors on key functional groups in the benthic community growing on simulated, post-disturbance reef patches within a system recovering from large-scale natural disturbances (corallivorous seastar outbreak and cyclone). Our study revealed that sedimentation, nutrient enrichment, and overfishing (simulated using exclusion cages) interactively affected coral survival and algal growth, with taxon-specific effects at multiple scales. First, our treatments affected corals and algae differently, with sedimentation being more detrimental to macroalgal growth but less detrimental to coral ( Porites rus) survival in caged plots, driving significant interactions between sedimentation and caging for both taxa. We also observed distinct responses between coral species and between algal functional groups, with the most extensive responses from algal turf biomass, for which sedimentation suppressed the synergistic (positive) combined effect of nutrient enrichment and caging. Our findings suggest that different combinations of ubiquitous anthropogenic stressors, related to either sea- or land-based activities, interactively influence community recovery from disturbance and may alter species compositions in the resulting community. Our findings further suggest that anthropogenic stressors could promote further degradation of coral reefs following natural disturbances by inhibiting recovery to coral-dominated states that provide vital ecosystem services to coastal populations worldwide.
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Large shift in source of fine sediment in the upper Mississippi River
Belmont, P.; Gran, K.B.; Schottler, S.P.; Wilcock, P.R.; Day, S.S.; Jennings, C.; Lauer, J.W.; Viparelli, E.; Willenbring, J.K.; Engstrom, D.R.; Parker, G.
2011-01-01
Although sediment is a natural constituent of rivers, excess loading to rivers and streams is a leading cause of impairment and biodiversity loss. Remedial actions require identification of the sources and mechanisms of sediment supply. This task is complicated by the scale and complexity of large watersheds as well as changes in climate and land use that alter the drivers of sediment supply. Previous studies in Lake Pepin, a natural lake on the Mississippi River, indicate that sediment supply to the lake has increased 10-fold over the past 150 years. Herein we combine geochemical fingerprinting and a suite of geomorphic change detection techniques with a sediment mass balance for a tributary watershed to demonstrate that, although the sediment loading remains very large, the dominant source of sediment has shifted from agricultural soil erosion to accelerated erosion of stream banks and bluffs, driven by increased river discharge. Such hydrologic amplification of natural erosion processes calls for a new approach to watershed sediment modeling that explicitly accounts for channel and floodplain dynamics that amplify or dampen landscape processes. Further, this finding illustrates a new challenge in remediating nonpoint sediment pollution and indicates that management efforts must expand from soil erosion to factors contributing to increased water runoff. ?? 2011 American Chemical Society.
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Fourney, Francesca; Figueiredo, Joana
2017-09-28
Corals worldwide are facing population declines due to global climate change and local anthropogenic impacts. Global climate change effects are hard to tackle but recent studies show that some coral species can better handle climate change stress when provided with additional energy resources. The local stressor that most undermines energy acquisition is sedimentation because it impedes coral heterotrophic feeding and their ability to photosynthesize. To investigate if reducing local sedimentation will enable corals to better endure ocean warming, we quantitatively assessed the combined effects of increased temperature and sedimentation (concentration and turbidity) on the survival of coral recruits of the species, Porites astreoides. We used sediment from a reef and a boat basin to mimic natural sediment (coarse) and anthropogenic (fine) sediment (common in dredging), respectively. Natural sediment did not negatively impact coral survival, but anthropogenic sediment did. We found that the capacity of coral recruits to survive under warmer temperatures is less compromised when anthropogenic sedimentation is maintained at the lowest level (30 mg.cm -2 ). Our study suggests that a reduction of US-EPA allowable turbidity from 29 Nephelometric Turbidity Units (NTU) above background to less than 7 NTU near coral reefs would facilitate coral recruit survival under current and higher temperatures.
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NASA Astrophysics Data System (ADS)
Maier, D. B.; Bigler, C.; Diehl, S.
2017-12-01
Diatom sediment assemblages are among the most important proxies for past climate and ecological condition reconstruction in aquatic environments, but the role of seasonality in the formation of diatom records is poorly understood. In this study we combine the diatom record of a varved sediment with year-round physico-chemical water column monitoring and the corresponding sequential sediment trap diatom record to disentangle the process information contained in a diatom sediment signal. The comparison of three consecutive annual diatom records indicates that the entire annual diatom sediment signal can be driven by winter air temperature induced timing of ice and snow melt and persistent under-ice stratification promoting an early diatom bloom under ice before spring lake over-turn. By contrast, in a year of late ice thinning when the chlorophyll a maximum occurred after spring lake over-turn, a more annually integrated diatom sediment signal was built buy a continuous diatom flux. The contrasting diatom records produced during years of different winter conditions have important implications for diatom based paleoecological reconstructions. Decadal records of sediment trap samples as well as long-term varved sediment records provide further support for the role of late winter and early spring weather conditions in determining sediment diatom assemblages.
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Structure-function characterization and optimization of a plant-derived antibacterial peptide.
Suarez, Mougli; Haenni, Marisa; Canarelli, Stéphane; Fisch, Florian; Chodanowski, Pierre; Servis, Catherine; Michielin, Olivier; Freitag, Ruth; Moreillon, Philippe; Mermod, Nicolas
2005-09-01
Crushed seeds of the Moringa oleifera tree have been used traditionally as natural flocculants to clarify drinking water. We previously showed that one of the seed peptides mediates both the sedimentation of suspended particles such as bacterial cells and a direct bactericidal activity, raising the possibility that the two activities might be related. In this study, the conformational modeling of the peptide was coupled to a functional analysis of synthetic derivatives. This indicated that partly overlapping structural determinants mediate the sedimentation and antibacterial activities. Sedimentation requires a positively charged, glutamine-rich portion of the peptide that aggregates bacterial cells. The bactericidal activity was localized to a sequence prone to form a helix-loop-helix structural motif. Amino acid substitution showed that the bactericidal activity requires hydrophobic proline residues within the protruding loop. Vital dye staining indicated that treatment with peptides containing this motif results in bacterial membrane damage. Assembly of multiple copies of this structural motif into a branched peptide enhanced antibacterial activity, since low concentrations effectively kill bacteria such as Pseudomonas aeruginosa and Streptococcus pyogenes without displaying a toxic effect on human red blood cells. This study thus identifies a synthetic peptide with potent antibacterial activity against specific human pathogens. It also suggests partly distinct molecular mechanisms for each activity. Sedimentation may result from coupled flocculation and coagulation effects, while the bactericidal activity would require bacterial membrane destabilization by a hydrophobic loop.
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Structure-Function Characterization and Optimization of a Plant-Derived Antibacterial Peptide
Suarez, Mougli; Haenni, Marisa; Canarelli, Stéphane; Fisch, Florian; Chodanowski, Pierre; Servis, Catherine; Michielin, Olivier; Freitag, Ruth; Moreillon, Philippe; Mermod, Nicolas
2005-01-01
Crushed seeds of the Moringa oleifera tree have been used traditionally as natural flocculants to clarify drinking water. We previously showed that one of the seed peptides mediates both the sedimentation of suspended particles such as bacterial cells and a direct bactericidal activity, raising the possibility that the two activities might be related. In this study, the conformational modeling of the peptide was coupled to a functional analysis of synthetic derivatives. This indicated that partly overlapping structural determinants mediate the sedimentation and antibacterial activities. Sedimentation requires a positively charged, glutamine-rich portion of the peptide that aggregates bacterial cells. The bactericidal activity was localized to a sequence prone to form a helix-loop-helix structural motif. Amino acid substitution showed that the bactericidal activity requires hydrophobic proline residues within the protruding loop. Vital dye staining indicated that treatment with peptides containing this motif results in bacterial membrane damage. Assembly of multiple copies of this structural motif into a branched peptide enhanced antibacterial activity, since low concentrations effectively kill bacteria such as Pseudomonas aeruginosa and Streptococcus pyogenes without displaying a toxic effect on human red blood cells. This study thus identifies a synthetic peptide with potent antibacterial activity against specific human pathogens. It also suggests partly distinct molecular mechanisms for each activity. Sedimentation may result from coupled flocculation and coagulation effects, while the bactericidal activity would require bacterial membrane destabilization by a hydrophobic loop. PMID:16127062
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Wang, Jingfu; Chen, Jingan; Guo, Jianyang; Sun, Qingqing; Yang, Haiquan
2018-04-01
Release of phosphorus (P) from sediment is a major source of P in many freshwater lakes. Currently, assessing the ability of sediment to release P, which is valuable to the management of water eutrophication, remains a challenge. Thus, the purpose of this study was to find effective indexes for predicting the release potential of internal-P. In this study, high-resolution diffusive gradients in thin films (DGT) and conventional sequential extraction were used to characterize the distribution and speciation of P, iron (Fe), and sulfur (S) in the surface sediment of a mildly eutrophic reservoir in southwestern China. Sediment samples exhibited large variations in Fe, S, and P, thereby providing favorable conditions for investigating the effects of Fe and S on sediment P mobilization. In contrast to traditional knowledge, our results show that total P (TP) and redox-sensitive P(BD-P) are poorly correlated with releasable P(DGT-P). This implies that high levels of sedimentary TP and BD-P do not necessarily result in an elevated release of internal-P under anaerobic conditions. Sedimentary P release was greatly suppressed at ratios of Fe/P > 30 and Fe/S > 6. Significant positive correlations between DGT-P and DGT-Fe or DGT-S suggest that Fe and S play an important role in governing the mobility of sedimentary P. These results support the combined Fe/P and Fe/S ratios as an effective and practicable index for assessing the ability of sediment to release P. Thus, our study provides a new and simple method for assessing sedimentary P pollution in freshwater ecosystems.
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Kreitsberg, Randel; Baršienė, Janina; Freiberg, Rene; Andreikėnaitė, Laura; Tammaru, Toomas; Rumvolt, Kateriina; Tuvikene, Arvo
2013-12-01
In North-East Estonia, considerable amounts of toxicants (e.g. polycyclic aromatic hydrocarbons (PAHs), phenols, heavy metals) leach into water bodies through discharges from the oil-shale industry. In addition, natural and anthropogenic hypoxic events in water bodies affect the health of aquatic organisms. Here we report a study on the combined effects of contaminated sediment and hypoxia on the physiology of gibel carp (Carssius auratus gibelio). We conducted a laboratory exposure study that involved exposure to polluted sediments from oil-shale industries (River Purtse) and sediments from a relatively clean environment (River Selja), together with sediments spiked with PAHs. The oxygen content (saturation vs. hypoxia (< 2 mg/L)) was changed to reflect hypoxia. A multi-biomarker approach was chosen to enable the combined effects to be assessed comprehensively and integratively. We used HPLC to measure the PAH concentration in sediment and fish muscle, fixed wavelength fluorescence (FF) analyses to indicate the presence of PAH metabolites in fish bile, and nuclear abnormalities in erythrocytes as markers of geno- and cyto-toxicity; and we monitored the change in body condition and measured EROD activity to indicate CYP1A induction. High levels of PAH conjugates in fish bile were found in the group exposed to the Purtse River sediment under hypoxia. The results suggested that induction of the CYP1A gene was modulated by hypoxia as well as by heavy metals. We found a correlation between several erythrocyte abnormalities (8-shaped nuclei and blebbed nuclei) and PAH metabolite content in fish. In conclusion, a measurable effect of pollution from the oil-shale industry on fish health parameters was clear under different oxygen levels. © 2013 Elsevier Inc. All rights reserved.
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Effects of Sediment Loading in Northern Europe During the Last Glacial
NASA Astrophysics Data System (ADS)
van der Wal, W.; IJpelaar, M.
2014-12-01
Over the years the framework of GIA modelling has been subject to continuous improvements, e.g. the addition of time dependent coastal margins and rotational feedback. The latest addition to this framework is the incorporation of sediment as a time-varying surface load while accounting for sea-level variations associated with the sediment transport (Dalca et al., GJI 2013). The effects of sediment loading during a glacial cycle have not been extensively investigated even though it is known that large sediment transport took place, for example in the Barents Sea region and Fennoscandia. This study investigates the effect of sediment transport on relative sea level change and present-day rates of gravity and vertical deformation in those regions. While the ice sheet history during the last glacial period has been modelled extensively there are no full-scale models of paleo-erosion and -deposition rates for regions such as Fennoscandia. Here we create end-member paleo-sedimentary models by combining geological observations of continuous erosion and deposition and large scale failure events. These models, in combination with the ICE-5G ice sheet history, serve as an input for a GIA model for a spherically symmetric incompressible Earth with the full sea-level equation. The results from this model, i.e. (rates of) relative sea level change and crustal deformation, are obtained for different viscosity models fitting best with the local rheology of Fennoscandia. By comparing GPS measurements, GRACE observations and relative sea level records with these modelled predictions the effects of sedimentary isostasy in the Fennoscandian region are studied. The sediment load does not significantly affect the modelled relative sea level curves, nor vertical deformation rates at the location of GPS measurements. However, gravity rates over the Barents Sea region are influenced significantly
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Late Quaternary glaciation of the Upper Soca River Region (Southern Julian Alps, NW Slovenia)
Bavec, Milos; Tulaczyk, Slawek M.; Mahan, Shannon; Stock, Gregory M.
2004-01-01
Extent of Late Quaternary glaciers in the Upper Soc??a River Region (Southern Julian Alps, SE Europe) has been analyzed using a combination of geological mapping, glaciological modeling, and sediment dating (radiocarbon, U/Th series and Infrared Stimulated Luminescence-IRSL). Field investigations focused mainly on relatively well preserved Quaternary sequences in the Bovec Basin, an intramontane basin located SW of the Mediterranean/Black Sea divide and surrounded by mountain peaks reaching from approximately 2100 up to 2587 m a.s.l. Within the Basin we recognized two Late Quaternary sedimentary assemblages, which consist of the same facies association of diamictons, laminated lacustrine deposits and sorted fluvial sediments. Radiocarbon dating of the upper part of the lake sediments sequence (between 12790??85 and 5885??60 14C years b.p.) indicates that the younger sedimentary assemblage was deposited during the last glacial maximum and through early Holocene (Marine Isotope Stage 21, MIS 2-1). Sediment ages obtained for the older assemblage with U/Th and IRSL techniques (between 154.74??22.88 and 129.93??7.90 ka b.p. for selected samples) have large errors but both methods yield results consistent with deposition during the penultimate glacial-interglacial transition (MIS 6-5). Based on analyses of field data combined with glaciological modeling, we argue that both sediment complexes formed due to high sediment productivity spurred by paraglacial conditions with glaciers present in the uplands around the Bovec Basin but not extending down to the basin floor. Our study shows that the extent and intensity of direct glacial sedimentation by Late Quaternary glaciers in the region was previously significantly overestimated. ?? 2004 Elsevier B.V. All rights reserved.
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Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik
2017-01-01
Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO 2 ) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase ( amoA ) and bacterial nitrite reductase ( nirS ) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO 2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes ( amoA and nirS ) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.
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Macdonald, Tara A; Burd, Brenda J; van Roodselaar, Albert
2012-01-01
Size distributions of biotic assemblages are important modifiers of productivity and function in marine sediments. We investigated the distribution of proportional organic biomass among logarithmic size classes (2(-6)J to 2(16)J) in the soft-bottom macrofaunal communities of the Strait of Georgia, Salish Sea on the west coast of Canada. The study examines how size structure is influenced by 3 fundamental habitat descriptors: depth, sediment percent fines, and organic flux (modified by quality). These habitat variables are uncorrelated in this hydrographically diverse area, thus we examine their effects in combination and separately. Cluster analyses and cumulative biomass size spectra reveal clear and significant responses to each separate habitat variable. When combined, habitat factors result in three distinct assemblages: (1) communities with a high proportion of biomass in small organisms, typical of shallow areas (<10 m) with coarse sediments (<10% fines) and low accumulation of organic material (<3.0 gC/m(2)/yr/δ(15)N); (2) communities with high proportion of biomass in the largest organisms found in the Strait, typical of deep, fine sediments with high modified organic flux (>3 g C/m(2)/yr/δ(15)N) from the Fraser River; and (3) communities with biomass dominated by moderately large organisms, but lacking the smallest and largest size classes, typical of deep, fine sediments experiencing low modified organic flux (<3.0 gC/m(2)/yr/δ(15)N). The remaining assemblages had intermediate habitat types and size structures. Sediment percent fines and flux appear to elicit threshold responses in size structure, whereas depth has the most linear influence on community size structure. The ecological implications of size structure in the Strait of Georgia relative to environmental conditions, secondary production and sediment bioturbation are discussed.
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Sensitivity analysis of non-cohesive sediment transport formulae
NASA Astrophysics Data System (ADS)
Pinto, Lígia; Fortunato, André B.; Freire, Paula
2006-10-01
Sand transport models are often based on semi-empirical equilibrium transport formulae that relate sediment fluxes to physical properties such as velocity, depth and characteristic sediment grain sizes. In engineering applications, errors in these physical properties affect the accuracy of the sediment fluxes. The present analysis quantifies error propagation from the input physical properties to the sediment fluxes, determines which ones control the final errors, and provides insight into the relative strengths, weaknesses and limitations of four total load formulae (Ackers and White, Engelund and Hansen, van Rijn, and Karim and Kennedy) and one bed load formulation (van Rijn). The various sources of uncertainty are first investigated individually, in order to pinpoint the key physical properties that control the errors. Since the strong non-linearity of most sand transport formulae precludes analytical approaches, a Monte Carlo method is validated and used in the analysis. Results show that the accuracy in total sediment transport evaluations is mainly determined by errors in the current velocity and in the sediment median grain size. For the bed load transport using the van Rijn formula, errors in the current velocity alone control the final accuracy. In a final set of tests, all physical properties are allowed to vary simultaneously in order to analyze the combined effect of errors. The combined effect of errors in all the physical properties is then compared to an estimate of the errors due to the intrinsic limitations of the formulae. Results show that errors in the physical properties can be dominant for typical uncertainties associated with these properties, particularly for small depths. A comparison between the various formulae reveals that the van Rijn formula is more sensitive to basic physical properties. Hence, it should only be used when physical properties are known with precision.
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NASA Astrophysics Data System (ADS)
Lantzsch, Hendrik; Hanebuth, Till J. J.; Horry, Jan; Grave, Marina; Rebesco, Michele; Schwenk, Tilmann
2017-10-01
High-resolution sediment echosounder data combined with radiocarbon-dated sediment cores allowed us to reconstruct the Late Quaternary stratigraphic architecture of the Kveithola Trough and surrounding Spitsbergenbanken. The deposits display the successive deglacial retreat of the Svalbard-Barents Sea Ice Sheet. Basal subglacial till indicates that the grounded ice sheet covered both bank and trough during the Late Weichselian. A glaciomarine blanket inside the trough coinciding with laminated plumites on the bank formed during the initial ice-melting phase from at least 16.1 to 13.5 cal ka BP in close proximity to the ice margin. After the establishment of open-marine conditions at around 13.5 cal ka BP, a sediment drift developed in the confined setting of the Kveithola Trough, contemporary with crudely laminated mud, an overlying lag deposit, and modern bioclastic-rich sand on Spitsbergenbanken. The Kveithola Drift shows a remarkable grain-size coarsening from the moat towards the southern flank of the trough. This trend contradicts the concept of a separated drift (which would imply coarser grain sizes in proximity of the moat) and indicates that the southern bank is the main sediment source for the coarse material building up the Kveithola Drift. This depocenter represents, therefore, a yet undescribed combination of off-bank wedge and confined drift. Although the deposits inside Kveithola Trough and on Spitsbergenbanken display different depocenter geometries, time-equivalent grain-size changes imply a region-wide sediment-dynamic connection. We thus relate a phase of coarsest sediment supply (8.8-6.3 cal ka BP) to an increase in bottom current strength, which might be related to a stronger Atlantic Water inflow from the Southeast across the bank leading to winnowing and off-bank export of sandy sediments.
