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

Hraber, Peter; Korber, Bette; Wagh, Kshitij

Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

Development of Hydrologic Characterization Methodology of Faults: Outline of the Project in Berkeley, California

NASA Astrophysics Data System (ADS)

Goto, J.; Miwa, T.; Tsuchi, H.; Karasaki, K.

2009-12-01

The Nuclear Waste Management Organization of Japan (NUMO), after volunteering municipalities arise, will start a three-staged program for selecting a HLW and TRU waste repository site. It is recognized from experiences from various site characterization programs in the world that the hydrologic property of faults is one of the most important parameters in the early stage of the program. It is expected that numerous faults of interest exist in an investigation area of several tens of square kilometers. It is, however, impossible to characterize all these faults in a limited time and budget. This raises problems in the repository designing and safety assessment that we may have to accept unrealistic or over conservative results by using a single model or parameters for all the faults in the area. We, therefore, seek to develop an efficient and practical methodology to characterize hydrologic property of faults. This project is a five year program started in 2007, and comprises the basic methodology development through literature study and its verification through field investigations. The literature study tries to classify faults by correlating their geological features with hydraulic property, to search for the most efficient technology for fault characterization, and to develop a work flow diagram. The field investigation starts from selection of a site and fault(s), followed by existing site data analyses, surface geophysics, geological mapping, trenching, water sampling, a series of borehole investigations and modeling/analyses. Based on the results of the field investigations, we plan to develop a systematic hydrologic characterization methodology of faults. A classification method that correlates combinations of geological features (rock type, fault displacement, fault type, position in a fault zone, fracture zone width, damage zone width) with widths of high permeability zones around a fault zone was proposed through a survey on available documents of the site characterization programs. The field investigation started in 2008, by selecting the Wildcat Fault that cut across the Laurence Berkeley National Laboratory (LBNL) site as the target. Analyses on site-specific data, surface geophysics, geological mapping and trenching have confirmed the approximate location and characteristics of the fault (see Session H48, Onishi, et al). The plan for the remaining years includes borehole investigations at LBNL, and another series of investigations in the northern part of the Wildcat Fault.

Level 1 remedial investigation work plan, 300 Area Process Ponds

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

Not Available

This report discusses the objectives of the site characterization for the 300 Area Process Ponds which are to identify and quantify contamination at the ponds and to estimate their potential impact on human health and the environment. The results of the site characterization will be used to identify any future actions related to contamination at the site and to identify any additional data requirements needed to support selection of a remedial action. 9 refs., 12 figs., 8 tabs.

Importance Of Solid Phase Characterization To MNA Assessment

EPA Science Inventory

Technical recommendations have recently been published by the U.S. Environmental Protection Agency to address site characterization needed to support selection of Monitored Natural Attenuation (MNA) for cleanup of inorganic contaminant plumes in groundwater. Immobilization onto ...

Sound settlement: noise surpasses land cover in explaining breeding habitat selection of secondary cavity-nesting birds.

PubMed

Kleist, Nathan J; Guralnick, Robert P; Cruz, Alexander; Francis, Clinton D

2017-01-01

Birds breeding in heterogeneous landscapes select nest sites by cueing in on a variety of factors from landscape features and social information to the presence of natural enemies. We focus on determining the relative impact of anthropogenic noise on nest site occupancy, compared to amount of forest cover, which is known to strongly influence the selection process. We examine chronic, industrial noise from natural gas wells directly measured at the nest box as well as site-averaged noise, using a well-established field experimental system in northwestern New Mexico. We hypothesized that high levels of noise, both at the nest site and in the environment, would decrease nest box occupancy. We set up nest boxes using a geospatially paired control and experimental site design and analyzed four years of occupancy data from four secondary cavity-nesting birds common to the Colorado Plateau. We found different effects of noise and landscape features depending on species, with strong effects of noise observed in breeding habitat selection of Myiarchus cinerascens, the Ash-throated Flycatcher, and Sialia currucoides, the Mountain Bluebird. In contrast, the amount of forest cover less frequently explained habitat selection for those species or had a smaller standardized effect than the acoustic environment. Although forest cover characterization and management is commonly employed by natural resource managers, our results show that characterizing and managing the acoustic environment should be an important tool in protected area management. © 2016 by the Ecological Society of America.

Site Characterization at a Tidal Energy Site in the East River, NY (usa)

NASA Astrophysics Data System (ADS)

Gunawan, B.; Neary, V. S.; Colby, J.

2012-12-01

A comprehensive tidal energy site characterization is performed using ADV measurements of instantaneous horizontal current magnitude and direction at the planned hub centerline of a tidal turbine over a two month period, and contributes to the growing data base of tidal energy site hydrodynamic conditions. The temporal variation, mean current statistics, and turbulence of the key tidal hydrodynamic parameters are examined in detail, and compared to estimates from two tidal energy sites in Puget Sound. Tidal hydrodynamic conditions, including mean annual current (at hub height), the speed of extreme gusts (instantaneous horizontal currents acting normal to the rotor plane), and turbulence intensity (as proposed here, relative to a mean current of 2 m s-1) can vary greatly among tidal energy sites. Comparison of hydrodynamic conditions measured in the East River tidal straight in New York City with those reported for two tidal energy sites in Puget Sound indicate differences of mean annual current speeds, difference in the instantaneous current speeds of extreme gusts, and differences in turbulence intensities. Significant differences in these parameters among the tidal energy sites, and with the tidal resource assessment map, highlight the importance of conducting site resource characterization with ADV measurements at the machine scale. As with the wind industry, which adopted an International Electrotechnical Commission (IEC) wind class standard to aid in the selection of wind turbines for a particular site, it is recommended that the tidal energy industry adopt an appropriate standard for tidal current classes. Such a standard requires a comprehensive field campaign at multiple tidal energy sites that can identify the key hydrodynamic parameters for tidal current site classification, select a list of tidal energy sites that exhibit the range of hydrodynamic conditions that will be encountered, and adopt consistent measurement practices (standards) for site classification.

Computational Optimization and Characterization of Molecularly Imprinted Polymers

NASA Astrophysics Data System (ADS)

Terracina, Jacob J.

Molecularly imprinted polymers (MIPs) are a class of materials containing sites capable of selectively binding to the imprinted target molecule. Computational chemistry techniques were used to study the effect of different fabrication parameters (the monomer-to-target ratios, pre-polymerization solvent, temperature, and pH) on the formation of the MIP binding sites. Imprinted binding sites were built in silico for the purposes of better characterizing the receptor - ligand interactions. Chiefly, the sites were characterized with respect to their selectivities and the heterogeneity between sites. First, a series of two-step molecular mechanics (MM) and quantum mechanics (QM) computational optimizations of monomer -- target systems was used to determine optimal monomer-to-target ratios for the MIPs. Imidazole- and xanthine-derived target molecules were studied. The investigation included both small-scale models (one-target) and larger scale models (five-targets). The optimal ratios differed between the small and larger scales. For the larger models containing multiple targets, binding-site surface area analysis was used to evaluate the heterogeneity of the sites. The more fully surrounded sites had greater binding energies. Molecular docking was then used to measure the selectivities of the QM-optimized binding sites by comparing the binding energies of the imprinted target to that of a structural analogue. Selectivity was also shown to improve as binding sites become more fully encased by the monomers. For internal sites, docking consistently showed selectivity favoring the molecules that had been imprinted via QM geometry optimizations. The computationally imprinted sites were shown to exhibit size-, shape-, and polarity-based selectivity. This represented a novel approach to investigate the selectivity and heterogeneity of imprinted polymer binding sites, by applying the rapid orientation screening of MM docking to the highly accurate QM-optimized geometries. Next, we sought to computationally construct and investigate binding sites for their enantioselectivity. Again, a two-step MM [special characters removed] QM optimization scheme was used to "computationally imprint" chiral molecules. Using docking techniques, the imprinted binding sites were shown to exhibit an enantioselective preference for the imprinted molecule over its enantiomer. Docking of structurally similar chiral molecules showed that the sites computationally imprinted with R- or S-tBOC-tyrosine were able to differentiate between R- and S-forms of other tyrosine derivatives. The cross-enantioselectivity did not hold for chiral molecules that did not share the tyrosine H-bonding functional group orientations. Further analysis of the individual monomer - target interactions within the binding site led us to conclude that H-bonding functional groups that are located immediately next to the target's chiral center, and therefore spatially fixed relative to the chiral center, will have a stronger contribution to the enantioselectivity of the site than those groups separated from the chiral center by two or more rotatable bonds. These models were the first computationally imprinted binding sites to exhibit this enantioselective preference for the imprinted target molecules. Finally, molecular dynamics (MD) was used to quantify H-bonding interactions between target molecules, monomers, and solvents representative of the pre-polymerization matrix. It was found that both target dimerization and solvent interference decrease the number of monomer - target H-bonds present. Systems were optimized via simulated annealing to create binding sites that were then subjected to molecular docking analysis. Docking showed that the presence of solvent had a detrimental effect on the sensitivity and selectivity of the sites, and that solvents with more H-bonding capabilities were more disruptive to the binding properties of the site. Dynamic simulations also showed that increasing the temperature of the solution can significantly decrease the number of H-bonds formed between the targets and monomers. It is believed that the monomer - target complexes formed within the pre-polymerization matrix are translated into the selective binding cavities formed during polymerization. Elucidating the nature of these interactions in silico improves our understanding of MIPs, ultimately allowing for more optimized sensing materials.