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Macdonald, Tara A.; Burd, Brenda J.; van Roodselaar, Albert
2012-01-01
Size distributions of biotic assemblages are important modifiers of productivity and function in marine sediments. We investigated the distribution of proportional organic biomass among logarithmic size classes (2−6J to 216J) in the soft-bottom macrofaunal communities of the Strait of Georgia, Salish Sea on the west coast of Canada. The study examines how size structure is influenced by 3 fundamental habitat descriptors: depth, sediment percent fines, and organic flux (modified by quality). These habitat variables are uncorrelated in this hydrographically diverse area, thus we examine their effects in combination and separately. Cluster analyses and cumulative biomass size spectra reveal clear and significant responses to each separate habitat variable. When combined, habitat factors result in three distinct assemblages: (1) communities with a high proportion of biomass in small organisms, typical of shallow areas (<10 m) with coarse sediments (<10% fines) and low accumulation of organic material (<3.0 gC/m2/yr/δ15N); (2) communities with high proportion of biomass in the largest organisms found in the Strait, typical of deep, fine sediments with high modified organic flux (>3 g C/m2/yr/δ15N) from the Fraser River; and (3) communities with biomass dominated by moderately large organisms, but lacking the smallest and largest size classes, typical of deep, fine sediments experiencing low modified organic flux (<3.0 gC/m2/yr/δ15N). The remaining assemblages had intermediate habitat types and size structures. Sediment percent fines and flux appear to elicit threshold responses in size structure, whereas depth has the most linear influence on community size structure. The ecological implications of size structure in the Strait of Georgia relative to environmental conditions, secondary production and sediment bioturbation are discussed. PMID:22911694
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Moisture and Structural Analysis for High Performance Hybrid Wall Assemblies
DOE Office of Scientific and Technical Information (OSTI.GOV)
Grin, A.; Lstiburek, J.
2012-09-01
Based on past experience in the Building America program, BSC has found that combinations of materials and approaches—in other words, systems—usually provide optimum performance. Integration is necessary, as described in this research project. The hybrid walls analyzed utilize a combination of exterior insulation, diagonal metal strapping, and spray polyurethane foam and leave room for cavity-fill insulation. These systems can provide effective thermal, air, moisture, and water barrier systems in one assembly and provide structure.
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The nature and pollutant role of solids at the water-sediment interface in combined sewer networks.
Chebbo, G; Ashley, R; Gromaire, M C
2003-01-01
Solids at the water-sediment interface in combined sewers are known to be important for pollution potential during storm washout via CSOs. They have been investigated in several studies, but nonetheless, little is known about the origins, build-up, transport and nature of these solids. From a review of current knowledge it is apparent that whilst there is general agreement that these solids are largely organic and have high polluting potential, their modes of transport and definition are not generally agreed upon. It is possible that there may be several "types" of these solids, defined as either: "near bed solids" or "fluid sediments/dense undercurrents", possibly representing transport modes in flows with different ranges of ambient (dry weather) velocities and with differing sewerage layouts. Current knowledge is presented and new ideas for resolving the uncertainties regarding the nature, movement and effects of this material are outlined.
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Xing, Zi-Peng; Sun, De-Zhi
2009-09-15
Attempts were made in this study to examine the combined polyferric sulfate (PFS) coagulation, Fenton and sedimentation process for treatment of non-degradable antibiotic fermentation wastewater. The experimental results indicated that 66.6% of color and 72.4% of chemical oxygen demand (COD) were removed under the optimum conditions of PFS dosage 200mg/L and pH 4.0. In addition, optimal parameters of Fenton process were determined to be 150 mg/L of H(2)O(2) dosage, 120 mg/L of FeSO(4) and 1h of reaction time. When Fenton treated effluent was controlled at pH 7.0, the pollutants could be further removed by sedimentation process. The overall color, COD and suspended solids (SS) removal reached 97.3%, 96.9% and 86.7% under selected conditions, respectively. Thus this study might offer an effective way for wastewater treatment of antibiotics manufacturer and pharmaceutical industry.
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Monitoring stream sediment loads in response to agriculture in Prince Edward Island, Canada.
Alberto, Ashley; St-Hilaire, Andre; Courtenay, Simon C; van den Heuvel, Michael R
2016-07-01
Increased agricultural land use leads to accelerated erosion and deposition of fine sediment in surface water. Monitoring of suspended sediment yields has proven challenging due to the spatial and temporal variability of sediment loading. Reliable sediment yield calculations depend on accurate monitoring of these highly episodic sediment loading events. This study aims to quantify precipitation-induced loading of suspended sediments on Prince Edward Island, Canada. Turbidity is considered to be a reasonably accurate proxy for suspended sediment data. In this study, turbidity was used to monitor suspended sediment concentration (SSC) and was measured for 2 years (December 2012-2014) in three subwatersheds with varying degrees of agricultural land use ranging from 10 to 69 %. Comparison of three turbidity meter calibration methods, two using suspended streambed sediment and one using automated sampling during rainfall events, revealed that the use of SSC samples constructed from streambed sediment was not an accurate replacement for water column sampling during rainfall events for calibration. Different particle size distributions in the three rivers produced significant impacts on the calibration methods demonstrating the need for river-specific calibration. Rainfall-induced sediment loading was significantly greater in the most agriculturally impacted site only when the load per rainfall event was corrected for runoff volume (total flow minus baseflow), flow increase intensity (the slope between the start of a runoff event and the peak of the hydrograph), and season. Monitoring turbidity, in combination with sediment modeling, may offer the best option for management purposes.
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NASA Astrophysics Data System (ADS)
Hürkamp, Kerstin; Völkel, Jörg; Winkelbauer, Jennifer; Leopold, Matthias; Bens, Oliver; Heine, Klaus
2010-05-01
Many studies deal with geoarchives such as dunes, fluvial and slope sediments, pans, speleothems and paleosoils, but often investigations are spatially limited or carried out on isolated landforms. Large-scaled, geochronologic and geomorphologic stratigraphies as well as generally accepted reconstructions of the paleoclimate are still missing for the southern African subcontinent. Only combining records of all geoarchives, and particularly the analysis of sediment interstratifications, would promise good results. For several relief generations of southern Africa, lots of sediment dating already exists, even if methodological and environmental problems delimit the radiocarbon (14C), optic stimulated or thermic luminescence (OSL/TL) chronologies. They illustrate fluctuating climates with a general trend to increasing aridity throughout the Quaternary. Periods of less precipitation led to the development of eolian sediments, while moister periods led to the development of lacustrine-fluvial sediments. Other investigations indicate both processes coexisted, as they did in the SW-Kalahari during the last glacial maximum (LGM). The study areas will be selected according to results of the authors' former field trips and using remote sensing methods. The Molopo River catchment in the south Kalahari is already selected as one major study site. It is highly applicable for paleoclimate research because of its location within the semi-arid to semi-humid Kalahari, which is a region with enormous climatic fluctuations due to recent and former shifts of tropical and subtropical circulation patterns and changing climatic factors. During the Last Glacial Maximum at approximately 24°S, a transition zone existed that was characterized by the overlap of alternating dry and cool climates in the north (summer rains), and cold and moist winters in the south. In the Late Glacial and Holocene period this boundary was shifted southwards. Here dunes and pans coexist as major Kalahari geomorphological types in an ideal way, with the Molopo River valley, including different fluvial sediment facies, interbedded with slope and eolian sediments, as well as the confluence of the Molopo and Orange River systems. Regarding the methods, a combination of sedimentologic, pedologic and geomorphologic field and laboratory work, as well as geophysical prospection of the shallow subsurface and remote sensing will be carried out. Chronological records of erosion and accumulation processes will be obtained by 14C- and OSL sediment datings. The combination of remote sensing methods by the means of aerial photographs (hyperspectral data of HyMAP and CHRIS-Proba) and geomorphological/sedimentological field and laboratory work (ground truth) provides diagnostic parameters of the sediments which will help to differentiate the geoarchives to improve the paleoenvironmental interpretation. The results of two first field campaigns in 2009 are presented including sediment descriptions, laboratory analyses and 14C-ages. The results of OSL dating are not yet available.
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Superrepression through Altered Corepressor-Activated Protein:Protein Interactions.
He, Chenlu; Custer, Gregory; Wang, Jingheng; Matysiak, Silvina; Beckett, Dorothy
2018-02-20
Small molecules regulate transcription in both eukaryotes and prokaryotes by either enhancing or repressing assembly of transcription regulatory complexes. For allosteric transcription repressors, superrepressor mutants can exhibit increased sensitivity to small molecule corepressors. However, because many transcription regulatory complexes assemble in multiple steps, the superrepressor phenotype can reflect changes in any or all of the individual assembly steps. Escherichia coli biotin operon repression complex assembly, which responds to input biotin concentration, occurs via three coupled equilibria, including corepressor binding, holorepressor dimerization, and binding of the dimer to DNA. A genetic screen has yielded superrepressor mutants that repress biotin operon transcription in vivo at biotin concentrations much lower than those required by the wild type repressor. In this work, isothermal titration calorimetry and sedimentation measurements were used to determine the superrepressor biotin binding and homodimerization properties. The results indicate that, although all variants exhibit biotin binding affinities similar to that measured for BirA wt , five of the six superrepressors show altered homodimerization energetics. Molecular dynamics simulations suggest that the altered dimerization results from perturbation of an electrostatic network that contributes to allosteric activation of BirA for dimerization. Modeling of the multistep repression complex assembly for these proteins reveals that the altered sensitivity of the transcription response to biotin concentration is readily explained solely by the altered superrepressor homodimerization energetics. These results highlight how coupled equilibria enable alterations in a transcription regulatory response to input signal through an indirect mechanism.
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The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity.
Zhao, Huaying; Balbo, Andrea; Brown, Patrick H; Schuck, Peter
2011-05-01
Sedimentation velocity (SV) experiments of heterogeneous interacting systems exhibit characteristic boundary structures that can usually be very easily recognized and quantified. For slowly interacting systems, the boundaries represent concentrations of macromolecular species sedimenting at different rates, and they can be interpreted directly with population models based solely on the mass action law. For fast reactions, migration and chemical reactions are coupled, and different, but equally easily discernable boundary structures appear. However, these features have not been commonly utilized for data analysis, for the lack of an intuitive and computationally simple model. The recently introduced effective particle theory (EPT) provides a suitable framework. Here, we review the motivation and theoretical basis of EPT, and explore practical aspects for its application. We introduce an EPT-based design tool for SV experiments of heterogeneous interactions in the software SEDPHAT. As a practical tool for the first step of data analysis, we describe how the boundary resolution of the sedimentation coefficient distribution c(s) can be further improved with a Bayesian adjustment of maximum entropy regularization to the case of heterogeneous interactions between molecules that have been previously studied separately. This can facilitate extracting the characteristic boundary features by integration of c(s). In a second step, these are assembled into isotherms as a function of total loading concentrations and fitted with EPT. Methods for addressing concentration errors in isotherms are discussed. Finally, in an experimental model system of alpha-chymotrypsin interacting with soybean trypsin inhibitor, we show that EPT provides an excellent description of the experimental sedimentation boundary structure of fast interacting systems. Published by Elsevier Inc.
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Sediment cores were collected at three sites from the Lower Taunton River in Narragansett Bay, MA, dated and examined for PCBs. At each site, PCBs first appear in the sediment cores at depths corresponding to 1929 based on a combination of radiometric and anthropogenic dating pr...
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NASA Astrophysics Data System (ADS)
Belyaev, Vladimir; Feoktistov, Artem; Huygens, Dries; Shamshurina, Eugenia; Golosov, Valentin
2014-05-01
Understanding hydrological response and geomorphic behavior of small catchments in urban environments, especially those experiencing urban expansion, represents serious and important problem which has not yet been given an adequate research attention. Urbanization exerts profound and diverse impacts on catchment characteristics, particularly by increasing surface runoff coefficients, peak flow discharges and rates of flash flood waves propagation as a result of widespread appearance of buildings and paved surfaces with practically zero infiltration capacities. Another essential influence of urbanization on small catchment hydrological regimes is associated with significant changes of natural topography (from relatively minor modifications such as grading of steeper slopes to complete transformations including total filling of gullies and small valleys, transfer of small streams from surface into underground pipes or collectors, etc.) combined with creation of systems of concrete-protected surface drainages and underground storm flow sewages. Such activities can result in substantial changes of runoff- and sediment-contributing areas for the remaining gullies and small valleys in comparison to the pre-urbanization conditions, causing dramatic increase of fluvial activity in some of those and much lower flow discharges in others. In addition, gullies and small valleys in urban settlements often become sites of dumping for both dry and liquid domestic and industrial wastes, thus being major pathways for dissolved and particle-bound pollutant transfer into perennial streams and rivers. All the problems listed require detailed hydrological and geomorphic investigations in order to provide sound basis for developing appropriate measures aimed to control and decrease urban erosion, sediment redistribution, pollution of water bodies, damage to constructions and communications. Recent advances in sediment tracing and fingerprinting techniques provide promising opportunities for distinguishing contributions of different sediment sources into catchment sediment budgets on a reliable quantitative basis. In combination with microstratigraphic differentiation and dating of sediment in continuous deposition zones by 137Cs depth distribution curves and available land use records, spatial and temporal variability of sediment sources and sinks can be reconstructed for the last several decades. That is especially important for catchments which experienced profound land use changes such as transition from pristine or agriculture-dominated to urbanized environment. The example presented here describes the results of reconstruction of changing sediment source types, contributions and spatial patterns for small reservoir catchment within the city of Kursk (Sredenerusskaya Upland, Central European Russia). Combination of compound specific stable isotopes, 137Cs, sediment grain size composition, land use information for several time intervals and daily rainfall record for the Kursk meteorological station (conveniently located within the study catchment) have been employed in order to evaluate major sediment sources within the catchment, their spatial pattern and temporal changes and compare those to history of reservoir sedimentation. The reservoir is situated on the Kur River - small river which gave its name to the city itself. The dam and reservoir were constructed and put into operation in 1969, thus the beginning of its infill is located stratigraphically later than the main peak of the global 137Cs fallout. It has been found that transition from dominantly agricultural land use to urbanized conditions caused decrease of contribution of soil erosion from cultivated land and increase of that of the active gullies into reservoir sedimentation. However, it is important to note that during extreme runoff events contribution of sediment originated from soil erosion on arable land still remains dominant, even though its area within the catchment recently became very limited.
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Chemistry and photochemistry of low-volatility organic chemicals on environmental surfaces
DOE Office of Scientific and Technical Information (OSTI.GOV)
Miller, G.C.; Hebert, V.R.; Zepp, R.G.
Hydrophobic organic xenobiotics such as polychlorinated dibenzodioxins and polycyclic aromatic hydrocarbons have strong tendencies to sorb on environmental surfaces. This paper summarizes a workshop in which scientists and modelers assembled to discuss nonbiological processes that affect sorption to soil or sediment surfaces and on atmospheric particles. The 20 scientists discussed a variety of topics with a major emphasis on the fate of chlorinated dioxins. The topics include transformation processes, mobility of organic pollutants, fate of organics, and evaluative fate models.
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Linking Monsoon Activity with River-Derived Sediment Deposition in the northern South China Sea
NASA Astrophysics Data System (ADS)
Ge, Q.; Xue, Z. G.; Liu, P.; Chu, F.
2016-02-01
Sediments retrieved from a gravity core were analyzed to examine the connection between East Asian Monsoon (EAM) and river-derived sediment deposition on the continental slope in the South China Sea since the Last Glacial Maximum. Combined clay mineralogy and grain size index analysis provided evidence of the sources of fine-grained sediment as well as for rebuilding the history of paleo-EAM. A shift of sediment source from the Pearl River to southwestern Taiwanese rivers was identified during the Holocene. The 4-8μm grain size fraction, as an environmental sensitive component and thus the EAM proxy, indicated the local deposition environment is mainly controlled by sea-level variations. And during the Holocene, the East Asian summer monsoon exhibited an in-phase relationship with East Asian winter monsoon, both following variations of the insolation intensity.
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Brakebill, J.W.; Ator, S.W.; Schwarz, G.E.
2010-01-01
We describe the sources and transport of fluvial suspended sediment in nontidal streams of the Chesapeake Bay watershed and vicinity. We applied SPAtially Referenced Regressions on Watershed attributes, which spatially correlates estimated mean annual flux of suspended sediment in nontidal streams with sources of suspended sediment and transport factors. According to our model, urban development generates on average the greatest amount of suspended sediment per unit area (3,928 Mg/km2/year), although agriculture is much more widespread and is the greatest overall source of suspended sediment (57 Mg/km2/year). Factors affecting sediment transport from uplands to streams include mean basin slope, reservoirs, physiography, and soil permeability. On average, 59% of upland suspended sediment generated is temporarily stored along large rivers draining the Coastal Plain or in reservoirs throughout the watershed. Applying erosion and sediment controls from agriculture and urban development in areas of the northern Piedmont close to the upper Bay, where the combined effects of watershed characteristics on sediment transport have the greatest influence may be most helpful in mitigating sedimentation in the bay and its tributaries. Stream restoration efforts addressing floodplain and bank stabilization and incision may be more effective in smaller, headwater streams outside of the Coastal Plain. ?? 2010 American Water Resources Association. No claim to original U.S. government works.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Bombardier, M.; Bermingham, N.
1999-04-01
This article introduces the sediment Toxicity (SED-TOX) Index for the assessment and ranking of toxic hazards in sediment. Major features include expression of toxicity responses on a single scale of measurement (dry weight-based toxic units), consideration of multiple routes of exposure (pore water, organic extract, wet sediment, and whole sediment), application of differential treatments to toxicity data depending on the level of response, and use of weighting factors to discriminate sediment exposure phases and effect endpoints on the basis of sensitivity. A battery of seven bioassays with four test species (Vibrio fischeri, Escherichia coli, Lytechinus pictus, and Amphiporeia virginiana) wasmore » conducted on 49 marine sediment samples collected from six sites at Anse-a-Beaufils and Cap-aux-Meules, which are in the Gulf of St. Lawrence. The SED-TOX scores were calculated for each sampling station and compared with sediment contaminant concentrations. Results indicate that physico-chemical characterization is not sufficient to assess contaminated-sediment hazard for organisms; furthermore, using several exposure phases and test species belonging to various trophic levels increases the possibility of correctly identifying toxic sediments. The results of this study indicate that the SED-TOX approach is valuable as a toxicity assessment and ranking tool for sediments. It could easily be combined with other measures of ecosystem disturbance to discriminate between polluted and unpolluted sites.« less
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Al-Chokhachy, Robert K.; Black, Tom A.; Thomas, Cameron; Luce, Charlie H.; Rieman, Bruce; Cissel, Richard; Carlson, Anne; Hendrickson, Shane; Archer, Eric K.; Kershner, Jeffrey L.
2016-01-01
Unpaved forest roads remain a pervasive disturbance on public lands and mitigating sediment from road networks remains a priority for management agencies. Restoring roaded landscapes is becoming increasingly important for many native coldwater fishes that disproportionately rely on public lands for persistence. However, effectively targeting restoration opportunities requires a comprehensive understanding of the effects of roads across different ecosystems. Here, we combine a review and a field study to evaluate the status of knowledge supporting the conceptual framework linking unpaved forest roads with streambed sediment. Through our review, we specifically focused on those studies linking measures of the density of forest roads or sediment delivery with empirical streambed sediment measures. Our field study provides an example of a targeted effort of linking spatially explicit estimates of sediment production with measures of streambed sediment. Surprisingly, our review uncovered few studies (n = 8) that empirically tested the conceptual framework linking unpaved forest roads and streambed sediment, and the results varied considerably. Field results generally supported the conceptual model that unpaved forest roads can control streambed sediment quality, but demonstrated high-spatial variability in the effects of forest roads on streambed sediment and the need to address hotspots of sediment sources. The importance of context in the effects of forest roads is apparent in both our review and field data, suggesting the need for in situ studies to avoid misdirected restoration actions.