New Synthesis and Tritium Labeling of a Selective Ligand for Studying High-affinity γ-Hydroxybutyrate (GHB) Binding Sites

PubMed Central

Vogensen, Stine B.; Marek, Aleš; Bay, Tina; Wellendorph, Petrine; Kehler, Jan; Bundgaard, Christoffer; Frølund, Bente; Pedersen, Martin H.F.; Clausen, Rasmus P.

2013-01-01

3-Hydroxycyclopent-1-enecarboxylic acid (HOCPCA, 1) is a potent ligand for the high-affinity GHB binding sites in the CNS. An improved synthesis of 1 together with a very efficient synthesis of [3H]-1 is described. The radiosynthesis employs in situ generated lithium trimethoxyborotritide. Screening of 1 against different CNS targets establishes a high selectivity and we demonstrate in vivo brain penetration. In vitro characterization of [3H]-1 binding shows high specificity to the high-affinity GHB binding sites. PMID:24053696

Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses.

PubMed

Chen, Haifen; Zhou, Xinrui; Zheng, Jie; Kwoh, Chee-Keong

2016-12-05

The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune system. Therefore, the vaccine has to be updated every year to stay effective. There is a need to characterize the evolution of influenza viruses for better selection of vaccine candidates and the prediction of pandemic strains. Studies have shown that the influenza hemagglutinin evolution is driven by the simultaneous mutations at antigenic sites. Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution. We obtain the rules of mutation co-occurrence using association rule mining after extracting HA1 sequences and detect co-mutation sites under strong selective pressure. Then we predict the potential drifts with specific mutations of the viruses based on the rules and compare the results with the "observed" mutations in different years. The sites under frequent mutations are in antigenic regions (epitopes) or receptor binding sites. Our study demonstrates the co-occurring site mutations obtained by rule mining can capture the evolution of influenza viruses, and confirms that cooperative interactions among sites of HA1 protein drive the influenza antigenic evolution.

Characterization of Seismic Noise at Selected Non-Urban Sites

DTIC Science & Technology

2010-03-01

Field sites for seismic recordings: Scottish moor (upper left), Enfield, NH (upper right), and vicinity of Keele, England (bottom). ERDC...three sites. The sites are: a wind farm on a remote moor in Scotland, a ~13 acre field bounded by woods in a rural Enfield, NH neigh- borhood, and a site...in a rural Enfield, NH, neighborhood, and a site transitional from developed land to farmland within 1 km of the six-lane M6 motorway near Keele

Correlations Between Life-Detection Techniques and Implications for Sampling Site Selection in Planetary Analog Missions

NASA Astrophysics Data System (ADS)

Gentry, Diana M.; Amador, Elena S.; Cable, Morgan L.; Chaudry, Nosheen; Cullen, Thomas; Jacobsen, Malene B.; Murukesan, Gayathri; Schwieterman, Edward W.; Stevens, Adam H.; Stockton, Amanda; Tan, George; Yin, Chang; Cullen, David C.; Geppert, Wolf

2017-10-01

We conducted an analog sampling expedition under simulated mission constraints to areas dominated by basaltic tephra of the Eldfell and Fimmvörðuháls lava fields (Iceland). Sites were selected to be "homogeneous" at a coarse remote sensing resolution (10-100 m) in apparent color, morphology, moisture, and grain size, with best-effort realism in numbers of locations and replicates. Three different biomarker assays (counting of nucleic-acid-stained cells via fluorescent microscopy, a luciferin/luciferase assay for adenosine triphosphate, and quantitative polymerase chain reaction (qPCR) to detect DNA associated with bacteria, archaea, and fungi) were characterized at four nested spatial scales (1 m, 10 m, 100 m, and >1 km) by using five common metrics for sample site representativeness (sample mean variance, group F tests, pairwise t tests, and the distribution-free rank sum H and u tests). Correlations between all assays were characterized with Spearman's rank test. The bioluminescence assay showed the most variance across the sites, followed by qPCR for bacterial and archaeal DNA; these results could not be considered representative at the finest resolution tested (1 m). Cell concentration and fungal DNA also had significant local variation, but they were homogeneous over scales of >1 km. These results show that the selection of life detection assays and the number, distribution, and location of sampling sites in a low biomass environment with limited a priori characterization can yield both contrasting and complementary results, and that their interdependence must be given due consideration to maximize science return in future biomarker sampling expeditions.

Identification and Characterization of a Secondary Sodium-Binding Site and the Main Selectivity Determinants in the Human Concentrative Nucleoside Transporter 3.

PubMed

Arimany-Nardi, C; Claudio-Montero, A; Viel-Oliva, A; Schmidtke, P; Estarellas, C; Barril, X; Bidon-Chanal, A; Pastor-Anglada, M

2017-06-05

The family of concentrative Na + /nucleoside cotransporters in humans is constituted by three subtypes, namely, hCNT1, hCNT2, and hCNT3. Besides their different nucleoside selectivity, hCNT1 and hCNT2 have a Na + /nucleoside stoichiometry of 1:1, while for hCNT3 it is 2:1. This distinct stoichiometry of subtype 3 might hint the existence of a secondary sodium-binding site that is not present in the other two subtypes, but to date their three-dimensional structures remain unknown and the residues implicated in Na + binding are unclear. In this work, we have identified and characterized the Na + binding sites of hCNT3 by combining molecular modeling and mutagenesis studies. A model of the transporter was obtained by homology modeling, and key residues of two sodium-binding sites were identified and verified with a mutagenesis strategy. The structural model explains the altered sodium-binding properties of the hCNT3C602R polymorphic variant and supports previously generated data identifying the determinant residues of nucleoside selectivity, paving the way to understand how drugs can target this plasma membrane transporter.

Conversion of the Bayou Choctaw geological site characterization report to a three-dimensional model.

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

Stein, Joshua S.; Rautman, Christopher Arthur

2004-02-01

The geologic model implicit in the original site characterization report for the Bayou Choctaw Strategic Petroleum Reserve Site near Baton Rouge, Louisiana, has been converted to a numerical, computer-based three-dimensional model. The original site characterization model was successfully converted with minimal modifications and use of new information. The geometries of the salt diapir, selected adjacent sedimentary horizons, and a number of faults have been modeled. Models of a partial set of the several storage caverns that have been solution-mined within the salt mass are also included. Collectively, the converted model appears to be a relatively realistic representation of the geologymore » of the Bayou Choctaw site as known from existing data. A small number of geometric inconsistencies and other problems inherent in 2-D vs. 3-D modeling have been noted. Most of the major inconsistencies involve faults inferred from drill hole data only. Modem computer software allows visualization of the resulting site model and its component submodels with a degree of detail and flexibility that was not possible with conventional, two-dimensional and paper-based geologic maps and cross sections. The enhanced visualizations may be of particular value in conveying geologic concepts involved in the Bayou Choctaw Strategic Petroleum Reserve site to a lay audience. A Microsoft WindowsTM PC-based viewer and user-manipulable model files illustrating selected features of the converted model are included in this report.« less

Air/Superfund national technical guidance study series, Volume 2. Estimation of baseline air emission at Superfund sites. Interim report(Final)

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

Not Available

1989-01-01

This volume is one in a series of manuals prepared for EPA to assist its Remedial Project Managers in the assessment of the air contaminant pathway and developing input data for risk assessment. The manual provides guidance on developing baseline-emission estimates from hazardous waste sites. Baseline-emission estimates (BEEs) are defined as emission rates estimated for a site in its undisturbed state. Specifically, the manual is intended to: Present a protocol for selecting the appropriate level of effort to characterize baseline air emissions; Assist site managers in designing an approach for BEEs; Describe useful technologies for developing site-specific baseline emission estimatesmore » (BEEs); Help site managers select the appropriate technologies for generating site-specific BEEs.« less

Criteria for predicting scour of erodible rock in West Virginia.