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High-Rate Assembly of Nanomaterials on Insulating Surfaces Using Electro-Fluidic Directed Assembly.
Yilmaz, Cihan; Sirman, Asli; Halder, Aditi; Busnaina, Ahmed
2017-08-22
Conductive or semiconducting nanomaterials-based applications such as electronics and sensors often require direct placement of such nanomaterials on insulating surfaces. Most fluidic-based directed assembly techniques on insulating surfaces utilize capillary force and evaporation but are diffusion limited and slow. Electrophoretic-based assembly, on the other hand, is fast but can only be utilized for assembly on a conductive surface. Here, we present a directed assembly technique that enables rapid assembly of nanomaterials on insulating surfaces. The approach leverages and combines fluidic and electrophoretic assembly by applying the electric field through an insulating surface via a conductive film underneath. The approach (called electro-fluidic) yields an assembly process that is 2 orders of magnitude faster compared to fluidic assembly. By understanding the forces on the assembly process, we have demonstrated the controlled assembly of various types of nanomaterials that are conducting, semiconducting, and insulating including nanoparticles and single-walled carbon nanotubes on insulating rigid and flexible substrates. The presented approach shows great promise for making practical devices in miniaturized sensors and flexible electronics.
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Sediment retention in a bottomland hardwood wetland in Eastern Arkansas
Kleiss, B.A.
1996-01-01
One of the often-stated functions of wetlands is their ability to remove sediments and other particulates from water, thus improving water quality in the adjacent aquatic system. However, actual rates of suspended sediment removal have rarely been measured in freshwater wetland systems. To address this issue, suspended sediment dynamics were measured in a 85-km2 bottomland hardwood (BLH) wetland adjacent to the highly turbid Cache River in eastern Arkansas during the 1988-1990 water years. A suspended sediment mass balance was calculated using depth-integrated, flow-weighted daily measurements at wetland inflow and outflow points. Over the three-year period, suspended sediment load decreased an average of 14% between upstream and downstream sampling points. To test the idea that the suspended sediments were retained by the adjacent wetland and to determine what portion of the BLH forest was most responsible for retaining the suspended sediments, concurrent measurements of sediment accretion were made at 30 sites in the wetland using feldspar clay marker horizons, sedimentation disks, the 137cesium method, and dendrogeomorphic techniques. Sedimentation rates exceeding 1 cm/yr were measured in frequently flooded areas dominated by Nyssa aquatica and Taxodium distichum. Maximum sedimentation rates did not occur on the natural levee, as would be predicted by classical fluvial geomorphology, but in the "first bottom," where retention time of the water reached a maximum. Multiple regression was used to relate sedimentation rates with several physical and biological factors. A combination of distance from the river, flood duration, and tree basal area accounted for nearly 90% of the variation in sedimentation rates.
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NASA Astrophysics Data System (ADS)
Yang, Qi; Lan, Fang; Yi, Qiangying; Wu, Yao; Gu, Zhongwei
2015-10-01
A combination strategy of the inverse emulsion crosslinking approach and the colloidal assembly technique is first proposed to synthesize Fe3O4/histidine composite nanoclusters as new-type magnetic porous nanomaterials. The nanoclusters possess uniform morphology, high magnetic content and excellent protein adsorption capacity, exhibiting their great potential for bio-separation.A combination strategy of the inverse emulsion crosslinking approach and the colloidal assembly technique is first proposed to synthesize Fe3O4/histidine composite nanoclusters as new-type magnetic porous nanomaterials. The nanoclusters possess uniform morphology, high magnetic content and excellent protein adsorption capacity, exhibiting their great potential for bio-separation. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c5nr05800g
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Thomas, Michael; Anglim Lagones, Thomas; Judd, Martyna; Morshedi, Mahbod; O'Mara, Megan L; White, Nicholas G
2017-07-04
A combination of molecular dynamics (MD), NMR spectroscopy, and single crystal X-ray diffraction (SCXRD) techniques was used to probe the self-assembly of para- and meta-bis(amidinium) compounds with para-, meta-, and ortho-dicarboxylates. Good concordance was observed between the MD and experimental results. In DMSO solution, the systems form several rapidly exchanging assemblies, in part because a range of hydrogen bonding interactions is possible between the amidinium and carboxylate moieties. Upon crystallization, the majority of the systems form 1D supramolecular polymers, which are held together by short N-H⋅⋅⋅O hydrogen bonds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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NASA Astrophysics Data System (ADS)
Sinha, R.; Mishra, K.; Swrankar, S.; Jain, V.; Nepal, S.; Uddin, K.
2017-12-01
Sediment flux of large tropical rivers is strongly influenced by the degree of linkage between the sediments sources and sink (i.e. sediment connectivity). Sediment connectivity, especially at the catchment scale, depends largely on the morphological characteristics of the catchment such as relief, terrain roughness, slope, elevation, stream network density and catchment shape and the combined effects of land use, particularly vegetation. Understanding the spatial distribution of sediment connectivity and its temporal evolution can be useful for the characterization of sediment source areas. Specifically, these areas represent sites of instability and their connectivity influences the probability of sediment transfer at a local scale that will propagate downstream through a feedback system. This paper evaluates the morphodynamics and sediment connectivity of the Kosi basin in Nepal and India at various spatial and temporal scales. Our results provide the first order assessment of the spatial sediment connectivity in terms of the channel connectivity (IC outlet) and source to channel connectivity (IC channel) of the upstream and midstream Kosi basin. This assessment helped in the characterization of sediment dynamics in the complex morphological settings and in a mixed environment. Further, Revised Universal Soil Loss Equation (RUSLE) was used to quantify soil erosion and sediment transport capacity equation is used to quantify sediment flux at each cell basis. Sediment Delivery Ratio (SDR) was calculated for each sub-basin to identify the sediment production and transport capacity limited sub-basin. We have then integrated all results to assess the sediment flux in the Kosi basin in relation to sediment connectivity and the factors controlling the pathways of sediment delivery. Results of this work have significant implications for sediment management of the Kosi river in terms of identification of hotspots of sediment accumulation that will in turn be manifested in morphodynamics of the river in the alluvial reaches.
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NASA Astrophysics Data System (ADS)
Stroup, J. S.; Kelly, M. A.; Lowell, T. V.; Smith, C.; Beal, S. A., Jr.; Tapia, P. M.
2016-12-01
The past fluctuations of Quelccaya Ice Cap (QIC) are an indicator of tropical paleoclimate. At QIC, ice core and glacial geological records provide late Holocene climate constraints. However, early and middle Holocene QIC fluctuations are less well-known. To interpret past QIC fluctuations, we present Holocene-long lake sediment records from Challpacocha, a lake fed by QIC meltwater, and Yanacocha, a lake that has not received meltwater during the Holocene. To assess the clastic sediment delivered to Challpacocha by QIC meltwater, we compare visual stratigraphy, X-ray fluorescence chemistry, grainsize, loss on ignition and clastic flux records from both lakes (additional Yanacocha proxies are presented by Axford et al. (this meeting, abstract 157985)). We compare the meltwater derived clastic sediment record from Challpacocha with moraine and stratigraphic records of past ice extents during the late Holocene. This comparison indicates that clastic sediment flux in Challpacocha increased during QIC recession and decreased during QIC advance, or significantly reduced QIC extent. We then use the Challpacocha clastic sediment record to interpret early and middle Holocene QIC fluctuations. Based on the Challpacocha sediment record, combined with prior work, we suggest that from 11 to 6.5 ka QIC was similar to or smaller than its late Holocene extent. From 6.9 to 6.5 ka QIC may have been absent from the landscape. At 3-2.4 and 0.62-0.31 ka QIC experienced the most extensive Holocene fluctuations. We compare the clastic sediment fluxes from Challpacocha and Pacococha (a nearby lake fed by QIC; Rodbell et al., 2008) to infer QIC expansion between 6.5-5 ka. This is supported by 14C ages of in-situ subfossil plants which indicate ice advance at 6.3-4.7 ka (Thompson et al., 2006, 2013; Buffen et al., 2009). Our study highlights the value of using multiple datasets to improve lake sediment record interpretations.
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NASA Astrophysics Data System (ADS)
Miller, A. J.; Allison, M. A.; Bianchi, T. S.; Marcantonio, F.
2012-12-01
Sediment cores collected from Simpson Lagoon on the inner Beaufort Sea shelf adjacent to the Colville River delta, AK are being utilized to develop new, high-resolution (sub-decadal scale) archives of the 0-3,000 year Arctic paleoclimate record necessary to assess natural and anthropogenic climate variability. An imperative first step for developing a new paleoclimate archive is to establish methodologies for constraining the age-depth relationship. Naturally occurring and bomb-produced radioisotopes have been utilized in sediments to constrain downcore variability of accumulation rates on 100-103 y timescales, but this methodology is complicated by low activities of many of these tracers at high latitudes. The present study utilizes the combination of a (1) multi-tracer approach and a (2) tailored measurement strategy to overcome this limitation. 210Pb and 137Cs analyses were conducted on the fine (<32μm) sediment fraction to maximize measurable activity and to minimize radioisotope activity variability resulting from changes in grain size: 137Cs geochronologies proved more reliable in this setting and revealed mm/y sediment accumulation in the lagoon. To corroborate the 137Cs results, 239,240Pu activities were analyzed for selected sites using ICP-MS which has ultra-low detection limits, and yielded accumulation rates that matched the Cs geochronology. Age model development for the remainder of the core lengths (>~100 y in age) were completed using radiocarbon dating of benthic foraminifera tests, which proved the only datable in situ carbon available in this sediment archive. These dates have been used to constrain the ages of acoustic reflectors in CHIRP subbottom seismic records collected from the lagoon. Using this age control, spatial patterns of lagoonal sediment accumulation over the last ~3 ky were derived from the CHIRP data. Two depocenters are identified and validate combining age-dated coring with high-resolution seismic profiling to identify areas of the highest temporal resolution for Arctic paleoclimate research in coastal sediments.
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Spatial characterization of riparian buffer effects on sediment loads from watershed systems.
Momm, Henrique G; Bingner, Ronald L; Yuan, Yongping; Locke, Martin A; Wells, Robert R
2014-09-01
Understanding all watershed systems and their interactions is a complex, but critical, undertaking when developing practices designed to reduce topsoil loss and chemical/nutrient transport from agricultural fields. The presence of riparian buffer vegetation in agricultural landscapes can modify the characteristics of overland flow, promoting sediment deposition and nutrient filtering. Watershed simulation tools, such as the USDA-Annualized Agricultural Non-Point Source (AnnAGNPS) pollution model, typically require detailed information for each riparian buffer zone throughout the watershed describing the location, width, vegetation type, topography, and possible presence of concentrated flow paths through the riparian buffer zone. Research was conducted to develop GIS-based technology designed to spatially characterize riparian buffers and to estimate buffer efficiency in reducing sediment loads in a semiautomated fashion at watershed scale. The methodology combines modeling technology at different scales, at individual concentrated flow paths passing through the riparian zone, and at watershed scales. At the concentrated flow path scale, vegetative filter strip models are applied to estimate the sediment-trapping efficiency for each individual flow path, which are aggregated based on the watershed subdivision and used in the determination of the overall impact of the riparian vegetation at the watershed scale. This GIS-based technology is combined with AnnAGNPS to demonstrate the effect of riparian vegetation on sediment loadings from sheet and rill and ephemeral gully sources. The effects of variability in basic input parameters used to characterize riparian buffers, onto generated outputs at field scale (sediment trapping efficiency) and at watershed scale (sediment loadings from different sources) were evaluated and quantified. The AnnAGNPS riparian buffer component represents an important step in understanding and accounting for the effect of riparian vegetation, existing and/or managed, in reducing sediment loads at the watershed scale. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
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NASA Astrophysics Data System (ADS)
Leipe, T.; Naumann, M.; Tauber, F.; Radtke, H.; Friedland, R.; Hiller, A.; Arz, H. W.
2017-12-01
This study presents selected results of a sediment geochemical mapping program of German territorial waters in the south-western Baltic Sea. The field work was conducted mainly during the early 2000s. Due to the strong variability of sediment types in the study area, it was decided to separate and analyse the fine fraction (<63 μm, mud) from more than 600 surficial samples, combined with recalculations for the bulk sediment. For the contents of total organic carbon (TOC) and selected elements (P, Hg), the regional distribution maps show strong differences between the analysed fine fraction and the recalculated total sediment. Seeing that mud contents vary strongly between 0 and 100%, this can be explained by the well-known grain-size effect. To avoid (or at least minimise) this effect, further interpretations were based on the data for the fine fraction alone. Lateral transport from the large Oder River estuary combined with high abundances and activities of benthic fauna on the shallow-water Oder Bank (well sorted fine sand) could be some main causes for hotspots identified in the fine-fraction element distribution. The regional pattern of primary production as the main driver of nutrient element fixation (C, N, P, Si) was found to be only weakly correlated with, for example, the TOC distribution in the fine fraction. This implies that, besides surface sediment dynamics, local conditions (e.g. benthic secondary production) also have strong impacts. To the best of the authors' knowledge, there is no comparable study with geochemical analyses of the fine fraction of marine sediments to this extent (13,600 km2) and coverage (between 600 and 800 data points) in the Baltic Sea. This aspect proved pivotal in confidently pinpointing geochemical "anomalies" in surface sediments of the south-western Baltic Sea.
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Move! - a deep Ocean Underwater Robot for Bio-Geochemical Research
NASA Astrophysics Data System (ADS)
Waldmann, C.; Epping, E.; Move! Team
2003-04-01
Within the framework of the binationally funded project MOVE! the partners from the Netherlands and Germany are pursuing the development of a versatile, autonomous vehicle for benthic research. The system acts as a modular platform for different scientific sensors and by moving on the sea floor will allow for taking measurements at defined locations. By combining acoustical navigation methods with other new position tracking devices an accurate positioning can be achieved. Both the vehicle subsystems and the scientific sensors will be powered by a dedicated energy source. The scientific application lies in the area of multidisciplinary studies (physics, chemistry, sedimentology and biology) with an emphasis on element cycling in marine sediments and benthic boundary layer from coastal areas to deep sea. Application of the vehicle should enable timed monitoring and experimentation to study temporal dynamics in forcing and effects, and allow for multiple sites to be studied in a single area to cover spatial variability. Typical experiments would require (1) enclosing an area of sediment and overlying water to monitor the chemical exchange between sediment and water to study the actual base line activities (2) manipulation of the sediment-overlying water by adding dissolved substances or particulate substances (food+ inert tracers) and the subsequent monitoring of overlying water chemistry (oxygen, DIC, pH, nitrate, ammonium, silicate) in order to assess biological responses to chemical disturbances. Sediments should be recovered after the experiment. (3)The monitoring of pore water chemistry by use of microelectrodes and HR-DET probes baseline and after addition in preceding chamber experiment (requires careful repositioning with high accuracy or a combined chamber-profiling unit) (4) Injection of labeled organic and inorganic substrates in the sediment and recovery of sediment cores in order to measure specific activities and to disentangle trophic relationships within sediments. The presentation will explain details of the design concept and how the envisaged scientific goals will be reached.
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NASA Astrophysics Data System (ADS)
Gobeil, C.; Kuzyk, Z. Z. A.; Goni, M. A.; Macdonald, R. W.
2016-02-01
Concentrations of elements (S, Mn, Mo, U, Cd, Re) providing insights on organic C metabolized through oxidative processes at the sea floor were measured in 27 sediment cores collected along a section extending from the North Bering Sea to Davis Strait via the Canadian Archipelago. Sedimentary distributions and accumulation rates of these elements were used to i) document the relative importance of aerobic versus anaerobic degradation of organic C in NAAM sediments, ii) infer variations in water column carbon flux and iii) estimate the importance of this margin as a sink for key elements in the Arctic and global ocean. Distributions of Mn, total S and reduced inorganic S demonstrated that most sediments along the NAAM had relatively thick (>1 cm) surface oxic layers, underlain by sediments with weakly reducing conditions and limited sulphate reduction. Strongly reducing conditions accompanied by substantial sedimentary pyrite burial occurred only in certain subregions, including the Bering-Chukchi Shelves, shallow portions of Barrow Canyon. Estimated accumulation rates of authigenic S, Mo, Cd and U, and total Re displayed marked spatial variability that was related to sedimentary redox conditions induced by the supply of labile C to the seabed, as shown by significant relationships between the accumulation rates and vertical C flux, estimated from regional primary production values and water depth at the coring sites. High primary production combined with shallow water columns drive elevated rates of authigenic trace element accumulation in sediments from the Bering-Chukchi Shelves whereas low production combined with moderately deep conditions drive low rates of accumulation in sediments in the Beaufort Shelf, Davis Strait and Canadian Archipelago. Using the average authigenic trace element accumulation rates in sediments from the various regions, we submit that the shelves along the NAAM margin are important sinks in global marine biogeochemical budgets.
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NASA Astrophysics Data System (ADS)
Carlier, Benoit; Arnaud-Fassetta, Gilles; Fort, Monique; Bouccara, Fanny; Sourdot, Grégoire; Tassel, Adrien; Lissak, Candide; Betard, François; Cossart, Etienne; Madelin, Malika; Viel, Vincent; Charnay, Bérengère; Bletterie, Xavier
2014-05-01
The upper Guil catchment (Southern Alps) is prone to hydro-geomorphic hazards. Major hazards are related to catastrophic floods, with an amplification of their impacts due to strong hillslope-channel connectivity as observed in 1957 and 2000. In both cases, the rainfall intensity, aggravated by the pre-existing saturated soils, explained the instantaneous response of the fluvial system, such as destabilisation of slopes, high sediment discharge, and subsequent damages to exposed structures and settlements present in the floodplain and at confluence sites. The Peynin junction with the Guil River is one of these sites, where significant land-use change during the last decades in relation to the development of handicraft and tourism economy has increased debris flow threat to population. Here, we adopt a sediment budget analysis aimed at better understanding the functioning of this small subcatchment. This latter offers a combination of factors that favour torrential and gravitational activity. It receives abundant and intense rainfall during "Lombarde" events (moist air mass from Mediterranean Sea). Its elongated shape and small surface area (15 km²) together with asymmetric slopes (counter dip slope on the left bank) accelerate runoff on a short response time. In addition highly tectonised shaly schists supply a large volume of debris (mostly platy clasts and fine, micaceous sediment). The objectives of this study, carried out in the frame of SAMCO (ANR) project, are threefold: Identify the different sediment storages; Characterise the processes that put sediment into motion; Quantify volumes of sediment storages. We produced a geomorphic map using topographic surveys and aerial photos in order to locate the different sediment storage types and associated processes. This analysis was made with respect to geomorphic coupling and sediment flux activity. In terms of surface area, the dominant landforms in the valley were found to be mass wasting, talus slopes and alluvial fans and plains. Most of these forms are relict landforms, decoupled from the present geomorphic system. Notable sediment transport is limited to avalanche tracks, debris flows, and along floodplains. Sediment volumes were calculated using a combination of polynomial functions of cross sections and GIS modelling. We calculated the overall sediment volume of the valley fill deposits to be 1.05 km3. This corresponds to a mean sediment thickness of 90.2 m. Landslides appear as the major sediment storage, representing more than 35% of the sediment volume stored in the Peynin subcatchment. For some locations, the polynomial-generated cross sections resulted in overestimations of sediment thickness, therefore, these results have to be considered as an order of magnitude. Future investigations will include seismic refraction profiles that may provide bedrock depth, hence a better control on sediment thickness (estimates generated thanks to GIS). Eventually, we expect our results to be used to better model, hence prevent future debris-flow events at the confluence of Peynin stream with the Guil River.