DOT National Transportation Integrated Search

2013-09-01

The research project Criteria for Predicting Scour of Erodible Rock in West Virginia (RP-273) was conducted to characterize the hydraulic scour of rock at : 15 selected bridge sites in West Virginia (at least one site in each of WVDOHs ten d...

Engineering peptide ligase specificity by proteomic identification of ligation sites.

PubMed

Weeks, Amy M; Wells, James A

2018-01-01

Enzyme-catalyzed peptide ligation is a powerful tool for site-specific protein bioconjugation, but stringent enzyme-substrate specificity limits its utility. We developed an approach for comprehensively characterizing peptide ligase specificity for N termini using proteome-derived peptide libraries. We used this strategy to characterize the ligation efficiency for >25,000 enzyme-substrate pairs in the context of the engineered peptide ligase subtiligase and identified a family of 72 mutant subtiligases with activity toward N-terminal sequences that were previously recalcitrant to modification. We applied these mutants individually for site-specific bioconjugation of purified proteins, including antibodies, and in algorithmically selected combinations for sequencing of the cellular N terminome with reduced sequence bias. We also developed a web application to enable algorithmic selection of the most efficient subtiligase variant(s) for bioconjugation to user-defined sequences. Our methods provide a new toolbox of enzymes for site-specific protein modification and a general approach for rapidly defining and engineering peptide ligase specificity.

Thermal conditions in selected urban and semi-natural habitats, important for the forensic entomology.

PubMed

Michalski, Marek; Nadolski, Jerzy

2018-06-01

A long-term study on thermal conditions in selected urban and semi-natural habitats, where human corpses are likely to be found, was conducted in the city of Lodz (Central Poland). Thermal data were collected during two years at nine sites and compared with corresponding data from the nearest permanent meteorological station at Lodz Airport (ICAO code: EPLL). The conditions closest to those at the meteorological station prevailed in the deciduous forest, coefficient of determination R 2 for those sets of data was above 0.96. The open field was characterized by high daily amplitudes, especially during spring, while the site in the allotment gardens was characterized by relatively high winter temperatures. The conditions prevailing in all closed space sites were very diverse and only slightly similar to the external ones. The most distinct site was an unheated basement in a tenement house, where temperature was almost always above 0°C and daily amplitudes were negligible. Copyright © 2018 Elsevier B.V. All rights reserved.

Analytical methods for characterization of explosives-contaminated sites on U.S. Army installations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas F.; Walsh, Marianne E.; Thorne, Philip G.

1995-10-01

The U.S. Army manufactures munitions at facilities throughout the United States. Many of these facilities are contaminated with residues of explosives from production, disposal of off- specification, and out-of-data munitions. The first step in remediating these sites is careful characterization. Currently sites are being characterized using a combination of on-site field screening and off-site laboratory analysis. Most of the contamination is associated with TNT (2,4,6-trinitrotoluene) and RDX (hexahydro-1,3,5-tri-nitro-1,3,5-triazine) and their manufacturing impurities and environmental transformation products. Both colorimetric and enzyme immunoassay-based field screening methods have been used successfully for on-site characterization. These methods have similar detection capabilities but differ in their selectivity. Although field screening is very cost-effective, laboratory analysis is still required to fully characterize a site. Laboratory analysis for explosives residues in the United States is generally conducted using high-performance liquid chromatography equipped with a UV detector. Air-dried soils are extracted with acetonitrile in an ultrasonic bath. Water is analyzed directly if detection limits in the range of 10 - 20 (mu) g/L are acceptable, or preconcentrated using either salting-out solvent extraction with acetonitrile or solid phase extraction.

Stennis Space Center Verification & Validation Capabilities

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Ryan, Robert E.; Holekamp, Kara; O'Neal, Duane; Knowlton, Kelly; Ross, Kenton; Blonski, Slawomir

2007-01-01

Scientists within NASA#s Applied Research & Technology Project Office (formerly the Applied Sciences Directorate) have developed a well-characterized remote sensing Verification & Validation (V&V) site at the John C. Stennis Space Center (SSC). This site enables the in-flight characterization of satellite and airborne high spatial resolution remote sensing systems and their products. The smaller scale of the newer high resolution remote sensing systems allows scientists to characterize geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the techniques used to characterize data from the earlier, coarser spatial resolution systems. Scientists have used the SSC V&V site to characterize thermal infrared systems. Enhancements are being considered to characterize active lidar systems. SSC employs geodetic targets, edge targets, radiometric tarps, atmospheric monitoring equipment, and thermal calibration ponds to characterize remote sensing data products. Similar techniques are used to characterize moderate spatial resolution sensing systems at selected nearby locations. The SSC Instrument Validation Lab is a key component of the V&V capability and is used to calibrate field instrumentation and to provide National Institute of Standards and Technology traceability. This poster presents a description of the SSC characterization capabilities and examples of calibration data.

Astronomical Extinction Over The ELT Moroccan Sites From Aerosol Satellite Data

NASA Astrophysics Data System (ADS)

Siher, E. A.; Benkhaldoun, Z.; Bounhir, A.

2006-08-01

Two Moroccan sites are selected to be characterized for the ELT telescopes. These sites are in the Atlas, between Oukaimeden (where is the national observatory) and The Canaries Islands. For a preliminary study, we will use the TOMS/Nimbus7 aerosol index (AI), threshold 0.7, to extract the astronomical extinction (AE), threshold 0.2 mag/airmass. In fact, on the one hand, one previously work showed the link between these parameters over the Canaries Islands (ORM Observatory). On the other hand, many studies proposed the dust characterization for the future extremely large telescope for a mandatory qualification.

BOREAS TE-23 Map Plot Data

NASA Technical Reports Server (NTRS)

Rich, Paul M.; Fournier, Robert; Hall, Forrest G. (Editor); Papagno, Andrea (Editor)

2000-01-01

The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-23 (Terrestrial Ecology) team collected map plot data in support of its efforts to characterize and interpret information on canopy architecture and understory cover at the BOREAS tower flux sites and selected auxiliary sites from May to August 1994. Mapped plots (typical dimensions 50 m x 60 m) were set up and characterized at all BOREAS forested tower flux and selected auxiliary sites. Detailed measurement of the mapped plots included: (1) stand characteristics (location, density, basal area); (2) map locations diameter at breast height (DBH) of all trees; (3) detailed geometric measures of a subset of trees (height, crown dimensions); and (4) understory cover maps. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Microcapsules with three orthogonal reactive sites

PubMed Central

Mason, Brian P.; Hira, Steven M.; Strouse, Geoffrey F.; McQuade, D. Tyler

2009-01-01

Polymeric microcapsules containing reactive sites on the shell surface and two orthogonally reactive polymers encapsulated within the interior are selectively labeled. The capsules provide three spatially separate and differentially reactive sites. Confocal fluorescence microscopy is used to characterize the distribution of labels. Polymers encapsulated are distributed homogeneously within the core and do not interact with the shell even when oppositely charged. PMID:19254010

Highly dispersed SiO x/Al 2O 3 catalysts illuminate the reactivity of isolated silanol sites

DOE PAGES

Mouat, Aidan R.; George, Cassandra; Kobayashi, Takeshi; ...

2015-09-23

The reaction of γ-alumina with tetraethylorthosilicate (TEOS) vapor at low temperatures selectively yields monomeric SiO x species on the alumina surface. These isolated (-AlO) 3Si(OH) sites are characterized by PXRD, XPS, DRIFTS of adsorbed NH 3, CO, and pyridine, and 29Si and 27Al DNP-enhanced solid-state NMR spectroscopy. The formation of isolated sites suggests that TEOS reacts preferentially at strong Lewis acid sites on the γ-Al 2O 3 surface, functionalizing the surface with “mild” Brønsted acid sites. As a result, for liquid-phase catalytic cyclohexanol dehydration, these SiO x sites exhibit up to 3.5-fold higher specific activity than the parent alumina withmore » identical selectivity.« less

Pine snake (Pituophis ruthveni and Pituophis mellanoleucus lodingi) hibernacula

Treesearch

D.C. Rudolph; R.R. Schaefer; S.J. Burgdorf; M. Duran; R.N. Conner

2007-01-01

Snakes are often highly selective in the choice of sites for hibernation, and suitable sites can potentially be a limiting resource. Hibernating Louisiana Pine Snakes (Pituopllis ruthveni; N = 7) in eastern Texas and Black Pine Snakes (Pituophis melanoleucus lodingi; N = 5) in Mississippi were excavated to characterize their...

Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals.

PubMed

Neves, Fabiana; Abrantes, Joana; Esteves, Pedro J

2016-07-01

The interactions between chemokines and their receptors are crucial for differentiation and activation of inflammatory cells. CC chemokine ligand 11 (CCL11) binds to CCR3 and to CCR5 that in leporids underwent gene conversion with CCR2. Here, we genetically characterized CCL11 in lagomorphs (leporids and pikas). All lagomorphs have a potentially functional CCL11, and the Pygmy rabbit has a mutation in the stop codon that leads to a longer protein. Other mammals also have mutations at the stop codon that result in proteins with different lengths. By employing maximum likelihood methods, we observed that, in mammals, CCL11 exhibits both signatures of purifying and positive selection. Signatures of purifying selection were detected in sites important for receptor binding and activation. Of the three sites detected as under positive selection, two were located close to the stop codon. Our results suggest that CCL11 is functional in all lagomorphs, and that the signatures of purifying and positive selection in mammalian CCL11 probably reflect the protein's biological roles. © The Author(s) 2016.

Correlations Between Life-Detection Techniques and Implications for Sampling Site Selection in Planetary Analog Missions.

PubMed

Gentry, Diana M; Amador, Elena S; Cable, Morgan L; Chaudry, Nosheen; Cullen, Thomas; Jacobsen, Malene B; Murukesan, Gayathri; Schwieterman, Edward W; Stevens, Adam H; Stockton, Amanda; Tan, George; Yin, Chang; Cullen, David C; Geppert, Wolf

2017-10-01

We conducted an analog sampling expedition under simulated mission constraints to areas dominated by basaltic tephra of the Eldfell and Fimmvörðuháls lava fields (Iceland). Sites were selected to be "homogeneous" at a coarse remote sensing resolution (10-100 m) in apparent color, morphology, moisture, and grain size, with best-effort realism in numbers of locations and replicates. Three different biomarker assays (counting of nucleic-acid-stained cells via fluorescent microscopy, a luciferin/luciferase assay for adenosine triphosphate, and quantitative polymerase chain reaction (qPCR) to detect DNA associated with bacteria, archaea, and fungi) were characterized at four nested spatial scales (1 m, 10 m, 100 m, and >1 km) by using five common metrics for sample site representativeness (sample mean variance, group F tests, pairwise t tests, and the distribution-free rank sum H and u tests). Correlations between all assays were characterized with Spearman's rank test. The bioluminescence assay showed the most variance across the sites, followed by qPCR for bacterial and archaeal DNA; these results could not be considered representative at the finest resolution tested (1 m). Cell concentration and fungal DNA also had significant local variation, but they were homogeneous over scales of >1 km. These results show that the selection of life detection assays and the number, distribution, and location of sampling sites in a low biomass environment with limited a priori characterization can yield both contrasting and complementary results, and that their interdependence must be given due consideration to maximize science return in future biomarker sampling expeditions. Key Words: Astrobiology-Biodiversity-Microbiology-Iceland-Planetary exploration-Mars mission simulation-Biomarker. Astrobiology 17, 1009-1021.

Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

NASA Technical Reports Server (NTRS)

Solomon, B. D.; Haynes, K. E.

1982-01-01

The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

Implementing Classification on a Munitions Response Project

DTIC Science & Technology

2011-12-01

Detection Dig List  IVS/Seed Site Planning Decisions Dig All  Anomalies Site Characterization Implementing Classification on a Munitions Response...Details ● Seed emplacement ● EM61-MK2 detection survey  RTK GPS ● Select anomalies for further investigation ● Collect cued data using MetalMapper...5.2 mV in channel 2  938 anomalies selected ● All QC seeds detected using this threshold  Some just inside the 60-cm halo ● IVS reproducibility

Proceedings of the tenth annual DOE low-level waste management conference: Session 2: Site performance assessment

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

Not Available

1988-12-01

This document contains twelve papers on various aspects of low-level radioactive waste management. Topics of this volume include: performance assessment methodology; remedial action alternatives; site selection and site characterization procedures; intruder scenarios; sensitivity analysis procedures; mathematical models for mixed waste environmental transport; and risk assessment methodology. Individual papers were processed separately for the database. (TEM)

Genotype-environment interaction and stability in ten-year height growth of Norway spruce Clones (Picea abies Karst.).

Treesearch

J.B. St. Clair; J. Kleinschmit

1986-01-01

Norway spruce cuttings of 40 clones were tested on seven contrasting sites in northern Germany. Analysis of variance for ten-year height growth indicate a highly significant clone x site interaction. This interaction may be reduced by selection of stable clones. Several measures of stability were calculated and discussed. Characterization of sites by the method of...

Site Selection for Mars Surveyor Landing Sites: Some Key Factors for 2001 and Relation to Long-Term Exploration of Mars

NASA Astrophysics Data System (ADS)

Head, James W.

1999-01-01

The Site Selection Process: Site selection as a process can be subdivided into several main elements and these can be represented as the corners of a tetrahedron. Successful site selection outcome requires the interactions between these elements or corners, and should also take into account several other external factors or considerations. In principle, elements should be defined in approximately the following order: (1) major scientific and programmatic goals and objectives: What are the major questions that are being asked, goals that should be achieved, and objectives that must be accomplished. Do programmatic goals (e.g., sample return) differ from mission goals (e.g., precursor to sample return)? It is most helpful if these questions can be placed in the context of site characterization and hypothesis testing (e.g., Was Mars warm and wet in the Noachian? Land at a Noachian-aged site that shows evidence of surface water and characterize it specifically to address this question). Goals and objectives, then, help define important engineering factors such as type of payload, landing regions of interest (highlands, lowlands, smooth, rough, etc.), mobility, mission duration, etc. Goals and objectives then lead to: (2) spacecraft design and engineering landing site constraints: the spacecraft is designed to optimize the areas that will meet the goals and objectives, but this in turn introduces constraints that must be met in the selection of a landing site. Scientific and programmatic goals and objectives also help to define (3), the specific lander scientific payload requirements and capabilities. For example, what observations and experiments are required to address the major questions? How do we characterize the site in reference to the specific questions? Is mobility required and if so, how much? Which experiments are on the spacecraft, which on the rover? The results of these deliberations should lead to a surface exploration strategy, in which the goals and objectives can in principle be achieved through the exploration of a site meeting the basic engineering constraints. Armed with all of this important background information, one can then proceed to (4) the selection of optimum sites to address major scientific and programmatic objectives. Following the successful completion of this process and the selection of a site or region, there is a further step of mission optimization, in which a detailed mission profile and surface exploration plan is developed. In practice, the process never works in a linear fashion. Scientific goals are influenced by ongoing discoveries and developments and simple crystallization of thinking. Programmatic goals are influenced by evolving fiscal constraints, perspectives on program duration, and roles of specific missions in the context of the larger program. Engineering constraints are influenced by evolving fiscal constraints, decisions on hardware design that may have little to do with scientific goals (e.g., lander clearance; size of landing ellipse), and evolving understanding (e.g., assessment of engineering constraint space reveals further the degree to which mission duration is severely influenced by available solar energy and thus latitude). Lander scientific payload is influenced by fiscal constraints, total mass, evolving complexity, technological developments, and a payload selection process that may involve very long-term goals (e.g., human exploration) as well as shorter term scientific and programmatic goals. Site selection activities commonly involve scientists who are actively trying to decipher the complex geology of the crust of Mars and to unravel its geologic history through geological mapping. By the nature of the process, they are thinking in terms of broad morphostratigraphic units which may have multiple possible origins, defined using images with resolutions of many tens to hundreds of meters, and whose surfaces at the scale of the lander and rover are virtually unknown; this approach and effort is crucially important but does not necessarily readily lend itself to integration with the other elements.