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NASA Astrophysics Data System (ADS)
Hentschke, Reinhard; Herzfeld, Judith
1991-06-01
The reversible association of globular protein molecules in concentrated solution leads to highly polydisperse fibers, e.g., actin filaments, microtubules, and sickle-cell hemoglobin fibers. At high concentrations, excluded-volume interactions between the fibers lead to spontaneous alignment analogous to that in simple lyotropic liquid crystals. However, the phase behavior of reversibly associating proteins is complicated by the threefold coupling between the growth, alignment, and hydration of the fibers. In protein systems aggregates contain substantial solvent, which may cause them to swell or shrink, depending on osmotic stress. Extending previous work, we present a model for the equilibrium phase behavior of the above-noted protein systems in terms of simple intra- and interaggregate interactions, combined with equilibration of fiber-incorporated solvent with the bulk solvent. Specifically, we compare our model results to recent osmotic pressure data for sickle-cell hemoglobin and find excellent agreement. This comparison shows that particle interactions sufficient to cause alignment are also sufficient to squeeze significant amounts of solvent out of protein fibers. In addition, the model is in accord with findings from independent sedimentation and birefringence studies on sickle-cell hemoglobin.
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Magnitudes and Sources of Catchment Sediment: When A + B Doesn't Equal C
NASA Astrophysics Data System (ADS)
Simon, A.
2015-12-01
The export of land-based sediments to receiving waters can cause degradation of water quality and habitat, loss of reservoir capacity and damage to reef ecosystems. Predictions of sources and magnitudes generally come from simulations using catchment models that focus on overland flow processes at the expense of gully and channel processes. This is not appropriate for many catchments where recent research has shown that the dominant erosion sources have shifted from the uplands and fields following European Settlement, to the alluvial valleys today. Still, catchment models which fail to adequately address channel and bank processes are still the overwhelming choice by resource agencies to help manage sediment export. These models often utilize measured values of sediment load at the river mouth to "calibrate" the magnitude of loads emanating from uplands and fields. The difference between the sediment load at the mouth and the simulated upland loading is then proportioned to channel sources.Bank erosion from the Burnett River (a "Reef Catchment" in eastern Queensland) was quantified by comparisons of bank-top locations and by numerical modeling using BSTEM. Results show that bank-derived sediment contributes between 44 and 73% of the sediment load being exported to the Coral Sea. In comparison reported results from a catchment model showed bank contributions of 8%. In absolute terms, this is an increase in the reported average, annual rate of bank erosion from 0.175 Mt/y to 2.0 Mt/y.In the Hoteo River, New Zealand, a rural North Island catchment characterized by resistant cohesive sediments, bank erosion was found to contribute at least 48% of the total specific yield of sediment. Combining the bank-derived, fine-grained loads from some of the major tributaries gives a total, average annual loading rate for fine material of about 10,900 t/y for the studied reaches in the Hoteo River System. If the study was extended to include the lower reaches of the main stem channel and other tributary reaches, this percentage would be higher. Similar studies in the United States using combinations of empirical and numerical modeling techniques have also disclosed that bank-derived sediment can be the major source of sediment in many catchments. An approach to improve the accuracy of predictions is proposed.
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Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
Hubalek, Valerie; Buck, Moritz; Tan, BoonFei; Foght, Julia; Wendeberg, Annelie; Berry, David; Bertilsson, Stefan
2017-01-01
ABSTRACT Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems. PMID:29104938
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Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.
Sharon, Itai; Kertesz, Michael; Hug, Laura A; Pushkarev, Dmitry; Blauwkamp, Timothy A; Castelle, Cindy J; Amirebrahimi, Mojgan; Thomas, Brian C; Burstein, David; Tringe, Susannah G; Williams, Kenneth H; Banfield, Jillian F
2015-04-01
Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads. © 2015 Sharon et al.; Published by Cold Spring Harbor Laboratory Press.
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Bioinspired Assemblies of Plant Cell Walls for Measuring Protein-Carbohydrate Interactions by FRAP.
Paës, Gabriel
2017-01-01
The interactions of proteins involved in plant cell wall hydrolysis, such as enzymes and CBMs, significantly determine their role and efficiency. In order to go beyond the characterization of interactions with simple ligands, bioinspired assemblies combined with the measurement of diffusion and interaction by FRAP offer a relevant alternative for highlighting the importance of different parameters related to the protein affinity and to the assembly.
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1969-01-01
In one of the initial assembly steps for the Saturn IB launch vehicle's S-IB (first) stage, workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, position the thrust structure. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.
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1969-01-01
In one of the initial assembly steps for the Saturn IB launch vehicle's S-IB (first) stage, workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, complete the thrust structure. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.
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Miller, Helen; Croudace, Ian W; Bull, Jonathan M; Cotterill, Carol J; Dix, Justin K; Taylor, Rex N
2014-07-01
A high-resolution record of pollution is preserved in recent sediments from Windermere, the largest lake in the English Lake District. Data derived from X-ray core scanning (validated against wavelength dispersive X-ray fluorescence), radiochronological techniques ((210)Pb and (137)Cs) and ultrahigh precision, double-spike mass spectrometry for lead isotopes are combined to decipher the anthropogenic inputs to the lake. The sediment record suggests that while most element concentrations have been stable, there has been a significant increase in lead, zinc, and copper concentrations since the 1930s. Lead isotope down-core variations identify three major contributory sources of anthropogenic (industrial) lead, comprising gasoline lead, coal combustion lead (most likely source is coal-fired steam ships), and lead derived from Carboniferous Pb-Zn mineralization (mining activities). Periods of metal workings do not correlate with peaks in heavy metals due to the trapping efficiency of up-system lakes in the catchment. Heavy metal increases could be due to flood-induced metal inwash after the cessation of mining and the weathering of bedrock in the catchment. The combination of sediment analysis techniques used provides new insights into the pollutant depositional history of Windermere and could be similarly applied to other lake systems to determine the timing and scale of anthropogenic inputs.
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Xu, Peng; Xiao, Enrong; Xu, Dan; Li, Juan; Zhang, Yi; Dai, Zhigang; Zhou, Qiaohong; Wu, Zhenbin
2018-05-01
The phosphorus reduction in water column was attempted by integrating sediment microbial fuel cells (SMFCs) with the submerged macrophyte Vallisneria spiralis. A comparative study was conducted to treat simulated water rich in phosphate with a control and three treatments: SMFC alone (SMFC), submerged macrophytes alone (macophyte), and combined macrophytes and fuel cells (M-SMFC). All treatments promoted phosphorus flux from the water column to sediments. Maximum phosphorus reduction was obtained in proportion to the highest stable phosphorus level in sediments in M-SMFC. For the initial phosphate concentrations of 0.2, 1, 2, and 4 mg/L, average phosphate values in the overlying water during four phases decreased by 33.3% (25.0%, 8.3%), 30.8% (5.1%, 17.9%), 36.5% (27.8%, 15.7%), and 36.2% (0.7%, 22.1%) for M-SMFC (macrophyte, SMFC), compared with the control. With macrophyte treatment, the obvious phosphorus release from sediments was observed during the declining period. However, such phenomenon was significantly inhibited with M-SMFC. The electrogenesis bacteria achieved stronger phosphorus adsorption and assimilation was significantly enriched on the closed-circuit anodes. The higher abundance of Geobacter and Pseudomonas in M-SMFC might in part explain the highest phosphorus reduction in the water column. M-SMFC treatment could be promising to control the phosphorus in eutrophic water bodies.
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Li, Juan-Ying; Tang, Janet Yat Man; Jin, Ling; Escher, Beate I
2013-12-01
Bioavailable and bioaccessible fractions of sediment-associated contaminants are considered as better dose metrics for sediment-quality assessment than total concentrations. The authors applied exhaustive solvent extraction and nondepletive equilibrium sampling techniques to sediment samples collected along the Brisbane River in South East Queensland, Australia, which range from pristine environments to urban and industry-impacted areas. The wide range of chemicals expected prevents comprehensive chemical analysis, but a battery of cell-based bioassays sheds light on mixture effects of chemicals in relation to various modes of toxic action. Toxic effects were expressed as bioanalytical equivalent concentrations (BEQs) normalized to the organic carbon content of each sediment sample. Bioanalytical equivalent concentrations from exhaustive extraction agreed fairly well with values estimated from polydimethylsiloxane passive sampling extracts via the constant organic carbon to polydimethylsiloxane partition coefficient. Agreement was best for bioassays indicative of photosynthesis inhibition and oxidative stress response and discrepancy within a factor of 3 for the induction of the aryl hydrocarbon receptor. For nonspecific cytotoxicity, BEQ from exhaustive extraction were 1 order of magnitude higher than values from equilibrium sampling, possibly because of coextraction of bioactive natural organic matter that led to an overestimation of toxicity in the exhaustive extracts, which suggests that passive sampling is better suited in combination with bioanalytical assessment than exhaustive extraction. © 2013 SETAC.
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SedFoam-2.0: a 3-D two-phase flow numerical model for sediment transport
NASA Astrophysics Data System (ADS)
Chauchat, Julien; Cheng, Zhen; Nagel, Tim; Bonamy, Cyrille; Hsu, Tian-Jian
2017-11-01
In this paper, a three-dimensional two-phase flow solver, SedFoam-2.0, is presented for sediment transport applications. The solver is extended from twoPhaseEulerFoam available in the 2.1.0 release of the open-source CFD (computational fluid dynamics) toolbox OpenFOAM. In this approach the sediment phase is modeled as a continuum, and constitutive laws have to be prescribed for the sediment stresses. In the proposed solver, two different intergranular stress models are implemented: the kinetic theory of granular flows and the dense granular flow rheology μ(I). For the fluid stress, laminar or turbulent flow regimes can be simulated and three different turbulence models are available for sediment transport: a simple mixing length model (one-dimensional configuration only), a k - ɛ, and a k - ω model. The numerical implementation is demonstrated on four test cases: sedimentation of suspended particles, laminar bed load, sheet flow, and scour at an apron. These test cases illustrate the capabilities of SedFoam-2.0 to deal with complex turbulent sediment transport problems with different combinations of intergranular stress and turbulence models.
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Ecology of Legionella pneumophila within water distribution systems.
Stout, J E; Yu, V L; Best, M G
1985-01-01
The reservoir for hospital-acquired Legionnaires disease has been shown to be the potable water distribution system. We investigated the influence of the natural microbial population and sediment (scale and organic particulates) found in water systems as growth-promoting factors for Legionella pneumophila. Our in vitro experiments showed that: (i) water from hot-water storage tank readily supported the survival of L. pneumophila, (ii) the concentration of sediment was directly related to the survival of L. pneumophila, (iii) the presence of environmental bacteria improved the survival of L. pneumophila via nutritional symbiosis, (iv) the combination of sediment and environmental bacteria acted synergistically to improve the survival of L. pneumophila, and (v) the role of sediment in this synergistic effect was determined to be nutritional. Sediment was found to stimulate the growth of environmental microflora, which in turn stimulated the growth of L. pneumophila. These findings confirm the empiric observations of the predilection of L. pneumophila for growth in hot-water tanks and its localization to sediment. L. pneumophila occupies an ecological niche within the potable water system, with interrelationships between microflora, sediment, and temperature. Images PMID:3977311
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Spatial Patterns of Road-Induced Backwater Sediment Storage Across A Rural to Urban Gradient
NASA Astrophysics Data System (ADS)
Copeland, M.; Bain, D.
2017-12-01
Road networks dominate many landscapes and often interact with stream networks to alter basin sediment dynamics. Currently, conceptual models of catchment-scale sediment fluxes remain at a coarse scale (i.e., the entire catchment) and are unable to resolve important human-driven sediment storage processes. The spatio-temporal complexity of the interactions between road networks and streams has made it challenging to infer the fine-scale impacts of road crossings on fluvial systems. Here, road crossings in multiple drainage networks and the associated backwater sediment accumulations are examined along a rural to urban gradient around Pittsburgh, PA. Preliminary results indicate that upstream drainage area, channel slope, and human activities control stream crossing type and therefore drive associated sediment accumulation, particularly in urban headwater channels. The data indicate that the combination of land use intensity and infrastructure age influences the volume of sediment trapped in road-induced backwaters. Clarification of the coupled human, road-building, and natural stream adjustments will allow for more effective treatments of fluvial impacts, such as the "urban stream syndrome."
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Song, Weiling; Zhang, Qiao; Sun, Wenbo
2015-02-11
An ultrasensitive protocol for fluorescent detection of DNA is designed by combining the template enhanced hybridization process (TEHP) with Rolling Circle Amplification (RCA) and Catalytic Hairpin Assembly (CHA), showing a remarkable amplification efficiency.
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ARSENIC MOBILIZATION FROM SEDIMENTS IN MICROCOSMS UNDER SULFATE REDUCTION
Sun, Jing; Quicksall, Andrew N.; Chillrud, Steven N.; Mailloux, Brian J.; Bostick, Benjamin C.
2016-01-01
Arsenic is often assumed to be immobile in sulfidic environments. Here, laboratory-scale microcosms were conducted to investigate whether microbial sulfate reduction could control dissolved arsenic concentrations sufficiently for use in groundwater remediation. Sediments from the Vineland Superfund site and the Coeur d'Alene mining district were amended with different combination of lactate and sulfate and incubated for 30 to 40 days. In general, sulfate reduction in Vineland sediments resulted in transient and incomplete arsenic removal, or arsenic release from sediments. Sulfate reduction in the Coeur d'Alene sediments was more effective at removing arsenic from solution than the Vineland sediments, probably by arsenic substitution and adsorption within iron sulfides. X-ray absorption spectroscopy indicated that the Vineland sediments initially contained abundant reactive ferrihydrite, and underwent extensive sulfur cycling during incubation. As a result, arsenic in the Vineland sediments could not be effectively converted to immobile arsenic-bearing sulfides, but instead a part of the arsenic was probably converted to soluble thioarsenates. These results suggest that coupling between the iron and sulfur redox cycles must be fully understood for in situ arsenic immobilization by sulfate reduction to be successful. PMID:27037658
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Evaluation and application of regional turbidity-sediment regression models in Virginia
Hyer, Kenneth; Jastram, John D.; Moyer, Douglas; Webber, James S.; Chanat, Jeffrey G.
2015-01-01
Conventional thinking has long held that turbidity-sediment surrogate-regression equations are site specific and that regression equations developed at a single monitoring station should not be applied to another station; however, few studies have evaluated this issue in a rigorous manner. If robust regional turbidity-sediment models can be developed successfully, their applications could greatly expand the usage of these methods. Suspended sediment load estimation could occur as soon as flow and turbidity monitoring commence at a site, suspended sediment sampling frequencies for various projects potentially could be reduced, and special-project applications (sediment monitoring following dam removal, for example) could be significantly enhanced. The objective of this effort was to investigate the turbidity-suspended sediment concentration (SSC) relations at all available USGS monitoring sites within Virginia to determine whether meaningful turbidity-sediment regression models can be developed by combining the data from multiple monitoring stations into a single model, known as a “regional” model. Following the development of the regional model, additional objectives included a comparison of predicted SSCs between the regional model and commonly used site-specific models, as well as an evaluation of why specific monitoring stations did not fit the regional model.
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Ionic self-assembly for functional hierarchical nanostructured materials.
Faul, Charl F J
2014-12-16
CONSPECTUS: The challenge of constructing soft functional materials over multiple length scales can be addressed by a number of different routes based on the principles of self-assembly, with the judicious use of various noncovalent interactions providing the tools to control such self-assembly processes. It is within the context of this challenge that we have extensively explored the use of an important approach for materials construction over the past decade: exploiting electrostatic interactions in our ionic self-assembly (ISA) method. In this approach, cooperative assembly of carefully chosen charged surfactants and oppositely charged building blocks (or tectons) provides a facile noncovalent route for the rational design and production of functional nanostructured materials. Generally, our research efforts have developed with an initial focus on establishing rules for the construction of novel noncovalent liquid-crystalline (LC) materials. We found that the use of double-tailed surfactant species (especially branched double-tailed surfactants) led to the facile formation of thermotropic (and, in certain cases, lyotropic) phases, as demonstrated by extensive temperature-dependent X-ray and light microscopy investigations. From this core area of activity, research expanded to cover issues beyond simple construction of anisotropic materials, turning to the challenge of inclusion and exploitation of switchable functionality. The use of photoactive azobenzene-containing ISA materials afforded opportunities to exploit both photo-orientation and surface relief grating formation. The preparation of these anisotropic LC materials was of interest, as the aim was the facile production of disposable and low-cost optical components for display applications and data storage. However, the prohibitive cost of the photo-orientation processes hampered further exploitation of these materials. We also expanded our activities to explore ISA of biologically relevant tectons, specifically deoxyguanosine monophosphate. This approach proved, in combination with block copolymer (BCP) self-assembly, very fruitful for the construction of complex and hierarchical functional materials across multiple length scales. Molecular frustration and incommensurability, which played a major role in structure formation in combination with nucleotide assembly, have now become important tools to tune supramolecular structure formation. These concepts, that is, the use of BCP assembly and incommensurability, in combination with metal-containing polymeric materials, have provided access to novel supramolecular morphologies and, more importantly, design rules to prepare such constructs. These design rules are now also being applied to the assembly of electroactive oligo(aniline)-based materials for the preparation of highly ordered functional soft materials, and present an opportunity for materials development for applications in energy storage. In this Account, we therefore discuss investigations into (i) the inclusion and preparation of supramolecular photoactive and electroactive materials; (ii) the exploitation and control over multiple noncovalent interactions to fine-tune function, internal structure, and long-range order and (iii) exploration of construction over multiple length scales by combination of ISA with well-known BCP self-assembly. Combination of ISA with tuning of volume fractions, mutual compatibility, and molecular frustration now provides a versatile tool kit to construct complex and hierarchical functional materials in a facile noncovalent way. A direct challenge for future ISA activities would certainly be the construction of functional mesoscale objects. However, within a broader scientific context, the challenge would be to exploit this powerful assembly tool for application in areas of research with societal impact, for example, energy storage and generation. The hope is that this Account will provide a platform for such future research activities and opportunities.
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NASA Astrophysics Data System (ADS)
Baasch, B.; Müller, H.; von Dobeneck, T.
2018-07-01
In this work, we present a new methodology to predict grain-size distributions from geophysical data. Specifically, electric conductivity and magnetic susceptibility of seafloor sediments recovered from electromagnetic profiling data are used to predict grain-size distributions along shelf-wide survey lines. Field data from the NW Iberian shelf are investigated and reveal a strong relation between the electromagnetic properties and grain-size distribution. The here presented workflow combines unsupervised and supervised machine-learning techniques. Non-negative matrix factorization is used to determine grain-size end-members from sediment surface samples. Four end-members were found, which well represent the variety of sediments in the study area. A radial basis function network modified for prediction of compositional data is then used to estimate the abundances of these end-members from the electromagnetic properties. The end-members together with their predicted abundances are finally back transformed to grain-size distributions. A minimum spatial variation constraint is implemented in the training of the network to avoid overfitting and to respect the spatial distribution of sediment patterns. The predicted models are tested via leave-one-out cross-validation revealing high prediction accuracy with coefficients of determination (R2) between 0.76 and 0.89. The predicted grain-size distributions represent the well-known sediment facies and patterns on the NW Iberian shelf and provide new insights into their distribution, transition and dynamics. This study suggests that electromagnetic benthic profiling in combination with machine learning techniques is a powerful tool to estimate grain-size distribution of marine sediments.
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NASA Astrophysics Data System (ADS)
Baasch, B.; M"uller, H.; von Dobeneck, T.