ROLE OF LABORATORY SAMPLING DEVICES AND LABORATORY SUBSAMPLING METHODS IN OPTIMIZING REPRESENTATIVENESS STRATEGIES

EPA Science Inventory

Sampling is the act of selecting items from a specified population in order to estimate the parameters of that population (e.g., selecting soil samples to characterize the properties at an environmental site). Sampling occurs at various levels and times throughout an environmenta...

Mars Exploration Rovers Launch Performance and TCM-1 Maneuver Design

NASA Technical Reports Server (NTRS)

Kangas, Julie A.; Potts, Christopher L.; Raofi, Behzad

2004-01-01

The Mars Exploration Rover (MER) project successfully landed two identical rovers on Mars in order to remotely conduct geologic investigations, including characterization of rocks and soils that may hold clues to past water activity. Two landing sites, Gusev crater and Meridiani Planum, were selected out of nearly 200 candidate sites after balancing science returns and flight system engineering and safety. Precise trajectory targeting and control was necessary to achieve the atmospheric entry requirements for the selected landing sites within the flight system constraints. This paper discusses the expected and achieved launch vehicle performance and the impacts of that performance on the first Trajectory Correction Maneuver (TCM-1) while maintaining targeting flexibility in accommodating additional project concerns about landing site safety and possible in-flight retargeting to alternate landing sites.

A fractured rock geophysical toolbox method selection tool

USGS Publications Warehouse

Day-Lewis, F. D.; Johnson, C.D.; Slater, L.D.; Robinson, J.L.; Williams, J.H.; Boyden, C.L.; Werkema, D.D.; Lane, J.W.

2016-01-01

Geophysical technologies have the potential to improve site characterization and monitoring in fractured rock, but the appropriate and effective application of geophysics at a particular site strongly depends on project goals (e.g., identifying discrete fractures) and site characteristics (e.g., lithology). No method works at every site or for every goal. New approaches are needed to identify a set of geophysical methods appropriate to specific project goals and site conditions while considering budget constraints. To this end, we present the Excel-based Fractured-Rock Geophysical Toolbox Method Selection Tool (FRGT-MST). We envision the FRGT-MST (1) equipping remediation professionals with a tool to understand what is likely to be realistic and cost-effective when contracting geophysical services, and (2) reducing applications of geophysics with unrealistic objectives or where methods are likely to fail.

Logging utilization in Idaho: Current and past trends

Treesearch

Eric A. Simmons; Todd A. Morgan; Erik C. Berg; Stanley J. Zarnoch; Steven W. Hayes; Mike T. Thompson

2014-01-01

A study of commercial timber-harvesting activities in Idaho was conducted during 2008 and 2011 to characterize current tree utilization, logging operations, and changes from previous Idaho logging utilization studies. A two-stage simple random sampling design was used to select sites and felled trees for measurement within active logging sites. Thirty-three logging...

Multivariate analysis of early and late nest sites of Abert's Towhees

Treesearch

Deborah M. Finch

1985-01-01

Seasonal variation in nest site selection by the Abert's towhee (Pipilo aberti) was studied in honey mesquite (Prosopis glandulosa) habitat along the lower Colorado River from March to July, 1981. Stepwise discriminant function analysis identified nest vegetation type, nest direction, and nest height as the three most important variables that characterized the...

Evolutionary characterization of hemagglutinin gene of H9N2 influenza viruses isolated from Asia.

PubMed

Shahsavandi, Shahla; Salmanian, Ali-Hatef; Ghorashi, Seyed Ali; Masoudi, Shahin; Ebrahimi, Mohammad Majid

2012-08-01

The full length hemagglutinin (HA) genes of 287 H9N2 AI strains isolated from chickens in Asia during the period 1994-2009 were genetically analyzed. Phylogenetic analysis showed that G1-like viruses circulated in the Middle East and Indian sub-continent countries, whereas other sublineages existed in Far East countries. It also revealed G1-like viruses with an average 96.7% identity clustered into two subgroups largely based on their time of isolation. The Ka/Ks ratio was calculated 0.34 for subgroup 1 and 0.57 for subgroup 2 indicates purifying/stabilizing selection, but despite this there is evidence of localized positive selection when comparing the subgroups 1 and 2 protein sequences. Five sites in HA H9N2 viruses had a posterior probability >0.5 using the Bayesian method, indicating these sites were under positive selection. These sites were found to be associated with the globular head region of HA. To identify sites under positive selection; amino acid substitution classified depends on their radicalism and neutrality. The results indicate that, although most positions in HAs were under purifying selection and can be eliminated, a few positions located in the antigenic regions and receptor binding sites were subject to positive selection. Copyright © 2011 Elsevier Ltd. All rights reserved.

Selective Amnesia and Racial Transcendence in News Coverage of President Obama's Inauguration

ERIC Educational Resources Information Center

Hoerl, Kristen

2012-01-01

The mainstream press frequently characterized the election of President Barack Obama, the first African American US President, as the realization of Martin Luther King's dream, thus crafting a postracial narrative of national transcendence. I argue that this routine characterization of Obama's election functions as a site for the production of…

Regulatory controls on the hydrogeological characterization of a mixed waste disposal site, Radioactive Waste Management Complex, Idaho National Engineering Laboratory

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

Ruebelmann, K.L.

1990-01-01

Following the detection of chlorinated volatile organic compounds in the groundwater beneath the SDA in the summer of 1987, hydrogeological characterization of the Radioactive Waste Management Complex (RWMC), Idaho National Engineering Laboratory (INEL) was required by the Resource Conservation and Recovery Act (RCRA). The waste site, the Subsurface Disposal Area (SDA), is the subject of a RCRA Corrective Action Program. Regulatory requirements for the Corrective Action Program dictate a phased approach to evaluation of the SDA. In the first phase of the program, the SDA is the subject of a RCRA Facility Investigation (RIF), which will obtain information to fullymore » characterize the physical properties of the site, determine the nature and extent of contamination, and identify pathways for migration of contaminants. If the need for corrective measures is identified during the RIF, a Corrective Measures Study (CMS) will be performed as second phase. Information generated during the RIF will be used to aid in the selection and implementation of appropriate corrective measures to correct the release. Following the CMS, the final phase is the implementation of the selected corrective measures. 4 refs., 1 fig.« less

Characterization of U.S. Wave Energy Converter (WEC) Test Sites: A Catalogue of Met-Ocean Data, 2nd Edition

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

Ann R. Dallman; Neary, Vincent S.

This report presents met-ocean data and wave energy characteristics at eight U.S. wave energy converter (WEC) test and potential deployment sites. Its purpose is to enable the comparison of wave resource characteristics among sites as well as the selection of test sites that are most suitable for a developer's device and that best meet their testing needs and objectives. It also provides essential inputs for the design of WEC test devices and planning WEC tests, including the planning of deployment, and operations and maintenance. For each site, this report catalogues wave statistics recommended in the International Electrotechnical Commission Technical Specimore » cation (IEC 62600-101 TS) on Wave Energy Characterization, as well as the frequency of occurrence of weather windows and extreme sea states, and statistics on wind and ocean currents. It also provides useful information on test site infrastructure and services.« less

Site Selection for the Disposal of LLW in Taiwan

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

Chuang, W.S.; Chi, L.M.; Tien, N.C.

2006-07-01

This paper presents the implementation status of the low-level radioactive waste (LLW) disposal program in Taiwan, including the disposal facility regulations, status of waste management, final disposal program, licensing procedures, waste acceptance criteria, site selection criteria and processes and preliminary disposal concepts. The first phase of site selection for low-level radioactive waste final disposal in Taiwan was implemented between 1992 and 2002. The site selection process adopted a Geographic Information System (GIS), Hierarchical Analysis System, Expert Evaluation System, and site reconnaissance. An incentive program for voluntary sites was also initiated. After a series of evaluations and discussion of 30 potentialmore » candidate sites, including 8 recommended sites, 5 qualified voluntary townships, and several remote uninhabited small islets, Hsiao-chiou islet was selected as the first priority candidate site in February 1998. The geological investigation work in Hsiao-chiou was conducted from March 1999 through October 2000. An Environmental Impact Statement Report (EIS) and the Investment Feasibility Study Report (IFS) were submitted to the Environmental Protection Agency (EPA) in November 2000 and to the Ministry of Economic Affairs (MOEA) in June 2001, respectively. Unfortunately, the site investigation was discontinued in 2002 due to political and public acceptance consideration. After years of planning, the second phase of the site selection process was launched in August 2004 and will be conducted through 2008. It is planned that a repository will be constructed in early 2009 and start to operate in 2014. The site selection process for the second phase is based on the earlier work and four potential candidate sites were selected for evaluation until 2005. A near surface disposal concept is proposed for a site located in the Taiwan strait, and cavern disposal concepts are proposed for three other sites located on the main island. This paper presents the implementation status of the LLW disposal program in Taiwan, including the disposal facility regulations, status of waste management, final disposal program, licensing procedures, waste acceptance criteria, site selection criteria and processes, and preliminary disposal concepts 'NIMBY' (Not in my backyard) is a critical problem for implementation of the final disposal project. Resistance from local communities has been continuously received during site characterization. To overcome this, an incentive program to encourage community acceptance has been approved by the Government. Programs for community promotion are being proposed and negotiations are also underway. (authors)« less

Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol*

PubMed Central

Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.; Fiamengo, Bryan A.; Foley, Sage E.; Frank, Kristine E.; George, Jonathan S.; Harris, Christopher M.; Hobson, Adrian D.; Ihle, David C.; Marcotte, Douglas; Merta, Philip J.; Michalak, Mark E.; Murdock, Sara E.; Tomlinson, Medha J.; Voss, Jeffrey W.

2015-01-01

The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC50 < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases. PMID:25552479

Position specific variation in the rate of evolution in transcription factor binding sites

PubMed Central

Moses, Alan M; Chiang, Derek Y; Kellis, Manolis; Lander, Eric S; Eisen, Michael B

2003-01-01

Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA. PMID:12946282

Evaluating β Diversity as a Surrogate for Species Representation at Fine Scale.

PubMed

Beier, Paul; Albuquerque, Fábio

2016-01-01

Species turnover or β diversity is a conceptually attractive surrogate for conservation planning. However, there has been only 1 attempt to determine how well sites selected to maximize β diversity represent species, and that test was done at a scale too coarse (2,500 km2 sites) to inform most conservation decisions. We used 8 plant datasets, 3 bird datasets, and 1 mammal dataset to evaluate whether sites selected to span β diversity will efficiently represent species at finer scale (sites sizes < 1 ha to 625 km2). We used ordinations to characterize dissimilarity in species assemblages (β diversity) among plots (inventory data) or among grid cells (atlas data). We then selected sites to maximize β diversity and used the Species Accumulation Index, SAI, to evaluate how efficiently the surrogate (selecting sites for maximum β diversity) represented species in the same taxon. Across all 12 datasets, sites selected for maximum β diversity represented species with a median efficiency of 24% (i.e., the surrogate was 24% more effective than random selection of sites), and an interquartile range of 4% to 41% efficiency. β diversity was a better surrogate for bird datasets than for plant datasets, and for atlas datasets with 10-km to 14-km grid cells than for atlas datasets with 25-km grid cells. We conclude that β diversity is more than a mere descriptor of how species are distributed on the landscape; in particular β diversity might be useful to maximize the complementarity of a set of sites. Because we tested only within-taxon surrogacy, our results do not prove that β diversity is useful for conservation planning. But our results do justify further investigation to identify the circumstances in which β diversity performs well, and to evaluate it as a cross-taxon surrogate.

Cloning and characterization of wnt4a gene and evidence for positive selection in half-smooth tongue sole (Cynoglossus semilaevis).

PubMed

Hu, Qiaomu; Zhu, Ying; Liu, Yang; Wang, Na; Chen, Songlin

2014-11-24

Wnt4 gene plays a role in developmental processes in mammals. However, little is known regarding its function in teleosts. We cloned and characterized the full-length half-smooth tongue sole (Cynoglossus semilaevis) wnt4a gene (CS-wnt4a). CS-wnt4a cDNA was 1746 bp in length encoding 353aa. CS-wnt4a expression level was highest in the testis, and gradually increased in the developing gonads until 1 year of age. In situ hybridization revealed that CS-wnt4a expression level was highest in stage II oocytes and sperm in the adult ovary and testis, respectively. CS-wnt4a expression level was significantly up-regulated in the gonads after exposure to high temperature. The level of methylation of the CS-wnt4a first exon was negatively correlated with the expression of CS-wnt4a. The branch-site model suggested that vertebrate wnt4a differed significantly from that of wnt4b, and that the selective pressures differed between ancestral aquatic and terrestrial organisms. Two positively selected sites were found in the ancestral lineages of teleost fish, but none in the ancestral lineages of mammals. One positively selected site was located on the α-helices of the 3D structure, the other on the random coil. Our results are of value for further study of the function of wnt4 and the mechanism of selection.

Cloning and characterization of wnt4a gene and evidence for positive selection in half-smooth tongue sole (Cynoglossus semilaevis)

NASA Astrophysics Data System (ADS)

Hu, Qiaomu; Zhu, Ying; Liu, Yang; Wang, Na; Chen, Songlin

2014-11-01

Wnt4 gene plays a role in developmental processes in mammals. However, little is known regarding its function in teleosts. We cloned and characterized the full-length half-smooth tongue sole (Cynoglossus semilaevis) wnt4a gene (CS-wnt4a). CS-wnt4a cDNA was 1746 bp in length encoding 353aa. CS-wnt4a expression level was highest in the testis, and gradually increased in the developing gonads until 1 year of age. In situ hybridization revealed that CS-wnt4a expression level was highest in stage II oocytes and sperm in the adult ovary and testis, respectively. CS-wnt4a expression level was significantly up-regulated in the gonads after exposure to high temperature. The level of methylation of the CS-wnt4a first exon was negatively correlated with the expression of CS-wnt4a. The branch-site model suggested that vertebrate wnt4a differed significantly from that of wnt4b, and that the selective pressures differed between ancestral aquatic and terrestrial organisms. Two positively selected sites were found in the ancestral lineages of teleost fish, but none in the ancestral lineages of mammals. One positively selected site was located on the α-helices of the 3D structure, the other on the random coil. Our results are of value for further study of the function of wnt4 and the mechanism of selection.

Structural characterization of nonactive site, TrkA-selective kinase inhibitors

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

Su, Hua-Poo; Rickert, Keith; Burlein, Christine

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residuesmore » from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.« less

Selective staining of proteins with hydrophobic surface sites on a native electrophoretic gel.

PubMed

Bertsch, Martina; Kassner, Richard J

2003-01-01

Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings.

Bed site selection by a subordinate predator: an example with the cougar (Puma concolor) in the Greater Yellowstone Ecosystem.

PubMed

Kusler, Anna; Elbroch, L Mark; Quigley, Howard; Grigione, Melissa

2017-01-01

As technology has improved, our ability to study cryptic animal behavior has increased. Bed site selection is one such example. Among prey species, bed site selection provides thermoregulatory benefits and mitigates predation risk, and may directly influence survival. We conducted research to test whether a subordinate carnivore also selected beds with similar characteristics in an ecosystem supporting a multi-species guild of competing predators. We employed a model comparison approach in which we tested whether cougar ( Puma concolor ) bed site attributes supported the thermoregulatory versus the predator avoidance hypotheses, or exhibited characteristics supporting both hypotheses. Between 2012-2016, we investigated 599 cougar bed sites in the Greater Yellowstone Ecosystem and examined attributes at two scales: the landscape (second-order, n  = 599) and the microsite (fourth order, n  = 140). At the landscape scale, cougars selected bed sites in winter that supported both the thermoregulatory and predator avoidance hypotheses: bed sites were on steeper slopes but at lower elevations, closer to the forest edge, away from sagebrush and meadow habitat types, and on southern, eastern, and western-facing slopes. In the summer, bed attributes supported the predator avoidance hypothesis over the thermoregulation hypothesis: beds were closer to forest edges, away from sagebrush and meadow habitat classes, and on steeper slopes. At the microsite scale, cougar bed attributes in both the winter and summer supported both the predator avoidance and thermoregulatory hypotheses: they selected bed sites with high canopy cover, high vegetative concealment, and in a rugged habitat class characterized by cliff bands and talus fields. We found that just like prey species, a subordinate predator selected bed sites that facilitated both thermoregulatory and anti-predator functions. In conclusion, we believe that measuring bed site attributes may provide a novel means of measuring the use of refugia by subordinate predators, and ultimately provide new insights into the habitat requirements and energetics of subordinate carnivores.