2018-04-01
In this work we present a new methodology to predict grain-size distributions from geophysical data. Specifically, electric conductivity and magnetic susceptibility of seafloor sediments recovered from electromagnetic profiling data are used to predict grain-size distributions along shelf-wide survey lines. Field data from the NW Iberian shelf are investigated and reveal a strong relation between the electromagnetic properties and grain-size distribution. The here presented workflow combines unsupervised and supervised machine learning techniques. Nonnegative matrix factorisation is used to determine grain-size end-members from sediment surface samples. Four end-members were found which well represent the variety of sediments in the study area. A radial-basis function network modified for prediction of compositional data is then used to estimate the abundances of these end-members from the electromagnetic properties. The end-members together with their predicted abundances are finally back transformed to grain-size distributions. A minimum spatial variation constraint is implemented in the training of the network to avoid overfitting and to respect the spatial distribution of sediment patterns. The predicted models are tested via leave-one-out cross-validation revealing high prediction accuracy with coefficients of determination (R2) between 0.76 and 0.89. The predicted grain-size distributions represent the well-known sediment facies and patterns on the NW Iberian shelf and provide new insights into their distribution, transition and dynamics. This study suggests that electromagnetic benthic profiling in combination with machine learning techniques is a powerful tool to estimate grain-size distribution of marine sediments.
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Ramos-Scharrón, Carlos E; Figueroa-Sánchez, Yasiel
2017-11-01
The combination of a topographically abrupt wet-tropical setting with the high level of soil exposure that typifies many sun-grown coffee farms represents optimal conditions for high erosion rates. Although traditionally considered as a main cause for water resource degradation, limited empirical evidence has existed to document its true contribution. This study relies on plot-scale experimental results conducted in western Puerto Rico to assess the impact of cultivated surfaces and farm access roads on runoff and sediment production from the plot to the farm and watershed scales. Results show that unsurfaced and graveled road surfaces produce one- to two-orders of magnitude more per unit area runoff than cultivated lands. Similarly, erosion rates from unsurfaced roads are about 102 g m -2 per cm of rainfall and these are two-orders of magnitude greater than from actively cultivated surfaces. Mitigation practices such as uncompacting road surfaces by ripping and gravel application reduce onsite erosion rates to 0.6% and 8% of unsurfaced conditions, respectively. At the farm scale, coffee farms are estimated to produce sediment at a rate of 12-18 Mg ha -1 yr -1 , and roads are undoubtedly the dominant sediment source responsible for 59-95% of the total sediment produced. The costs associated to ameliorating erosion problems through road graveling are high. Therefore, a combined approach that treats road erosion onsite with one that traps sediment before it reaches river networks is the viable solution to this problem. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Oceanographic controls over sediment water content: northern Bermuda rise
DOE Office of Scientific and Technical Information (OSTI.GOV)
Baker, M.; Laine, E.P.
1985-01-01
Cores taken from the plateaus of Northern Bermuda Rise show that the region is underlain at depths of 1-5 m by a 1-3 m thick layer of hemipelagic lutites with anomalously high water contents. The lack of visually apparent textural and lithological changes in this extremely fine grained sediment rule out these common causes for variation in water content. The water content averages 175% within this layer and 100% immediately above and below it. This is an increase of 9.5% in porosity. The high water content sediment is confined to a period between 12 and 16 ka. Current work onmore » the mineralogy of the sediments which comprise this layer suggest two oceanographic factors that may have influenced its formation. A meltwater spike associated with deglaciation may have altered the ecological conditions above the thermocline sufficiently to promote the increased production of radiolaria, resulting in the deposition of silica enriched sediment on the sea floor. A combination of textural and perhaps chemical factors caused by the silica enrichment may have influenced the increase in water content. Intensified bottom currents at this time also may have eroded smectite rich sediments from exposures of Neogene age and deposited them on the plateaus. An increase in smectite would increase the water content due to the extremely fine grain size and the chemistry of the clay. Thus, the lateral continuity and isochroniety of this layer, combined with its mineralogical characteristics suggests that oceanographic changes can influence water content and perhaps other geotechnical properties on a regional scale.« less
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NASA Astrophysics Data System (ADS)
Sugla, R.; Norris, R. D.; Lyakov, J.
2017-12-01
In his book The Nature of the Stratigraphical Record, Derek Ager made the remarkable observation that the geologic eras of the Phanerozoic could be identified by coloration patterns of carbonate sediments in outcrops. This observation, however, was never quantified nor explained by Ager. Here, we present a record of spectral reflectance of carbonate sediments collected from sections worldwide. While sediment color is governed by many factors, global and abrupt shifts in sediment color across depositional envrionments observed here may represent a shift towards rising oxygen concentrations. Such a shift would explain changes in redox state of iron or organic matter concentrations, both factors which influence sediment color. This record is combined with a simple model of physiological requirements of marine fauna in order to infer a minimum pO2 in the atmosphere to support life. Results indicate a strong threshold change in the Earth system near the Triassic-Jurassic boundary, potentially reflecting rising atmospheric oxygen concentrations not previously recorded.
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Baldock, T E; Golshani, A; Atkinson, A; Shimamoto, T; Wu, S; Callaghan, D P; Mumby, P J
2015-08-15
A one-dimensional wave model is combined with an analytical sediment transport model to investigate the likely influence of sea-level rise on net cross-shore sediment transport on fetch-limited barrier reef and lagoon island beaches. The modelling considers if changes in the nearshore wave height and wave period in the lagoon induced by different water levels over the reef flat are likely to lead to net offshore or onshore movement of sediment. The results indicate that the effects of SLR on net sediment movement are highly variable and controlled by the bathymetry of the reef and lagoon. A significant range of reef-lagoon bathymetry, and notably shallow and narrow reefs, appears to lead hydrodynamic conditions and beaches that are likely to be stable or even accrete under SLR. Loss of reef structural complexity, particularly on the reef flat, increases the chance of sediment transport away from beaches and offshore. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Méar, Yann; Poizot, Emmanuel; Murat, Anne; Beryouni, Khadija; Baux, Noémie; Dauvin, Jean-Claude
2018-04-01
Dredged sediments have different physical and chemical characteristics compared with the sediments in place, which generates multiple effects on the environment. In this study, we show that the sampling strategy used to monitor the effects of dredge spoil deposition on the surrounding environment can lead to different interpretations. It appears that sediment sample replicates may or may not be necessary, depending on the studied area, the prevailing environmental forcings before sediment sampling and the combination of these two factors. The proposed modus operandi allows us to optimize both the confidence on the obtained results and the cost of the sediment studies (sampling and laboratory analyses). The results are based on the sediment fine fraction, which is considered as a key environmental component due, for example, to its strong association with the structure of benthic faunal communities as well as its role in the build-up of pollutants. Copyright © 2017 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Hereford, Richard
1987-10-01
Alluvium deposited in a reservoir from 1937 to 1976 records the sediment-yield history of a small (2.8 km2), high-relief basin in semiarid southern Utah. Stratification in the alluvium shows that sediment was deposited in the reservoir only 21 times in 38 yr, a runoff recurrence interval of 1.8 yr. Thus, on average, the particular combination of rainfall intensity, duration, and antecedent moisture conditions producing runoff did not recur often. On the basis of the volume of beds in the reservoir fill, sediment yield of individual runoff events averaged 2500 m3/km2 (5.3 a-ft/mi2) with slightly less than one order of magnitude variation. This low variation is not expected of small basins and probably resulted from limited hillslope sediment supply, suggesting that transport processes were more rapid than weathering processes. Sediment yield, therefore, was evidently controlled by the availability of freshly weathered material.
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Coal-tar-based sealcoated pavement: a major PAH source to urban stream sediments.
Witter, Amy E; Nguyen, Minh H; Baidar, Sunil; Sak, Peter B
2014-02-01
We used land-use analysis, PAH concentrations and assemblages, and multivariate statistics to identify sediment PAH sources in a small (~1303 km(2)) urbanizing watershed located in South-Central, Pennsylvania, USA. A geographic information system (GIS) was employed to quantify land-use features that may serve as PAH sources. Urban PAH concentrations were three times higher than rural levels, and were significantly and highly correlated with combined residential/commercial/industrial land use. Principal components analysis (PCA) was used to group sediments with similar PAH assemblages, and correlation analysis compared PAH sediment assemblages to common PAH sources. The strongest correlations were observed between rural sediments (n = 7) and coke-oven emissions sources (r = 0.69-0.78, n = 5), and between urban sediments (n = 22) and coal-tar-based sealcoat dust (r = 0.94, n = 47) suggesting that coal-tar-based sealcoat is an important urban PAH source in this watershed linked to residential and commercial/industrial land use. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Influence of a dam on fine-sediment storage in a canyon river
Hazel, J.E.; Topping, D.J.; Schmidt, J.C.; Kaplinski, M.
2006-01-01
Glen Canyon Dam has caused a fundamental change in the distribution of fine sediment storage in the 99-km reach of the Colorado River in Marble Canyon, Grand Canyon National Park, Arizona. The two major storage sites for fine sediment (i.e., sand and finer material) in this canyon river are lateral recirculation eddies and the main-channel bed. We use a combination of methods, including direct measurement of sediment storage change, measurements of sediment flux, and comparison of the grain size of sediment found in different storage sites relative to the supply and that in transport, in order to evaluate the change in both the volume and location of sediment storage. The analysis shows that the bed of the main channel was an important storage environment for fine sediment in the predam era. In years of large seasonal accumulation, approximately 50% of the fine sediment supplied to the reach from upstream sources was stored on the main-channel bed. In contrast, sediment budgets constructed for two short-duration, high experimental releases from Glen Canyon Dam indicate that approximately 90% of the sediment discharge from the reach during each release was derived from eddy storage, rather than from sandy deposits on the main-channel bed. These results indicate that the majority of the fine sediment in Marble Canyon is now stored in eddies, even though they occupy a small percentage (???17%) of the total river area. Because of a 95% reduction in the supply of fine sediment to Marble Canyon, future high releases without significant input of tributary sediment will potentially erode sediment from long-term eddy storage, resulting in continued degradation in Marble Canyon. Copyright 2006 by the American Geophysical Union.
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Gao, Jinjuan; Shi, Huahong; Dai, Zhijun; Mei, Xuefei; Zong, Haibo; Yang, Hongwei; Hu, Lingling; Li, Shushi
2018-02-01
Anthropogenic activities are driving an increase in sediment contamination in coastal areas. This poses significant challenges for the management of estuarine ecosystems and their adjacent seas worldwide. However, few studies have been conducted on how dynamic mechanisms affect the sediment toxicity in the estuarine environment. This study was designed to investigate the linkages between sediment toxicity and hydrodynamics in the Yangtze River Estuary (YRE) area. High sediment toxicity was found in the Yangtze River mouth (Region I), the depocenter of the Yangtze River Delta (Region II), and the southeastern area of the adjacent sea (Region III), while low sediment toxicity was found in the northeastern offshore region (Region IV). A spatial comparison analysis and regression model indicated that the distributed pattern of sediment toxicity was likely related to hydrodynamics and circumfluence in the East China Sea (ECS) shelf. Specifically, high sediment toxicity in Region I may be affected by the Yangtze River Pump (YRP) and the low hydrodynamics there, and high toxicity in Region II can be influenced by the low sediment dynamics and fine sediment in the depocenter. The high sediment toxicity in Region III might be related to the combination of the YRP and Taiwan Warm Current, while the low toxicity in Region IV may be influenced by the local coarse-grained relict sand with strong sediment dynamics there. The present research results further suggest that it is necessary to link hydrodynamics and the spatial behavior of sediment and sediment-derived pollutants when assessing the pollution status of estuarine environments, especially for those mega-estuaries and their neighboring ocean environments with complex waves, tides and ocean currents. Copyright © 2017 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Yu, M.; Rhoads, B. L.; Stumpf, A.
2015-12-01
As the awareness of water pollution, eutrophication and other water related environmental concerns grows, the significance of sediment in the transport of nutrients and contaminants from agricultural areas to streams has received increasing attention. Both the physical and geochemical properties of suspended sediment are strongly controlled by sediment sources. Thus, tracing sources of suspended sediment in watersheds is important for the design of management practices to reduce sediment loads and contributions of sediment-adsorbed nutrients from agricultural areas to streams. However, the contributions of different sediment sources to suspended sediment loads within intensively managed watersheds in the Midwest still remain insufficiently explored. This study aims to assess the provenance of suspended sediment and the relation between channel morphology and production of suspended sediment in the Upper Sangamon River Basin, Illinois, USA. The 3,690-km2 Upper Sangamon River Basin is characterized by low-relief, agricultural lands dominated by row-crop agriculture. Sediment source samples were collected in the Saybrook from five potential sources: farmland, forests, floodplains, river banks, and grasslands. Event-based and accumulated suspended sediment samples were collected by ISCO automatic pump samplers and in situ suspended sediment samplers and from the stream at watershed outlet. A quantitative geochemical fingerprinting technique, combining statistically verified multicomponent signatures and an un-mixing model, was employed to estimate the relative contributions of sediment from five potential sources to the suspended sediment loads. Organic matter content, trace elements, and radionuclides from soil samples were used as potential tracers. Our preliminary results indicate that the majority of suspended sediment is derived from floodplains in the downstream portions of the watersheds, while only minor amounts of suspended sediment are derived from upland areas and banks. These results suggest that floodplain erosion during high flow events contributes to the suspended sediment.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Wade, T.L.; Velinsky, D.J.; Reinharz, E.
1994-06-01
Concentrations of aliphatic, aromatic, and chlorinated hydrocarbons were determined from 33 surface-sediment samples taken from the Tidal Basin, Washington Ship Channel, and the Anacostia and Potomac rivers in Washington, D.C. In conjunction with these samples, selected storm sewers and outfalls also were sampled to help elucidate general sources of contamination to the area. All of the sediments contained detectable concentrations of aliphatic and aromatic hydrocarbons, DDT (total dichlorodiphenytrichloroethande), DDE (dichlorodiphenyldichloroethene), DDD (dichlorodiphenyldichloroethane), PCBx (total polychlorinated biphenyls) and total chlordanes (oxy-, {alpha}-, and {gamma}-chlordane and cis + trans-nonachlor). Sediment concentrations of most contaminants were highest in the Anacostia River just downstreammore » of the Washington Navy Yard, except for total chlordane, which appeared to have upstream sources in addition to storm and combined sewer runoff. This area has the highest number of storm and combined sewer outfalls in the river. Potomac River stations had lower concentrations than other stations. Polycyclic aromatic hydrocarbons, saturated hydrocarbons, and the unresolved complex mixture (UCM) distributions reflect mixtures of combustion products and direct discharges of petroleum products. Sources of PCBs appear to be related to specific outfalls, while hydrocarbon inputs, especially PAHs, are diffuse, and may be related to street runoff. This study indicates that in large urban areas, nonpoint sources deliver substantial amounts of contaminants to ecosystems through storm and combined sewer systems, and control of these inputs must be addressed. 33 refs., 6 figs., 3 tabs.« less
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Software-assisted stacking of gene modules using GoldenBraid 2.0 DNA-assembly framework.
Vazquez-Vilar, Marta; Sarrion-Perdigones, Alejandro; Ziarsolo, Peio; Blanca, Jose; Granell, Antonio; Orzaez, Diego
2015-01-01
GoldenBraid (GB) is a modular DNA assembly technology for plant multigene engineering based on type IIS restriction enzymes. GB speeds up the assembly of transcriptional units from standard genetic parts and facilitates the stacking of several genes within the same T-DNA in few days. GBcloning is software-assisted with a set of online tools. The GBDomesticator tool assists in the adaptation of DNA parts to the GBstandard. The combination of GB-adapted parts to build new transcriptional units is assisted by the GB TU Assembler tool. Finally, the assembly of multigene modules is simulated by the GB Binary Assembler. All the software tools are available at www.gbcloning.org . Here, we describe in detail the assembly methodology to create a multigene construct with three transcriptional units for polyphenol metabolic engineering in plants.
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Links between sediment consolidation and Cascadia megathrust slip behaviour
NASA Astrophysics Data System (ADS)
Han, Shuoshuo; Bangs, Nathan L.; Carbotte, Suzanne M.; Saffer, Demian M.; Gibson, James C.
2017-12-01
At sediment-rich subduction zones, megathrust slip behaviour and forearc deformation are tightly linked to the physical properties and in situ stresses within underthrust and accreted sediments. Yet the role of sediment consolidation at the onset of subduction in controlling the downdip evolution and along-strike variation in megathrust fault properties and accretionary wedge structure is poorly known. Here we use controlled-source seismic data combined with ocean drilling data to constrain the sediment consolidation and in situ stress state near the deformation front of the Cascadia subduction zone. Offshore Washington where the megathrust is inferred to be strongly locked, we find over-consolidated sediments near the deformation front that are incorporated into a strong outer wedge, with little sediment subducted. These conditions are favourable for strain accumulation on the megathrust and potential earthquake rupture close to the trench. In contrast, offshore Central Oregon, a thick under-consolidated sediment sequence is subducting, and is probably associated with elevated pore fluid pressures on the megathrust in a region where reduced locking is inferred. Our results suggest that the consolidation state of the sediments near the deformation front is a key factor contributing to megathrust slip behaviour and its along-strike variation, and it may also have a significant role in the deformation style of the accretionary wedge.
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Zhang, Li-Mei; Duff, Aoife M; Smith, Cindy J
2018-04-24
Terrestrial-marine boundaries are significant sites of biogeochemical activity with delineated gradients from land to sea. While niche differentiation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) driven by pH and nitrogen is well known, the patterns and environmental drivers of AOA and AOB community structure and activity across soil-sediment boundaries have not yet been determined. In this study, nitrification potential rate, community composition and transcriptional activity of AOA and AOB in soil, soil/sediment interface and sediments of two coastal Bays were characterized using a combination of field investigations and microcosm incubations. At DNA level, amoA gene abundances of AOA were significantly greater than AOB in soil, while in sediments AOB were significantly more abundant than AOA, but at the soil/sediment interface there were equal numbers of AOA and AOB amoA genes. Microcosm incubations provided further evidence, through qPCR and DGGE-sequencing analysis of amoA transcripts, that AOA were active in soil, AOB in sediment and both AOA and AOB were active at the soil/sediment interface. The AOA and AOB community composition shifted across the coastal soil-interface-sediment gradient with salinity and pH identified as major environmental drivers. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Modeling runoff and sediment yield from a terraced watershed using WEPP
Mary Carla McCullough; Dean E. Eisenhauer; Michael G. Dosskey
2008-01-01
The watershed version of WEPP (Water Erosion Prediction Project) was used to estimate 50-year runoff and sediment yields for a 291 ha watershed in eastern Nebraska that is 90% terraced and which has no historical gage data. The watershed has a complex matrix of elements, including terraced and non-terraced subwatersheds, multiple combinations of soils and land...
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WEPPCAT is an on-line tool that provides a flexible capability for creating user-determined climate change scenarios for assessing the potential impacts of climate change on sediment loading to streams using the USDA’s Water Erosion Prediction Project (WEPP) Model. In combination...
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Concentration-Driven Assembly and Sol–Gel Transition of π-Conjugated Oligopeptides
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhou, Yuecheng; Li, Bo; Li, Songsong
Advances in supramolecular assembly have enabled the design and synthesis of functional materials with well-defined structures across multiple length scales. Biopolymer-synthetic hybrid materials can assemble into supramolecular structures with a broad range of structural and functional diversity through precisely controlled noncovalent interactions between subunits. Despite recent progress, there is a need to understand the mechanisms underlying the assembly of biohybrid/synthetic molecular building blocks, which ultimately control the emergent properties of hierarchical assemblies. Here in this work, we study the concentration-driven self-assembly and gelation of π-conjugated synthetic oligopeptides containing different π-conjugated cores (quaterthiophene and perylene diimide) using a combination of particlemore » tracking microrheology, confocal fluorescence microscopy, optical spectroscopy, and electron microscopy. Our results show that π-conjugated oligopeptides self-assemble into β-sheet-rich fiber-like structures at neutral pH, even in the absence of electrostatic screening of charged residues. A critical fiber formation concentration c fiber and a critical gel concentration c gel are determined for fiber-forming π-conjugated oligopeptides, and the linear viscoelastic moduli (storage modulus G' and loss modulus G") are determined across a wide range of peptide concentrations. These results suggest that the underlying chemical structure of the synthetic π-conjugated cores greatly influences the self-assembly process, such that oligopeptides appended to π-conjugated cores with greater torsional flexibility tend to form more robust fibers upon increasing peptide concentration compared to oligopeptides with sterically constrained cores. Overall, our work focuses on the molecular assembly of π-conjugated oligopeptides driven by concentration, which is controlled by a combination of enthalpic and entropic interactions between oligopeptide subunits.« less
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Concentration-Driven Assembly and Sol–Gel Transition of π-Conjugated Oligopeptides
Zhou, Yuecheng; Li, Bo; Li, Songsong; ...
2017-08-17
Advances in supramolecular assembly have enabled the design and synthesis of functional materials with well-defined structures across multiple length scales. Biopolymer-synthetic hybrid materials can assemble into supramolecular structures with a broad range of structural and functional diversity through precisely controlled noncovalent interactions between subunits. Despite recent progress, there is a need to understand the mechanisms underlying the assembly of biohybrid/synthetic molecular building blocks, which ultimately control the emergent properties of hierarchical assemblies. Here in this work, we study the concentration-driven self-assembly and gelation of π-conjugated synthetic oligopeptides containing different π-conjugated cores (quaterthiophene and perylene diimide) using a combination of particlemore » tracking microrheology, confocal fluorescence microscopy, optical spectroscopy, and electron microscopy. Our results show that π-conjugated oligopeptides self-assemble into β-sheet-rich fiber-like structures at neutral pH, even in the absence of electrostatic screening of charged residues. A critical fiber formation concentration c fiber and a critical gel concentration c gel are determined for fiber-forming π-conjugated oligopeptides, and the linear viscoelastic moduli (storage modulus G' and loss modulus G") are determined across a wide range of peptide concentrations. These results suggest that the underlying chemical structure of the synthetic π-conjugated cores greatly influences the self-assembly process, such that oligopeptides appended to π-conjugated cores with greater torsional flexibility tend to form more robust fibers upon increasing peptide concentration compared to oligopeptides with sterically constrained cores. Overall, our work focuses on the molecular assembly of π-conjugated oligopeptides driven by concentration, which is controlled by a combination of enthalpic and entropic interactions between oligopeptide subunits.« less
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NASA Astrophysics Data System (ADS)
Yoshida, Masaki; Santosh, M.
2011-03-01
The periodic assembly and dispersal of supercontinents through the history of the Earth had considerable impact on mantle dynamics and surface processes. Here we synthesize some of the conceptual models on supercontinent amalgamation and disruption and combine it with recent information from numerical studies to provide a unified approach in understanding Wilson Cycle and supercontinent cycle. Plate tectonic models predict that superdownwelling along multiple subduction zones might provide an effective mechanism to pull together dispersed continental fragments into a closely packed assembly. The recycled subducted material that accumulates at the mantle transition zone and sinks down into the core-mantle boundary (CMB) provides the potential fuel for the generation of plumes and superplumes which ultimately fragment the supercontinent. Geological evidence related to the disruption of two major supercontinents (Columbia and Gondwana) attest to the involvement of plumes. The re-assembly of dispersed continental fragments after the breakup of a supercontinent occurs through complex processes involving 'introversion', 'extroversion' or a combination of both, with the closure of the intervening ocean occurring through Pacific-type or Atlantic-type processes. The timescales of the assembly and dispersion of supercontinents have varied through the Earth history, and appear to be closely linked with the processes and duration of superplume genesis. The widely held view that the volume of continental crust has increased over time has been challenged in recent works and current models propose that plate tectonics creates and destroys Earth's continental crust with more crust being destroyed than created. The creation-destruction balance changes over a supercontinent cycle, with a higher crustal growth through magmatic influx during supercontinent break-up as compared to the tectonic erosion and sediment-trapped subduction in convergent margins associated with supercontinent assembly which erodes the continental crust. Ongoing subduction erosion also occurs at the leading edges of dispersing plates, which also contributes to crustal destruction, although this is only a temporary process. The previous numerical studies of mantle convection suggested that there is a significant feedback between mantle convection and continental drift. The process of assembly of supercontinents induces a temperature increase beneath the supercontinent due to the thermal insulating effect. Such thermal insulation leads to a planetary-scale reorganization of mantle flow and results in longest-wavelength thermal heterogeneity in the mantle, i.e., degree-one convection in three-dimensional spherical geometry. The formation of degree-one convection seems to be integral to the emergence of periodic supercontinent cycles. The rifting and breakup of supercontinental assemblies may be caused by either tensional stress due to the thermal insulating effect, or large-scale partial melting resulting from the flow reorganization and consequent temperature increase beneath the supercontinent. Supercontinent breakup has also been correlated with the temperature increase due to upwelling plumes originating from the deeper lower mantle or CMB as a return flow of plate subduction occurring at supercontinental margins. The active mantle plumes from the CMB may disrupt the regularity of supercontinent cycles. Two end-member scenarios can be envisaged for the mantle convection cycle. One is that mantle convection with dispersing continental blocks has a short-wavelength structure, or close to degree-two structure as the present Earth, and when a supercontinent forms, mantle convection evolves into degree-one structure. Another is that mantle convection with dispersing continental blocks has a degree-one structure, and when a supercontinent forms, mantle convection evolves into degree-two structure. In the case of the former model, it would take longer time to form a supercontinent, because continental blocks would be trapped by different downwellings thus inhibiting collision. Although most of the numerical studies have assumed the continent/supercontinent to be rigid or nondeformable body mainly because of numerical limitations as well as a simplification of models, a more recent numerical study allows the modeling of mobile, deformable continents, including oceanic plates, and successfully reproduces continental drift similar to the processes and timescales envisaged in Wilson Cycle.
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2009-01-01
An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful. PMID:19495910
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Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway
NASA Astrophysics Data System (ADS)
Kim, Kyunghee; Pochan, Darrin
Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.
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NASA Astrophysics Data System (ADS)
Pernet-Fisher, John F.; Day, James M. D.; Howarth, Geoffrey H.; Ryabov, Victor V.; Taylor, Lawrence A.
2017-02-01
Organic carbon-rich sediment assimilation by basaltic magmas leads to enhanced emission of greenhouse gases during continental flood basalt eruptions. A collateral effect of these interactions is the generation of low oxygen fugacities (fO2) (below the iron-wüstite [IW] buffer curve) during magmatic crystallization, resulting in the precipitation of native-iron. The occurrence of native-iron bearing terrestrial basaltic rocks are rare, having been identified at three locations: Siberia, West Greenland, and Central Germany. We report the first combined study of Re-Os isotopes, highly siderophile element (HSE: Os, Ir, Ru, Pt, Pd, Re), and trace-element abundances for these three occurrences, in addition to host sediments at West Greenland. To quantify the amount of crustal assimilation experienced by the magmas, we present combined crystallization and assimilation models, together with fractional crystallization models, to assess how relative abundances of the HSE have been modified during crystallization. The radiogenic osmium isotopic compositions (γOsinitial +15 to +193) of mafic igneous samples are consistent with assimilation of old high Re/Os crustal contaminants with radiogenic 187Os/188Os, whereas the HSE inter-element fractionations (Pd/Os 2 to >10,000) suggest that some Siberian samples underwent an early stage of sulfide removal. Metalliferous samples from the Siberian intrusions of Khungtukun and Dzhaltul (associated with the Siberian flood basalts) yield internal 187Re-187Os ages of 266 ± 83Ma and 249 ± 50Ma, respectively, reflecting late-Permian emplacement ages. These results imply that crustal assimilation took place prior to crystallization of native-Fe. In contrast, metalliferous samples from Disko Island and Bühl (associated with the West Greenland flood basalts, and the Central European Volcanic Province, respectively) have trends in 187Re/188Os-187Os/188Os space corresponding to apparent ages older than their reported crystallization ages. These anomalous ages probably reflect concurrent assimilation of high Re/Os, radiogenic 187Os crust during crystallization of native-Fe, consistent with the character of local West Greenland sediments. In all three locations, calculations of combined assimilation of crustal sediments and fractional crystallization indicate between 1-7% assimilation can account for the Os-isotope systematics. In the case of Siberian samples, incompatible trace-element abundances indicate that lower crustal assimilation may have also occurred, consistent with the suggestion that crustal assimilation took place prior to native-Fe precipitation. The extent of local crustal contamination at Siberia, West Greenland, and Bühl necessitates that significant quantities of CH4, CO, CO2, SO2 and H2 O were released during assimilation of carbonaceous sediments. Consequently, carbonaceous sediment-basalt melt interactions have collateral effects on total gas output from flood basalt volcanism into the atmosphere. However, the amount of carbonaceous sediment contamination experienced by melts forming the Khungtukun and Dzhaltul intrusions alone, cannot explain the major C-isotope excursions at the Permo-Triassic mass-extinction event. Instead, further unsampled intrusions that also experienced significant carbonaceous sediment-melt interactions would be required. Enhanced greenhouse gas-emission during the Permo-Triassic mass extinction may have been facilitated by a combination of mantle melting and carbonaceous sediment-melt interactions, together with other proposed mechanisms, including wildfires, or by microbial metabolic exhalation.
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Brooks, G.R.; Holmes, C.W.
1990-01-01
Depositional patterns and sedimentary processes influencing modern southwest Florida carbonate slope development have been identified based upon slope morphology, seismic facies and surface sediment characteristics. Three slope-parallel zones have been identified: (1) an upper slope progradational zone (100-500 m) characterized by seaward-trending progradational clinoforms and sediments rich in shelf-derived carbonate material, (2) a lower gullied slope zone (500-800 m) characterized by numerous gullies formed by the downslope transport of gravity flows, and (3) a base-of-slope zone (> 800 m) characterized by thin, lens-shaped gravity flow deposits and irregular topography interpreted to be the result of bottom currents and slope failure along the basal extensions of gullies. Modern slope development is interpreted to have been controlled by the offshelf transport of shallow-water material from the adjacent west Florida shelf, deposition of this material along a seaward advancing sediment front, and intermittent bypassing of the lower slope by sediments transported in the form of gravity flows via gullies. Sediments are transported offshelf by a combination of tides and the Loop Current, augmented by the passage of storm frontal systems. Winter storm fronts produce cold, dense, sediment-laden water that cascades offshelf beneath the strong, eastward flowing Florida Current. Sediments are eventually deposited in a relatively low energy transition zone between the Florida Current on the surface and a deep westward flowing counter current. The influence of the Florida Current is evident in the easternmost part of the study area as eastward prograding sediments form a sediment drift that is progressively burying the Pourtales Terrace. The modern southwest Florida slope has seismic reflection and sedimentological characteristics in common with slopes bordering both the non-rimmed west Florida margin and the rimmed platform of the northern Bahamas, and shows many similarities to the progradational Miocene section along the west Florida slope. As with rimmed platform slopes, development of non-rimmed platform slopes can be complex and controlled by a combination of processes that result in a variety of configurations. Consequently, the distinction between the two slope types based solely upon seismic and sedimentological characteristics may not be readily discernible. ?? 1990.
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Active overbank deposition during the last century, South River, Virginia
NASA Astrophysics Data System (ADS)
Pizzuto, Jim; Skalak, Katherine; Pearson, Adam; Benthem, Adam
2016-03-01
We quantify rates of overbank deposition over decadal to centennial timescales along the South River in Virginia using four independent methods. Detailed mercury profiles sampled adjacent to the stream channel preserve the peak historic mercury concentration on suspended sediment dating from 1955 to 1961 and suggest sedimentation rates of 8 to 50 cm/100 years. Sediment accumulation over the roots of trees suggest rates of 0 to 100 cm/100 years, with significantly higher values on levees and lower values on floodplains farther from the channel. Profiles of 137Cs and 210Pb from two eroding streambanks are fit with an advection-diffusion model calibrated at an upland reference site; these methods suggest sedimentation rates of 44 to 73 cm/100 years. Mercury inventories from 107 floodplain cores, combined with a previously published reconstruction of the history of mercury concentration on suspended sediment, provide spatially comprehensive estimates of floodplain sedimentation: median sedimentation rates are 3.8 cm/100 years for the < 0.3-year floodplain, 1.37 cm/100 years for the 0.3- to 2-year floodplain, 0.4 cm/100 years for the 2- to 5-year floodplain, and 0.1 cm/100 years for the 5- to 62-year floodplain. While these sedimentation rates are relatively low, the total mass of sediment stored from 1930 to 2007 is 4.9 ± 1.7 (95% confidence interval) × 107 kg, corresponding to an average thickness of 2.5 cm (3.2 cm/100 years). These results demonstrate that floodplains of our 4.5-km-long study reach have stored 8 to 12% of the total suspended sediment supplied to the study reach of the South River. Hydrologic Engineering Center-River Analysis System (HEC-RAS) modeling demonstrates that the floodplain of the South River remains hydraulically connected to the channel: 56% of the 100-year floodplain is inundated every two years, and 83% of the floodplain is inundated every five years. These results, combined with previously published data, provide the basis for a regional synthesis of floodplain deposition rates since European settlement. Floodplain sedimentation rates were high following European settlement, with published estimates ranging from 50 to 200 cm/100 years. Sedimentation rates decreased by 1 to 2 orders of magnitude during the twentieth and twenty-first centuries; but despite these lower sedimentation rates, floodplains continue to store a significant fraction of total suspended sediment load. Many floodplains of the mid-Atlantic region are active landforms fully connected to the rivers that flow within them and should not be considered terraces isolated from contemporary fluvial processes by post-settlement aggradation.
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NASA Astrophysics Data System (ADS)
Buchty-Lemke, Michael; Frings, Roy; Hagemann, Lukas; Lehmkuhl, Frank; Maaß, Anna-Lisa; Schwarzbauer, Jan
2016-04-01
The Wurm River (Lower Rhine Embayment, Germany) is a small stream in a low mountain area near the Dutch-German border that has seen a lot of anthropogenic changes of its morphology since medieval times. Among other influencing factors, water mills, in particular, had an early impact on the sediment dynamics and created sediment traps. Several knickpoints in the long profile may represent the legacy of mill damming - or founded mill building at these spots. The knickpoints may also represent the aftermath of the colliery history. A study site in the upper reaches of the Wurm River features erosion terraces, incised following the demise of a mill dam in the early 20th century. The mill pond most likely collected sediment and additives e.g. used in agricultural and industrial processes. These legacy sediments from behind former mill dams provide information about anthropogenic pollution, particularly for the era of industrialization in the vicinity of the old industrial area of the city of Aachen. Along with the demise of the mill dam and the increased incision tendency, the sediments are also a secondary source for pollution in case of remobilization of contaminated sediments. Two major research questions are addressed. A) Which individual hydrological and geomorphological processes, both upstream and downstream, triggered the incision and the construction of the erosion terraces, which are preserved in the mill pond sediments? Is either the demised mill dam, or subsidence effects, or a combination of both the determining factor? B) Which contaminants are retained in the sediments? Is there a detectable point source for the pollutants or is it a mixture of diffuse anthropogenic (industry, agriculture, traffic, wastewater) and natural origin? To tackle these questions, sedimentological data are combined with geomorphological mapping and evaluation of historical data. A soil profile provides insight into the architecture of the floodplain, which is built of riverbed sediments overlain by stratified fine clastic and organic-rich material, representing the sediment being trapped when the mill dam existed. X-ray fluorescence and grain size analysis are used to determine the depositional process, provenance and chemostratigraphy. Knowledge about the distribution and fate of pollutants in sediments is valuable for river management purposes. Measures within the scope of the EU Water Framework Directive have been implemented at several breaches at the Wurm River, and further ones are planned. Potential risks due to remobilization of polluted alluvial sediments must thereby be taken into account. Furthermore, e.g. dismantling of transverse structures to improve passage for fish might trigger similar erosion processes and affects the sediment continuity.
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NASA Astrophysics Data System (ADS)
Ma, Wei-Wei; Zhu, Mao-Xu; Yang, Gui-Peng; Li, Tie
2018-02-01
In marine sediments factors that influence iron (Fe) geochemistry and its interactions with other elements are diverse and remain poorly understood. Here we comparatively study Fe speciation and reactive Fe-bound organic carbon (Fe-OC) in surface sediments of the East China Sea (ECS) and the south Yellow Sea (SYS). The objectives are to better understand the potential impacts of geochemically distinct sediment sources and depositional/diagenetic settings on Fe geochemistry and OC preservation by Fe (hydr)oxides in sediments of the two extensive shelf seas around the world. Contents of carbonate- and acid-volatile-sulfide (AVS)-associated Fe(II) (FeAVS + carb) and magnetite (Femag) in the ECS sediments are about 5 and 9 times higher, respectively, than in the SYS. This could be ascribed to the ferruginous conditions of the ECS sediments that favor the formation/accumulation of Fecarb and Femag, a unique feature of marine unsteady depositional regimes. Much lower total Fe(II) contents in the SYS than in the ECS suggest that lower availability of highly reactive Fe (FeHR) and/or weak Fe reduction is a factor limiting Fe(II) formation and accumulation in the SYS sediments. The ratio of FeHR to total Fe is, on average, markedly higher (2.4 times) in the ECS sediments than in the SYS, which may be a combined result of several factors relevant to different sediment sources and depositional/diagenetic settings. In comparison with many other marine sediments, the percent fractions (fFe-OC) of Fe-OC to total organic carbon (TOC) in the ECS and the SYS are low, which can be ascribed to surface adsorption of OC rather than coprecipitation or organic complexation as the dominant binding mechanisms. Based on the fFe-OC in this study, total Fe-OC estimated for global continental shelves is equivalent to 38% of the atmospheric CO2 pool, which indicates the important role of sorptive stabilization of Fe-OC in continental shelf sediments for buffering CO2 release to the atmosphere. In the SYS, consistently less 13C-depleted Fe-OC relative to 13C of non-Fe-bound OC (13Cnon-Fe-OC) suggests selective sequestration of labile marine OC in the marine OC-dominated sediments of the central SYS. In the ECS, however, efficient oxidation of OC and frequent redox cycling of Fe in the unsteady depositional regimes may complicate the isotopic compositions of Fe-OC. A combination of our results and literature data demonstrates that Fe-OC contents are strongly dependent on the availability of TOC and reactive Fe, but the fFe-OC is primarily controlled by the processes of Fe redox cycling in the sediments.
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Prediction of phenotypes of missense mutations in human proteins from biological assemblies.
Wei, Qiong; Xu, Qifang; Dunbrack, Roland L
2013-02-01
Single nucleotide polymorphisms (SNPs) are the most frequent variation in the human genome. Nonsynonymous SNPs that lead to missense mutations can be neutral or deleterious, and several computational methods have been presented that predict the phenotype of human missense mutations. These methods use sequence-based and structure-based features in various combinations, relying on different statistical distributions of these features for deleterious and neutral mutations. One structure-based feature that has not been studied significantly is the accessible surface area within biologically relevant oligomeric assemblies. These assemblies are different from the crystallographic asymmetric unit for more than half of X-ray crystal structures. We find that mutations in the core of proteins or in the interfaces in biological assemblies are significantly more likely to be disease-associated than those on the surface of the biological assemblies. For structures with more than one protein in the biological assembly (whether the same sequence or different), we find the accessible surface area from biological assemblies provides a statistically significant improvement in prediction over the accessible surface area of monomers from protein crystal structures (P = 6e-5). When adding this information to sequence-based features such as the difference between wildtype and mutant position-specific profile scores, the improvement from biological assemblies is statistically significant but much smaller (P = 0.018). Combining this information with sequence-based features in a support vector machine leads to 82% accuracy on a balanced dataset of 50% disease-associated mutations from SwissVar and 50% neutral mutations from human/primate sequence differences in orthologous proteins. Copyright © 2012 Wiley Periodicals, Inc.