Vegetation in group selection openings: ecology and manipulation

Treesearch

Philip M. McDonald; Gary O. Fiddler

1991-01-01

Group selection openings ranging from 0.1 to 2.0 acres in mixed conifer stands in northern and central California were evaluated for effect of site preparation, opening size, kind and amount of vegetation, and release treatment. Small openings, in general, are characterized by less sunlight and lower temperature extremes than clearcuttings. Roots from border trees...

Expert systems in civil engineering

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

Kostem, C.N.; Maher, M.L.

1986-01-01

This book presents the papers given at a symposium on expert systems in civil engineering. Topics considered at the symposium included problem solving using expert system techniques, construction schedule analysis, decision making and risk analysis, seismic risk analysis systems, an expert system for inactive hazardous waste site characterization, an expert system for site selection, knowledge engineering, and knowledge-based expert systems in seismic analysis.

Characterization of instrumented sites for the onsite fuel-cell field-test project. Volume 4. Topical report, 1983-1985

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

Racine, W.C.; Campillo, C.J.

During the site-selection phase of the Onsite Fuel-Cell Field Test, nearly one hundred sites throughout the U.S. were each instrumented with a standard data-acquisition system (DAS) to collect hourly electrical and thermal data for one year. Seventy of those sites are included in the report. Each site's electrical and thermal systems were instrumented including ambient temperature, electrical demands, building gas usage, and other parameters necessary to calculate building thermal loads. Multifamily residential, commercial, and light industrial sites were instrumented. Approximately twenty market sectors were represented including restaurants, hospitals, hotels, apartments, health clubs, nursing homes, and food-processing plants. The primary usemore » of the data was to determine site compatibility for the installation of 40-kW fuel-cell power plants. However, the collected energy data and site-specific information summarized in this comprehensive report may also be useful for other applications such as market characterization and simulation of new or improved energy-utilization equipment in actual sites. This volume covers metal-plating facilities, nurseries, nursing homes, office buildings and other industrial applications.« less

Post-parturition habitat selection by elk calves and adult female elk in New Mexico

USGS Publications Warehouse

Pitman, James W.; Cain, James W.; Liley, Stewart; Gould, William R.; Quintana, Nichole T.; Ballard, Warren

2014-01-01

Neonatal survival and juvenile recruitment are crucial to maintaining viable elk (Cervus elaphus) populations. Neonate survival is known to be influenced by many factors, including bed-site selection. Although neonates select the actual bed-site location, they must do so within the larger calf-rearing area selected by the mother. As calves age, habitat selection should change to meet the changing needs of the growing calf. Our main objectives were to characterize habitat selection at 2 spatial scales and in areas with different predator assemblages in New Mexico. We evaluated bed-site selection by calves and calf-rearing area selection by adult females. We captured 108 elk calves by hand and fitted them with ear tag transmitters in two areas in New Mexico: the Valle Vidal and Blue Range Wolf Recovery Area. In both study areas, we found that concealing cover structure and distance to that cover influenced bed-site selection of young calves (i.e., <2 weeks of age). Older calves (i.e., 3–10 weeks of age) still selected areas in relation to distance to cover, but also preferred areas with higher visibility. At the larger spatial scale of calf-rearing habitat selection by the adult female, concealing cover (e.g., rocks, shrubs, and logs) and other variables important to the hiding calves were still in the most supported models, but selection was also influenced by forage availability and indices of forage quality. Studies that seek to obtain insight into microhabitat selection of ungulate neonates should consider selection by the neonate and selection by the adult female, changes in selection as neonates age, and potential selection differences in areas of differing predation risk. By considering these influences together and at multiple scales, studies can achieve a broader understanding of neonatal ungulate habitat requirements. 

Evaluation of Suitability of Selected Set of Department of Defense Military Bases and Department of Energy Facilities for Siting a Small Modular Reactor

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

Poore III, Willis P; Belles, Randy; Mays, Gary T

This report summarizes the approach that ORNL developed for screening a sample set of US Department of Defense (DOD) military base sites and DOE sites for possible powering with an SMR; the methodology employed, including spatial modeling; and initial results for several sample sites. The objective in conducting this type of siting evaluation is demonstrate the capability to characterize specific DOD and DOE sites to identify any particular issues associated with powering the sites with an SMR using OR-SAGE; it is not intended to be a definitive assessment per se as to the absolute suitability of any particular site.

Energy technology characterizations handbook: environmental pollution and control factors. Third edition

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

Not Available

1983-03-01

This Handbook deals with environmental characterization information for a range of energy-supply systems and provides supplementary information on environmental controls applicable to a select group of environmentally characterized energy systems. Environmental residuals, physical-resource requirements, and discussion of applicable standards are the principal information provided. The quantitative and qualitative data provided are useful for evaluating alternative policy and technical strategies and for assessing the environmental impact of facility siting, energy production, and environmental controls.

Summary of interference measurements at selected radio observatories

NASA Technical Reports Server (NTRS)

Tarter, Jill C.

1990-01-01

Results are presented from a series of RF interference (RFI) observations conducted during 1989 and 1990 at selected radio astronomy observatories in order to choose a site for the SETI, where the local and orbital RFI would be as benign as possible for observations of weak electromagnetic signals. These observatories included the DSS13 at Goldstone (California), the Arecibo Observatory (Puerto Rico), the Algonquin Radio Observatory in Ottawa (Canada), the Ohio State University Radio Observatory in Columbus (Ohio), and the NRAO in Green Bank (West Virginia). The observations characterize the RFI environment at these sites from 1 to 10 GHz, using radio astronomy antennas, feeds, and receivers; SETI signal processors; and stand-alone equipment built specifically for this purpose. The results served as part of the basis for the selection (by the NASA SETI Microwave Observing Project) of NRAO as the site of choice for SETI observations.

Computer-assisted selection of donor sites for autologous grafts

NASA Astrophysics Data System (ADS)

Krol, Zdzislaw; Zeilhofer, Hans-Florian U.; Sader, Robert; Hoffmann, Karl-Heinz; Gerhardt, Paul; Horch, Hans-Henning

1997-05-01

A new method is proposed for a precise planning of autologous bone grafts in cranio- and maxillofacial surgery. In patients with defects of the facial skeleton, autologous bone transplants can be harvested from various donor sites in the body. The preselection of a donor site depends i.a. on the morphological fit of the available bone mass and the shape of the part that is to be transplanted. A thorough planning and simulation of the surgical intervention based on 3D CT studies leads to a geometrical description and the volumetric characterization of the bone part to be resected and transplanted. Both, an optimal fit and a minimal lesion of the donor site are guidelines in this process. We use surface similarity and voxel similarity measures in order to select the optimal donor region for an individually designed transplant.

Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol

DOE PAGES

Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.; ...

2014-12-31

The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. In this paper, we have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). Wemore » found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC 50 < 100 nM) inhibit Jak3 activity in cell-based assays. Finally, these results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases.« less

Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol

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

Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.

The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. In this paper, we have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). Wemore » found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC 50 < 100 nM) inhibit Jak3 activity in cell-based assays. Finally, these results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases.« less

Boundary layer pollution profiles from a rural site in South Korea

NASA Astrophysics Data System (ADS)

Sullivan, John; McGee, Thomas; Thompson, Anne; Twigg, Laurence; Sumnicht, Grant; Stauffer, Ryan

2018-04-01

During the NASA 2016 KORUS-AQ campaign, the ground based NASA GSFC ozone lidar and balloon borne instrumentation were deployed to the remote Taehwa Forest site (37.3 N, 127.3 E, 151 m AGL) to characterize the transport of pollution downwind of the Seoul metropolitan region. On most days from 02 May to 10 June 2016, continuous hours of lidar profiles of ozone were measured. Select days are shown to represent key ozone events that occurred at the rural site.