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Bickhart, Derek M; Rosen, Benjamin D; Koren, Sergey; Sayre, Brian L; Hastie, Alex R; Chan, Saki; Lee, Joyce; Lam, Ernest T; Liachko, Ivan; Sullivan, Shawn T; Burton, Joshua N; Huson, Heather J; Nystrom, John C; Kelley, Christy M; Hutchison, Jana L; Zhou, Yang; Sun, Jiajie; Crisà, Alessandra; Ponce de León, F Abel; Schwartz, John C; Hammond, John A; Waldbieser, Geoffrey C; Schroeder, Steven G; Liu, George E; Dunham, Maitreya J; Shendure, Jay; Sonstegard, Tad S; Phillippy, Adam M; Van Tassell, Curtis P; Smith, Timothy P L
2017-04-01
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
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Bickhart, Derek M.; Rosen, Benjamin D.; Koren, Sergey; Sayre, Brian L.; Hastie, Alex R.; Chan, Saki; Lee, Joyce; Lam, Ernest T.; Liachko, Ivan; Sullivan, Shawn T.; Burton, Joshua N.; Huson, Heather J.; Nystrom, John C.; Kelley, Christy M.; Hutchison, Jana L.; Zhou, Yang; Sun, Jiajie; Crisà, Alessandra; de León, F. Abel Ponce; Schwartz, John C.; Hammond, John A.; Waldbieser, Geoffrey C.; Schroeder, Steven G.; Liu, George E.; Dunham, Maitreya J.; Shendure, Jay; Sonstegard, Tad S.; Phillippy, Adam M.; Van Tassell, Curtis P.; Smith, Timothy P.L.
2018-01-01
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ~400-fold improvement in continuity due to properly assembled gaps compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex ever produced for an individual of a ruminant species. PMID:28263316
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Zhang, Peng; Chen, Xiaoling; Lu, Jianzhong; Zhang, Wei
2015-12-01
Numerical models are important tools that are used in studies of sediment dynamics in inland and coastal waters, and these models can now benefit from the use of integrated remote sensing observations. This study explores a scheme for assimilating remotely sensed suspended sediment (from charge-coupled device (CCD) images obtained from the Huanjing (HJ) satellite) into a two-dimensional sediment transport model of Poyang Lake, the largest freshwater lake in China. Optimal interpolation is used as the assimilation method, and model predictions are obtained by combining four remote sensing images. The parameters for optimal interpolation are determined through a series of assimilation experiments evaluating the sediment predictions based on field measurements. The model with assimilation of remotely sensed sediment reduces the root-mean-square error of the predicted sediment concentrations by 39.4% relative to the model without assimilation, demonstrating the effectiveness of the assimilation scheme. The spatial effect of assimilation is explored by comparing model predictions with remotely sensed sediment, revealing that the model with assimilation generates reasonable spatial distribution patterns of suspended sediment. The temporal effect of assimilation on the model's predictive capabilities varies spatially, with an average temporal effect of approximately 10.8 days. The current velocities which dominate the rate and direction of sediment transport most likely result in spatial differences in the temporal effect of assimilation on model predictions.
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Peng, Xianzhi; Xiong, Songsong; Ou, Weihui; Wang, Zhifang; Tan, Jianhua; Jin, Jiabin; Tang, Caiming; Liu, Jun; Fan, Yujuan
2017-02-05
A variety of personal care products have been classified as emerging contaminants (ECs). Occurrence, fate, spatial and vertical profiles of 13 ultraviolet absorbents, triclocarban (TCC) and its dechlorinated products, triclosan (TCS), 2-phenylphenol and parabens were investigated in riverine and estuarine sediment of the Pearl River catchment, China. Bisphenol A (BPA), a widely applied plasticizer, was also investigated. The ECs were widely present in the bed sediment. TCC was the most abundant with a maximum concentration of 332ngg -1 dry weight. The other prominent ECs included BPA, TCS, octocrylene, and benzotriazole UV stabilizers UV326 and UV328. Treated wastewater effluent was the major source of the ECs in the riverine sediment. TCC, BPA, TCS, methyparaben, UV531, UV326, and UV328 were also detected throughout the estuarine sediment cores, indicating their persistence in the sediment. Temporal trends of the ECs in the sediment cores reflected a combined effect of industrial development, population growth, human life quality improvement, and waste treatment capacity in the Pearl River Delta over the last decades. TCC dechlorination products were frequently detected in the bed sediment with higher levels near treated effluent outlets but only occasionally observed in the sediment cores, suggesting insignificant in-situ TCC dechlorination in the sediment. Copyright © 2016 Elsevier B.V. All rights reserved.
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Optical properties of three-dimensional P(St-MAA) photonic crystals on polyester fabrics
NASA Astrophysics Data System (ADS)
Liu, Guojin; Zhou, Lan; Wu, Yujiang; Wang, Cuicui; Fan, Qinguo; Shao, Jianzhong
2015-04-01
The three-dimensional (3D) photonic crystals with face-centered cubic (fcc) structure was fabricated on polyester fabrics, a kind of soft textile materials quite different from the conventional solid substrates, by gravitational sedimentation self-assembly of monodisperse P(St-MAA) colloidal microspheres. The optical properties of structural colors on polyester fabrics were investigated and the position of photonic band gap was characterized. The results showed that the color-tuning ways of the structural colors from photonic crystals were in accordance with Bragg's law and could be modulated by the size of P(St-MAA) colloidal microspheres and the viewing angles. The L∗a∗b∗ values of the structural colors generated from the assembled polyester fabrics were in agreement with their reflectance spectra. The photonic band gap position of photonic crystals on polyester fabrics could be consistently confirmed by reflectance and transmittance spectra.
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A deterministic (non-stochastic) low frequency method for geoacoustic inversion.
Tolstoy, A
2010-06-01
It is well known that multiple frequency sources are necessary for accurate geoacoustic inversion. This paper presents an inversion method which uses the low frequency (LF) spectrum only to estimate bottom properties even in the presence of expected errors in source location, phone depths, and ocean sound-speed profiles. Matched field processing (MFP) along a vertical array is used. The LF method first conducts an exhaustive search of the (five) parameter search space (sediment thickness, sound-speed at the top of the sediment layer, the sediment layer sound-speed gradient, the half-space sound-speed, and water depth) at 25 Hz and continues by retaining only the high MFP value parameter combinations. Next, frequency is slowly increased while again retaining only the high value combinations. At each stage of the process, only those parameter combinations which give high MFP values at all previous LF predictions are considered (an ever shrinking set). It is important to note that a complete search of each relevant parameter space seems to be necessary not only at multiple (sequential) frequencies but also at multiple ranges in order to eliminate sidelobes, i.e., false solutions. Even so, there are no mathematical guarantees that one final, unique "solution" will be found.
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A BPTTF-based self-assembled electron-donating triangle capable of C60 binding.
Goeb, Sébastien; Bivaud, Sébastien; Dron, Paul Ionut; Balandier, Jean-Yves; Chas, Marcos; Sallé, Marc
2012-03-25
A kinetically stable self-assembled redox-active triangle is isolated. The resulting electron-donating cavity, which incorporates three BPTTF units, exhibits a remarkable binding ability for electron-deficient C(60), supported by a favorable combination of structural and electronic features.
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FILTRATION OF SALT SMOKE FROM CHLORATE CANDLE OXYGEN.
their associated equipment for use on submarines. Rockwool -wire mesh combinations were first used in welded assemblies which were cleaned by water...washing when they became clogged. The rockwool was later replaced with fiberglass blanket, and two modifications of the assembly were made, but the
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In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway
NASA Astrophysics Data System (ADS)
Ning, Jiying; Erdemci-Tandogan, Gonca; Yufenyuy, Ernest L.; Wagner, Jef; Himes, Benjamin A.; Zhao, Gongpu; Aiken, Christopher; Zandi, Roya; Zhang, Peijun
2016-12-01
HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.
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Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics1
Weitemier, Kevin; Straub, Shannon C. K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron
2014-01-01
• Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. • Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. • Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics. PMID:25225629
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Durbin, Alan M.; Teske, Andreas
2012-01-01
Examining the patterns of archaeal diversity in little-explored organic-lean marine subsurface sediments presents an opportunity to study the association of phylogenetic affiliation and habitat preference in uncultured marine Archaea. Here we have compiled and re-analyzed published archaeal 16S rRNA clone library datasets across a spectrum of sediment trophic states characterized by a wide range of terminal electron-accepting processes. Our results show that organic-lean marine sediments in deep marine basins and oligotrophic open ocean locations are inhabited by distinct lineages of archaea that are not found in the more frequently studied, organic-rich continental margin sediments. We hypothesize that different combinations of electron donor and acceptor concentrations along the organic-rich/organic-lean spectrum result in distinct archaeal communities, and propose an integrated classification of habitat characteristics and archaeal community structure. PMID:22666218
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Hyperpycnal plume-derived fans in the Santa Barbara Channel, California
Warrick, Jonathan A.; Simms, Alexander R.; Ritchie, Andy; Steel, Elisabeth; Dartnell, Pete; Conrad, James E.; Finlayson, David P.
2013-01-01
Hyperpycnal gravity currents rapidly transport sediment across shore from rivers to the continental shelf and deep sea. Although these geophysical processes are important sediment dispersal mechanisms, few distinct geomorphic features on the continental shelf can be attributed to hyperpycnal flows. Here we provide evidence of large depositional features derived from hyperpycnal plumes on the continental shelf of the northern Santa Barbara Channel, California, from the combination of new sonar, lidar, and seismic reflection data. These data reveal lobate fans directly offshore of the mouths of several watersheds known to produce hyperpycnal concentrations of suspended sediment. The fans occur on an upwardly concave section of the shelf where slopes decrease from 0.04 to 0.01, and the location of these fans is consistent with wave- and auto-suspending sediment gravity current theories. Thus, we provide the first documentation that the morphology of sediment deposits on the continental shelf can be dictated by river-generated hyperpycnal flows.
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Sources of suspended sediment in the Lower Roanoke River, NC
NASA Astrophysics Data System (ADS)
Jalowska, A. M.; McKee, B. A.; Rodriguez, A. B.; Laceby, J. P.
2015-12-01
The Lower Roanoke River, NC, extends 220 km from the fall line to the bayhead delta front in the Albemarle Sound. The Lower Roanoke is almost completely disconnected from the upper reaches by a series of dams, with the furthest downstream dam located at the fall line. The dams effectively restrict the suspended sediment delivery from headwaters, making soils and sediments from the Lower Roanoke River basin, the sole source of suspended sediment. In flow-regulated rivers, bank erosion, especially mass wasting, is the major contributor to the suspended matter. Additional sources of the suspended sediment considered in this study are river channel, surface soils, floodplain surface sediments, and erosion of the delta front and prodelta. Here, we examine spatial and temporal variations in those sources. This study combined the use of flow and grain size data with a sediment fingerprinting method, to examine the contribution of surface and subsurface sediments to the observed suspended sediment load along the Lower Roanoke River. The fingerprinting method utilized radionuclide tracers 210Pb (natural atmospheric fallout), and 137Cs (produced by thermonuclear bomb testing). The contributions of surface and subsurface sources to the suspended sediment were calculated with 95% confidence intervals using a Monte-Carlo numerical mixing model. Our results show that with decreasing river slope and changing hydrography along the river, the contribution of surface sediments increases and becomes a main source of sediments in the Roanoke bayhead delta. At the river mouth, the surface sediment contribution decreases and is replaced by sediments eroded from the delta front and prodelta. The area of high surface sediment contribution is within the middle and upper parts of the delta, which are considered net depositional. Our study demonstrates that floodplains, often regarded to be a sediment sink, are also a sediment source, and they should be factored into sediment, carbon and nutrient budgets.
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Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.
Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung
2016-02-24
Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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1969-01-01
In the clustering procedure, an initial assembly step for the Saturn IB launch vehicle's S-IB (first) stage, workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, position the central liquid-oxygen tank. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.
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The effects of wildfire on the sediment yield of a coastal California watershed
Warrick, J.A.; Hatten, J.A.; Pasternack, G.B.; Gray, A.B.; Goni, M.A.; Wheatcroft, R.A.
2012-01-01
The occurrence of two wildfires separated by 31 yr in the chaparral-dominated Arroyo Seco watershed (293 km) of California provides a unique opportunity to evaluate the effects of wildfire on suspended-sediment yield. Here, we compile discharge and suspended-sediment sampling data from before and after the fires and show that the effects of the postfire responses differed markedly. The 1977 Marble Cone wildfire was followed by an exceptionally wet winter, which resulted in concentrations and fluxes of both fine and coarse suspended sediment that were ˜35 times greater than average (sediment yield during the 1978 water year was 11,000 t/km2/yr). We suggest that the combined 1977–1978 fire and flood had a recurrence interval of greater than 1000 yr. In contrast, the 2008 Basin Complex wildfire was followed by a drier than normal year, and although suspended-sediment fluxes and concentrations were significantly elevated compared to those expected for unburned conditions, the sediment yield during the 2009 water year was less than 1% of the post–Marble Cone wildfire yield. After the first postfire winters, sediment concentrations and yield decreased with time toward prefire relationships and continued to have significant rainfall dependence. We hypothesize that the differences in sediment yield were related to precipitation-enhanced hillslope erosion processes, such as rilling and mass movements. The millennial-scale effects of wildfire on sediment yield were explored further using Monte Carlo simulations, and these analyses suggest that infrequent wildfires followed by floods increase long-term suspended-sediment fluxes markedly. Thus, we suggest that the current approach of estimating sediment yield from sediment rating curves and discharge data—without including periodic perturbations from wildfires—may grossly underestimate actual sediment yields.
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Yi, Xiaoyi; Li, Huizhen; Ma, Ping; You, Jing
2015-08-01
Sediments in urban waterways of Guangzhou, China, were contaminated by a variety of chemicals and showed prevalent toxicity to benthic organisms. A combination of whole-sediment toxicity identification evaluation (TIE) and bioavailability-based extraction was used to identify the causes of sediment toxicity. Of the 6 sediment samples collected, 4 caused 100% mortality to Chironomus dilutus in 10-d bioassays, and the potential toxicants were assessed using TIE in these sediments after dilution. The results of phase I characterization showed that organic contaminants were the principal contributors to the mortality of the midges in 2 sediments and that metals and organics jointly caused the mortality in the other 2 sediments. Ammonia played no role in the mortality for any samples. Conventional toxic unit analysis in phase II testing identified Cr, Cu, Ni, Pb, and Zn as the toxic metals, with cypermethrin, lambda-cyhalothrin, deltamethrin, and fipronils being the toxic organics. To improve the accuracy of identifying the toxicants, 4-step sequential extraction and Tenax extraction were conducted to analyze the bioavailability of the metals and organics, respectively. Bioavailable toxic unit analysis narrowed the list of toxic contributors, and the putative toxicants included 3 metals (Zn, Ni, and Pb) and 3 pesticides (cypermethrin, lambda-cyhalothrin, and fipronils). Metals contributed to the mortality in all sediments, but sediment dilution reduced the toxicity and confounded the characterization of toxicity contribution from metals in 2 sediments in phase I. Incorporating bioavailability-based measurements into whole-sediment TIE improved the accuracy of identifying the causative toxicants in urban waterways where multiple stressors occurred and contributed to sediment toxicity jointly. © 2015 SETAC.
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East, Amy E.; Clift, Peter D.; Carter, Andrew; Alizai, Anwar; VanLaningham, Sam
2015-01-01
Sediment production and its subsequent preservation in the marine stratigraphic record offshore of large rivers are linked by complex sediment-transfer systems. To interpret the stratigraphic record it is critical to understand how environmental signals transfer from sedimentary source regions to depositional sinks, and in particular to understand the role of buffering in obscuring climatic or tectonic signals. In dryland regions, signal buffering can include sediment cycling through linked fluvial and eolian systems. We investigate sediment-routing connectivity between the Indus River and the Thar Desert, where fluvial and eolian systems exchanged sediment over large spatial scales (hundreds of kilometers). Summer monsoon winds recycle sediment from the lower Indus River and delta northeastward, i.e., downwind and upstream, into the desert. Far-field eolian recycling of Indus sediment is important enough to control sediment provenance at the downwind end of the desert substantially, although the proportion of Indus sediment of various ages varies regionally within the desert; dune sands in the northwestern Thar Desert resemble the Late Holocene–Recent Indus delta, requiring short transport and reworking times. On smaller spatial scales (1–10 m) along fluvial channels in the northern Thar Desert, there is also stratigraphic evidence of fluvial and eolian sediment reworking from local rivers. In terms of sediment volume, we estimate that the Thar Desert could be a more substantial sedimentary store than all other known buffer regions in the Indus basin combined. Thus, since the mid-Holocene, when the desert expanded as the summer monsoon rainfall decreased, fluvial-eolian recycling has been an important but little recognized process buffering sediment flux to the ocean. Similar fluvial-eolian connectivity likely also affects sediment routing and signal transfer in other dryland regions globally.
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Structures of ribonucleoprotein particle modification enzymes
Liang, Bo; Li, Hong
2016-01-01
Small nucleolar and Cajal body ribonucleoprotein particles (RNPs) are required for the maturation of ribosomes and spliceosomes. They consist of small nucleolar RNA or Cajal body RNA combined with partner proteins and represent the most complex RNA modification enzymes. Recent advances in structure and function studies have revealed detailed information regarding ribonucleoprotein assembly and substrate binding. These enzymes form intertwined RNA–protein assemblies that facilitate reversible binding of the large ribosomal RNA or small nuclear RNA. These revelations explain the specificity among the components in enzyme assembly and substrate modification. The multiple conformations of individual components and those of complete RNPs suggest a dynamic assembly process and justify the requirement of many assembly factors in vivo. PMID:21108865
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NASA Astrophysics Data System (ADS)
Karwan, D. L.; Pizzuto, J. E.; Skalak, K.; Benthem, A.
2016-12-01
The sources and transport of suspended sediments within watersheds of varying sizes remain an important area of study within the geosciences. Short term fallout radionuclides, such as Beryllium-7 (7Be) and Lead-210 (210Pb), and their ratios can be a valuable tool for gaining insight into suspended sediment transport dynamics. We use these techniques in combination with other sediment exchange and transport models to estimate residence and transport time of suspended sediment in nested reaches of the Difficult Run watershed (Virginia, USA) on timescales from storm events to centuries and longer. During several winter and spring 2015-2016 precipitation events, Beryllium-7 to excess Lead-210 ratios vary from 0.4 - 2.5 in direct channel precipitation and 0.2 - 1 on suspended sediment. Previously published age dating models would suggest that the suspended sediments were originally "tagged" by, or in contact with wet fallout of, by Beryllium7 fallout approximately 20-80 days before sampling. Sediments at the upstream reach (watershed size 14 km2) tend to be older ( 75 days), while sediments at the downstream reach (watershed size 117 km2) tend to be newer ( 20 days). We use multiple sediment transport models and hypothesize that fluvial sediments are tagged with direct channel precipitation between the upstream and downstream reach, explaining their apparently younger age. Our analysis includes error propagation as well as a comparison of radioisotope gamma analyses from different labs across multiple institutions.
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Kinetic and microbial community analysis of methyl ethyl ketone biodegradation in aquifer sediments.
Fahrenfeld, N; Pruden, A; Widdowson, M
2017-02-01
Methyl ethyl ketone (MEK) is a common groundwater contaminant often present with more toxic compounds of primary interest. Because of this, few studies have been performed to determine the effect of microbial community structure on MEK biodegradation rates in aquifer sediments. Here, microcosms were prepared with aquifer sediments containing MEK following a massive spill event and compared to laboratory-spiked sediments, with MEK biodegradation rates quantified under mixed aerobic/anaerobic conditions. Biodegradation was achieved in MEK-contaminated site sediment microcosms at about half of the solubility (356 mg/L) with largely Firmicutes population under iron-reducing conditions. MEK was biodegraded at a higher rate [4.0 ± 0.74 mg/(L days)] in previously exposed site samples compared to previously uncontaminated sediments [0.51 ± 0.14 mg/(L days)]. Amplicon sequencing and denaturing gradient gel electrophoresis of 16S rRNA genes were combined to understand the relationship between contamination levels, biodegradation, and community structure across the plume. More heavily contaminated sediments collected from an MEK-contaminated field site had the most similar communities than less contaminated sediments from the same site despite differences in sediment texture. The more diverse microbial community observed in the laboratory-spiked sediments reduced MEK concentration 47 % over 92 days. Results of this study suggest lower rates of MEK biodegradation in iron-reducing aquifer sediments than previously reported for methanogenic conditions and biodegradation rates comparable to previously reported nitrate- and sulfate-reducing conditions.
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Han, Xiaoyu; Liu, Jiahui; Zhao, Chaoyue; Zhang, Bao; Xu, Xiufang; Song, Jian
2018-09-01
Hydrogels induced by two-component gelator isomers based on the different amine/acid interactions were investigated. Scanning electron microscopy and atomic force microscopy images of the xerogel obtained from the two hydrogels revealed different assembly morphologies. While left-handed helical fibers were observed for the amine-acid based xerogel, acid-amine underwent self-assembly to afford smooth fibers. Fourier transform infrared spectroscopy, fluorescence, and X-ray diffraction measurements combined with density functional theory calculations suggested that the different self-assembly patterns of gelators resulted in opposite electric charges on the xerogel surfaces, in line with Zeta potential measurements. Based on these opposite charges resulting from their different self-assemblies, both xerogels demonstrated efficient dye adsorption abilities with different selectivities. Interestingly, the adsorption performance was not influenced by the salt in the dye solution. Furthermore, the xerogels still showed high dye adsorption efficiency after four cycles. These results provide a two-component hydrogel method for the purification of dye-polluted water systems, while also paving the way for future design of functionalized supramolecular self-assembly systems. Copyright © 2018 Elsevier Inc. All rights reserved.
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Berga, Mercè; Östman, Örjan; Lindström, Eva S; Langenheder, Silke
2015-07-01
Effects of dispersal and the presence of predators on diversity, assembly and functioning of bacterial communities are well studied in isolation. In reality, however, dispersal and trophic interactions act simultaneously and can therefore have combined effects, which are poorly investigated. We performed an experiment with aquatic metacommunities consisting of three environmentally different patches and manipulated dispersal rates among them as well as the presence or absence of the keystone species Daphnia magna. Daphnia magna reduced both local and regional diversity, whereas dispersal increased local diversity but decreased beta-diversity having no net effect on regional diversity. Dispersal modified the assembly mechanisms of bacterial communities by increasing the degree of determinism. Additionally, the combination of the D. magna and dispersal increased the importance of deterministic processes, presumably because predator-tolerant taxa were spread in the metacommunity via dispersal. Moreover, the presence of D. magna affected community composition, increased community respiration rates but did not affect bacterial production or abundance, whereas dispersal slightly increased bacterial production. In conclusion, our study suggests that predation by a keystone species such as D. magna and dispersal additively influence bacterial diversity, assembly processes and ecosystem functioning. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Benton, Matthew A; Kenny, Nathan J; Conrads, Kai H; Roth, Siegfried; Lynch, Jeremy A
2016-01-01
Despite recent efforts to sample broadly across metazoan and insect diversity, current sequence resources in the Coleoptera do not adequately describe the diversity of the clade. Here we present deep, staged transcriptomic data for two coleopteran species, Atrachya menetriesi (Faldermann 1835) and Callosobruchus maculatus (Fabricius 1775). Our sampling covered key stages in ovary and early embryonic development in each species. We utilized this data to build combined assemblies for each species which were then analysed in detail. The combined A. menetriesi assembly consists of 228,096 contigs with an N50 of 1,598 bp, while the combined C. maculatus assembly consists of 128,837 contigs with an N50 of 2,263 bp. For these assemblies, 34.6% and 32.4% of contigs were identified using Blast2GO, and 97% and 98.3% of the BUSCO set of metazoan orthologs were present, respectively. We also carried out manual annotation of developmental signalling pathways and found that nearly all expected genes were present in each transcriptome. Our analyses show that both transcriptomes are of high quality. Lastly, we performed read mapping utilising our timed, stage specific RNA samples to identify differentially expressed contigs. The resources presented here will provide a firm basis for a variety of experimentation, both in developmental biology and in comparative genomic studies.
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NASA Astrophysics Data System (ADS)
Wang, Junqiang; Wang, Qian; Wu, Zijian; Tan, Lin; Cai, Jian; Wang, Dejun
2017-05-01
A novel pretreatment of plasma combined self-assembled monolayer (PcSAM) was proposed to improve surface properties of electroplated Cu for low temperature Cu-Sn bonding in 3D integration. Measurement results revealed that self-assemble monolayer (SAM) would be easier absorbed on plasma-activated Cu surface and protect the clean surface from re-oxidation when storage. The absorbed SAM layer could be removed by thermal desorption during bonding process. With optimal PcSAM pretreatment, oxygen content of the Cu surface was reduced to as low as 1.39%. The followed Cu-Sn bonding was realized at low temperature of 200 °C. Finally, bonding interface exhibited a defect-free interconnection, and bonding strength has reached as high as 68.7 MPa.
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Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.
Kleftogiannis, Dimitrios; Kalnis, Panos; Bajic, Vladimir B
2013-01-01
A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memory by choosing suitable assembly methods. Our study reveals the minimum memory requirements for different assembly programs even when data volume exceeds memory capacity by orders of magnitude. By combining existing methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment on some findings regarding suitable computational resources for assembly.
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2010-01-01
Background Diagnostic options for pulmonary tuberculosis in resource-poor settings are commonly limited to smear microscopy. We investigated whether bleach concentration by sedimentation and sputum cytology analysis (SCA) increased the positivity rate of smear microscopy for smear-positive tuberculosis. Methods We did a prospective diagnostic study in a Médecins Sans Frontières-supported hospital in Mindouli, Republic of Congo. Three sputum samples were obtained from 280 consecutive pulmonary tuberculosis suspects, and were processed according to WHO guidelines for direct smear microscopy. The remainder of each sputum sample was homogenised with 2.6% bleach, sedimented overnight, smeared, and examined blinded to the direct smear result for acid-fast bacilli (AFB). All direct smears were assessed for quality by SCA. If a patient produced fewer than three good-quality sputum samples, further samples were requested. Sediment smear examination was performed independently of SCA result on the corresponding direct smear. Positivity rates were compared using McNemar's test. Results Excluding SCA, 43.2% of all patients were diagnosed as positive on direct microscopy of up to three samples. 47.9% were diagnosed on sediment microscopy, with 48.2% being diagnosed on direct microscopy, sediment microscopy, or both. The positivity rate increased from 43.2% to 47.9% with a case definition of one positive smear (≥1 AFB/100 high power fields) of three, and from 42.1% to 43.9% with two positive smears. SCA resulted in 87.9% of patients producing at least two good-quality sputum samples, with 75.7% producing three or more. Using a case definition of one positive smear, the incremental yield of bleach sedimentation was 14/121, or 11.6% (95% CI 6.5-18.6, p = 0.001) and in combination with SCA was 15/121, or 12.4% (95% CI 7.1-19.6, p = 0.002). Incremental yields with two positive smears were 5/118, or 4.2% (95% CI 1.4-9.6, p = 0.062) and 7/118, or 5.9% (95% CI 2.4-11.8, p = 0.016), respectively. Conclusions The combination of bleach sedimentation and SCA resulted in significantly increased microscopy positivity rates with a case definition of either one or two positive smears. Implementation of bleach sedimentation led to a significant increase in the diagnosis of smear-positive patients. Implementation of SCA did not result in significantly increased diagnosis of tuberculosis, but did result in improved sample quality. Requesting extra sputum samples based on SCA results, combined with bleach sedimentation, could significantly increase the detection of smear-positive patients if routinely implemented in resource-limited settings where gold standard techniques are not available. We recommend that a pilot phase is undertaken before routine implementation to determine the impact in a particular context. PMID:20858253
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Wu, Chi; Xie, Zuowei; Zhang, Guangzhao; Zi, Guofu; Tu, Yingfeng; Yang, Yali; Cai, Ping; Nie, Ting
2002-12-07
A combination of polymer physics and synthetic chemistry has enabled us to develop self-assembly assisted polymerization (SAAP), leading to the preparation of long multi-block copolymers with an ordered chain sequence and controllable block lengths.
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Cell-free protein synthesis and assembly on a biochip
NASA Astrophysics Data System (ADS)
Heyman, Yael; Buxboim, Amnon; Wolf, Sharon G.; Daube, Shirley S.; Bar-Ziv, Roy H.
2012-06-01
Biologically active complexes such as ribosomes and bacteriophages are formed through the self-assembly of proteins and nucleic acids. Recapitulating these biological self-assembly processes in a cell-free environment offers a way to develop synthetic biodevices. To visualize and understand the assembly process, a platform is required that enables simultaneous synthesis, assembly and imaging at the nanoscale. Here, we show that a silicon dioxide grid, used to support samples in transmission electron microscopy, can be modified into a biochip to combine in situ protein synthesis, assembly and imaging. Light is used to pattern the biochip surface with genes that encode specific proteins, and antibody traps that bind and assemble the nascent proteins. Using transmission electron microscopy imaging we show that protein nanotubes synthesized on the biochip surface in the presence of antibody traps efficiently assembled on these traps, but pre-assembled nanotubes were not effectively captured. Moreover, synthesis of green fluorescent protein from its immobilized gene generated a gradient of captured proteins decreasing in concentration away from the gene source. This biochip could be used to create spatial patterns of proteins assembled on surfaces.
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Classification of coordination polygons and polyhedra according to their mode of self-assembly.
Swiegers, G F; Malefetse, T J
2001-09-03
This work extends techniques for the controlled formation of synthetic molecular containers by metal-mediated self-assembly. A new classification system based on the self-assembly of such species is proposed. The system: 1) allows a systematic identification of suitable acceptor-donor combinations, 2) widens the variety of design possibilities available, 3) allows a ready comparison of the self-assembly of different compounds, 4) reveals useful commonalities between different compounds, 5) aids in the development of novel architectures, and 6) permits identification of systems capable of being switched back-and-forth between architectures.
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NASA Astrophysics Data System (ADS)
Griffiths, Ronald E.; Topping, David J.
2017-11-01
Sediment budgets are an important tool for understanding how riverine ecosystems respond to perturbations. Changes in the quantity and grain size distribution of sediment within river systems affect the channel morphology and related habitat resources. It is therefore important for resource managers to know if a river reach is in a state of sediment accumulation, deficit or stasis. Many sediment-budget studies have estimated the sediment loads of ungaged tributaries using regional sediment-yield equations or other similar techniques. While these approaches may be valid in regions where rainfall and geology are uniform over large areas, use of sediment-yield equations may lead to poor estimations of loads in regions where rainfall events, contributing geology, and vegetation have large spatial and/or temporal variability. Previous estimates of the combined mean-annual sediment load of all ungaged tributaries to the Colorado River downstream from Glen Canyon Dam vary by over a factor of three; this range in estimated sediment loads has resulted in different researchers reaching opposite conclusions on the sign (accumulation or deficit) of the sediment budget for particular reaches of the Colorado River. To better evaluate the supply of fine sediment (sand, silt, and clay) from these tributaries to the Colorado River, eight gages were established on previously ungaged tributaries in Glen, Marble, and Grand canyons. Results from this sediment-monitoring network show that previous estimates of the annual sediment loads of these tributaries were too high and that the sediment budget for the Colorado River below Glen Canyon Dam is more negative than previously calculated by most researchers. As a result of locally intense rainfall events with footprints smaller than the receiving basin, floods from a single tributary in semi-arid regions can have large (≥ 10 ×) differences in sediment concentrations between equal magnitude flows. Because sediment loads do not necessarily correlate with drainage size, and may vary by two orders of magnitude on an annual basis, using techniques such as sediment-yield equations to estimate the sediment loads of ungaged tributaries may lead to large errors in sediment budgets.
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Griffiths, Ronald; Topping, David
2017-01-01
Sediment budgets are an important tool for understanding how riverine ecosystems respond to perturbations. Changes in the quantity and grain size distribution of sediment within river systems affect the channel morphology and related habitat resources. It is therefore important for resource managers to know if a river reach is in a state of sediment accumulation, deficit or stasis. Many sediment-budget studies have estimated the sediment loads of ungaged tributaries using regional sediment-yield equations or other similar techniques. While these approaches may be valid in regions where rainfall and geology are uniform over large areas, use of sediment-yield equations may lead to poor estimations of loads in regions where rainfall events, contributing geology, and vegetation have large spatial and/or temporal variability.Previous estimates of the combined mean-annual sediment load of all ungaged tributaries to the Colorado River downstream from Glen Canyon Dam vary by over a factor of three; this range in estimated sediment loads has resulted in different researchers reaching opposite conclusions on the sign (accumulation or deficit) of the sediment budget for particular reaches of the Colorado River. To better evaluate the supply of fine sediment (sand, silt, and clay) from these tributaries to the Colorado River, eight gages were established on previously ungaged tributaries in Glen, Marble, and Grand canyons. Results from this sediment-monitoring network show that previous estimates of the annual sediment loads of these tributaries were too high and that the sediment budget for the Colorado River below Glen Canyon Dam is more negative than previously calculated by most researchers. As a result of locally intense rainfall events with footprints smaller than the receiving basin, floods from a single tributary in semi-arid regions can have large (≥ 10 ×) differences in sediment concentrations between equal magnitude flows. Because sediment loads do not necessarily correlate with drainage size, and may vary by two orders of magnitude on an annual basis, using techniques such as sediment-yield equations to estimate the sediment loads of ungaged tributaries may lead to large errors in sediment budgets.
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Nelson, C.H.; Maldonado, A.
1990-01-01
The Ebro continental margin sedimentation system originated with a Messinian fluvial system. This system eroded both a major subaerial canyon cutting the margin southeastward from the present Ebro Delta and an axial valley that drained northeastward down Valencia Trough. Post-Messinian submergence of this topography and the Pliocene regime of high sea levels resulted in a marine hemipelagic drape over the margin. Late Pliocene to Pleistocene glacial climatic cycles, drainagebasin deforestation, and sea-level lowstands combined to increase sediment supply, cause the margin to prograde, and create a regime of lowstand sediment-gravity flows in the deeper margin. The depositional patterns of regressive, transgressive and highstand sea-level regimes suggest that location of the sediment source near the present Ebro Delta throughout the late Cenozoic, southward current advection of sediment, and greater subsidence in the southern margin combined to cause generally asymmetric progradation of the margin to the southeast. Thicker, less stable deposits filling the Messinian subaerial canyon underwent multiple retrograde failures, eroded wide gullied canyons and formed unchanneled base-of-slope sediment aprons in the central margin area; other margin areas to the north and south developed a series of channel-levee complexes. On the basin floor, the formation of Valencia Valley over the Messinian subaerial valley and earlier faults led to draining of about 20% of the Ebro Pleistocene sediment from channel-levee complexes through the valley to prograde Valencia Fan as much as 500 km northeast of the margin. Thus, the Ebro margin has two growth directions, mainly southeastward during higher sea levels, and eastward to northeastward during lower sea levels. The northeastward draining of turbidity currents has produced unusually thin and widely dispersed turbidite systems compared to those on ponded basin floors. During the past few centuries, man's impact has exceeded natural controls on Ebro margin growth. Deforestation of the drainage basin more than doubled the normal Holocene sediment supply, and construction of dams then reduced the supply by 95%. This reduction of the past 50 years has caused erosion of the delta and contamination of bottom sediment because normal Holocene sediment discharge is not available to prograde the delta or help dilute pollutants. ?? 1990.
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NASA Astrophysics Data System (ADS)
Fricke, A. T.; Nittrouer, C. A.; Ogston, A. S.; Vo-Luong, H. P.
2017-09-01
Mangrove forests are an important means of coastal protection along many shorelines in the tropics, and are often associated with large rivers there. Isolating the contribution of any one factor to the progradation or retreat of a coastal mangrove forest is often hindered by the physical separation between sites that are subject to vastly different combinations of marine and fluvial influence. The mangrove forest at the seaward end of Cù Lao Dung, an island in the Mekong Delta, includes areas with progradation rates of 10 s m y-1, and areas that have experienced little to no progradation in recent decades. The physical proximity (<12 km) of these two environments allows detailed hydrodynamic and sediment-dynamic measurements to be related directly to morphologic change and century-scale stratigraphy. Contrary to conventional understanding, the region of mangrove forest prograding most rapidly is subject to the greatest wave attack, while progradation is slowest in the most quiescent area. Limited progradation here is the product of a reduction in the supply of sediment to certain parts of the mangrove forest due to nearby estuarine dynamics operating on spring-neap timescales. Measurements of sediment flux show net transport into the rapidly prograding part of the forest, and transport out from the part of the forest with minimal progradation. Century-scale rates of sediment accumulation determined using 210Pb geochronology are consistent with in-situ dynamical measurements and geomorphic evolution of the mangrove forest. Where progradation is most rapid, sediment accumulation rates (3.0-5.1 cm y-1) exceed the rate of local sea-level rise (∼1.5 cm y-1). In contrast, sediment-accumulation rates in the area of minimal progradation (0.8-2.8 cm y-1) only somewhat exceed the rate of local sea-level rise, if at all. Physical stratification is well preserved in cores from areas of rapid progradation, consistent with energetic transport processes and an ample sediment supply. Greater impact from bioturbation and episodic sediment delivery produce more variable bedding where progradation is less rapid. The presence of a supply-limited mangrove forest adjacent to a major sediment source highlights the complexity of sediment-supply pathways in coastal mangrove environments.
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NASA Astrophysics Data System (ADS)
Dume, Bayu; Amsalu, Nebiyu; Bode, Samuel; Mtei, Kelvin; Munishi, Linus; Navas, Ana; Semmens, Brice; Smith, Hugh; Stock, Brian; Blake, Will; Boeckx, Pascal
2017-04-01
Soil erosion and associated downstream siltation of dams and lakes is becoming serious threat to catchment ecosystem services supporting water, food and energy security in Ethiopia. Sediments originate on catchment hillslopes but mobilisation processes vary depending on land use and terrain. The Gilgel Gibe hydroelectric dam is one of a series of development projects launched by the Federal Government of Ethiopia. The catchment is characterised by erodible, deforested agricultural land which is also overgrazed. Siltation and nutrient enrichment are significant issues given 'hotspot' sheet erosion estimates of 2210 ton per square km. The annual contribution of sediment from the Gilgel Gibe River to the dam was estimated at 277 thousand tons per year leading to accumulations of 3.75 x 107 cubic metres per year of silt behind the dam. The primary driver for mobilisation and translocation to downstream is believed to be erosion on agricultural lands and collapse of steep banks, through landsliding into river channels in the highland headwaters. The relative importance of specific sources of siltation are unknown and sediment source apportionment has been identified as a first essential step before soil conservation measures can be implemented. Knowledge of sediment source and transfer dynamics is critical to inform management policy decisions to maintain and enhance future food, water and energy security To test the applicability of a new combination of Bayesian unmixing modelling with sediment fingerprinting in this terrain (IMIXSED approach) a demonstration sub-catchment was selected through field assessment in the upper Gilgel-Gibe water-supply catchments (Unta River) and sampling strategies designed. Accordingly, sources, i.e. soil samples from landslides (n=40), eroding channel bank (n = 5), cultivated land (n = 30), grasslands (n = 30), wooded areas (n = 10), homestead plots (n = 10) were collected alongside 10 spatially-integrated sediment deposits from the receptor cobble bed river after the 2016 rainy season. In order to extract reliable information on the sources of fine sediment delivered into rivers and dam, new isotopic techniques (e.g., Compound Specific Stable Isotopes (CSSIs)) combined with other isotopic techniques (fallout radionuclides) and geochemical tracer properties (via WD-XRF) were employed to quantify sediment sources. Results from this demonstration catchment are discussed in the context of the wider sediment pressures on the Hydro-Electric Power infrastructure of the Gilgel Gibe system.