Identification of a Novel Allosteric Inhibitory Site on Tryptophan Hydroxylase 1 Enabling Unprecedented Selectivity Over all Related Hydroxylases

PubMed Central

Petrassi, Mike; Barber, Rob; Be, Celine; Beach, Sarah; Cox, Brian; D’Souza, Anne-Marie; Duggan, Nick; Hussey, Martin; Fox, Roy; Hunt, Peter; Jarai, Gabor; Kosaka, Takatoshi; Oakley, Paul; Patel, Viral; Press, Neil; Rowlands, David; Scheufler, Clemens; Schmidt, Oliver; Srinivas, Honnappa; Turner, Mary; Turner, Rob; Westwick, John; Wolfreys, Alison; Pathan, Nuzhat; Watson, Simon; Thomas, Matthew

2017-01-01

Pulmonary arterial hypertension (PAH) has demonstrated multi-serotonin receptor dependent pathologies, characterized by increased tone (5-HT1B receptor) and complex lesions (SERT, 5-HT1B, 5-HT2B receptors) of the pulmonary vasculature together with right ventricular hypertrophy, ischemia and fibrosis (5-HT2B receptor). Selective inhibitors of individual signaling elements – SERT, 5-HT2A, 5HT2B, and combined 5-HT2A/B receptors, have all been tested clinically and failed. Thus, inhibition of tryptophan hydroxylase 1 (TPH1), the rate limiting step in 5-HT synthesis, has been suggested as a more broad, and thereby more effective, mode of 5-HT inhibition. However, selectivity over non-pathogenic enzyme family members, TPH2, phenylalanine hydroxylase, and tyrosine hydroxylase has hampered therapeutic development. Here we describe the site/sequence, biochemical, and biophysical characterization of a novel allosteric site on TPH1 through which selectivity over TPH2 and related aromatic amino acid hydroxylases is achieved. We demonstrate the mechanism of action by which novel compounds selectively inhibit TPH1 using surface plasma resonance and enzyme competition assays with both tryptophan ligand and BH4 co-factor. We demonstrate 15-fold greater potency within a human carcinoid cell line versus the most potent known TPH1/2 non-specific inhibitor. Lastly, we detail a novel canine in vivo system utilized to determine effective biologic inhibition of newly synthesized 5-HT. These findings are the first to demonstrate TPH1-selective inhibition and may pave the way to a truly effective means to reduce pathologic 5-HT and thereby treat complex remodeling diseases such as PAH. PMID:28529483

Characterizing the diversity of coral reef habitats and fish communities found in a UNESCO World Heritage Site: the strategy developed for Lagoons of New Caledonia.

PubMed

Andréfouët, S; Wantiez, L

2010-01-01

Since 1972, the UNESCO "World Heritage Convention" offers an international canvas for conservation and management that targets areas of high cultural and environmental significance. To support the designation of areas within the 36.000 km(2) of New Caledonia coral reefs and lagoons as a World Heritage Site, the natural value and diversity of the proposed zones needed to be demonstrated. To exhaustively identify each configuration of shallow habitats, high resolution remote sensing images were used to select the sampling sites. This optimal scheme resulted in the selection of nearly 1300 sampling sites, and was then simplified to render its application realistic. In the final sampling plan, only the most common or the most remarkable coral zones were selected. Following this selection, in situ habitat and fish surveys were conducted in 2006-2008 in five large areas spanning a 600 km-long latitudinal gradient. Habitats were described using line-intercept transects in parallel with underwater visual census of indicator and commercial coral reef fish species. We report here on the results achieved in terms of: (i) the actual diversity of coral habitats captured by the remote sensing based sampling strategy, (ii) the different reef fish communities captured from the different sites, and (iii) how well they represent New Caledonia diversity. We discuss the possible generalization of this scheme to other sites, in the context of World Heritage Site selection and for other large-scale conservation planning activities. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Geoscientific Site Evaluation Approach for Canada's Deep Geological Repository for Used Nuclear Fuel

NASA Astrophysics Data System (ADS)

Sanchez-Rico Castejon, M.; Hirschorn, S.; Ben Belfadhel, M.

2015-12-01

The Nuclear Waste Management Organization (NWMO) is responsible for implementing Adaptive Phased Management, the approach selected by the Government of Canada for long-term management of used nuclear fuel generated by Canadian nuclear reactors. The ultimate objective of APM is the centralized containment and isolation of Canada's used nuclear fuel in a Deep Geological Repository in a suitable crystalline or sedimentary rock formation. In May 2010, the NWMO published and initiated a nine-step site selection process to find an informed and willing community to host a deep geological repository for Canada's used nuclear fuel. The site selection process is designed to address a broad range of technical and social, economic and cultural factors. The site evaluation process includes three main technical evaluation steps: Initial Screenings; Preliminary Assessments; and Detailed Site Characterizations, to assess the suitability of candidate areas in a stepwise manner over a period of many years. By the end of 2012, twenty two communities had expressed interest in learning more about the project. As of July 2015, nine communities remain in the site selection process. To date (July 2015), NWMO has completed Initial Screenings for the 22 communities that expressed interest, and has completed the first phase of Preliminary Assessments (desktop) for 20 of the communities. Phase 2 of the Preliminary Assessments has been initiated in a number of communities, with field activities such as high-resolution airborne geophysical surveys and geological mapping. This paper describes the approach, methods and criteria being used to assess the geoscientific suitability of communities currently involved in the site selection process.

Isolation of Cu Atoms in Pd Lattice: Forming Highly Selective Sites for Photocatalytic Conversion of CO2 to CH4.

PubMed

Long, Ran; Li, Yu; Liu, Yan; Chen, Shuangming; Zheng, Xusheng; Gao, Chao; He, Chaohua; Chen, Nanshan; Qi, Zeming; Song, Li; Jiang, Jun; Zhu, Junfa; Xiong, Yujie

2017-03-29

Photocatalytic conversion of CO 2 to CH 4 , a carbon-neutral fuel, represents an appealing approach to remedy the current energy and environmental crisis; however, it suffers from the large production of CO and H 2 by side reactions. The design of catalytic sites for CO 2 adsorption and activation holds the key to address this grand challenge. In this Article, we develop highly selective sites for photocatalytic conversion of CO 2 to CH 4 by isolating Cu atoms in Pd lattice. According to our synchrotron-radiation characterizations and theoretical simulations, the isolation of Cu atoms in Pd lattice can play dual roles in the enhancement of CO 2 -to-CH 4 conversion: (1) providing the paired Cu-Pd sites for the enhanced CO 2 adsorption and the suppressed H 2 evolution; and (2) elevating the d-band center of Cu sites for the improved CO 2 activation. As a result, the Pd 7 Cu 1 -TiO 2 photocatalyst achieves the high selectivity of 96% for CH 4 production with a rate of 19.6 μmol g cat -1 h -1 . This work provides fresh insights into the catalytic site design for selective photocatalytic CO 2 conversion, and highlights the importance of catalyst lattice engineering at atomic precision to catalytic performance.

Importance of structural stability to success of mourning dove nests

USGS Publications Warehouse

Coon, R.A.; Nichols, J.D.; Percival, H.F.

1981-01-01

Studies of nest-site selection and nesting habitats often involve a "characterization" of nests and of habitats in which nests are found. Our objective in the present work is to identify nest-site characteristics that are associated with variation in components of Mourning Dove (Zenaida macroura) fitness (e.g. the probability of a nest succeeding), as opposed to simply "characterizing" dove nest sites. If certain nest- site characteristics affect the probability that a nest will succeed, then we suspect that these characteristics will be associated with either concealment (the probability of detection by certain predators) or structural stability (the probability of eggs or entire nests falling to the ground as a result of wind, rain storms, parental activity, etc.). Although other workers agree that structural stability is an important determinant of Mourning Dove nesting success (e.g. McClure 1944: 384; Woolfenden and Rohwer 1969: 59), we are aware of no actual tests of this hypothesis.

Miscellaneous chemical basin expedited site characterization report

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

Riha, B.D.; Pemberton, B.E.; Rossabi, J.

1996-12-01

A total of twenty nine cone penetrometer test (CPT) pushes in three weeks were conducted for vadose zone characterization of the Miscellaneous Chemical Basin (MCB) waste unit at the Savannah River Site. The shallow, unlined basin received liquid chemical wastes over an 18 year period beginning in 1956. This characterization was initiated to determine the vertical and lateral extent of contamination in the vadose zone and to install vadose zone wells for remediation by barometric pumping or active vapor extraction to help prevent further contamination of groundwater. The CPT locations within the waste site were selected based on results frommore » previous shallow soil gas surveys, groundwater contamination data, and the suspected basin center. Geophysical data and soil gas samples were collected at twenty five locations and twenty five vadose zone wells were installed. The wells were screened to target the clay zones and areas of higher soil gas concentrations. The well construction diagrams are provided in Appendix B. Baro-Ball{trademark} valves for enhanced barometric pumping were installed on each well upon completion to immediately begin the remediation treatability study at the site.« less

Multi-year high-frequency hydrothermal monitoring of selected high-threat Cascade Range volcanoes

NASA Astrophysics Data System (ADS)

Crankshaw, I. M.; Archfield, S. A.; Newman, A. C.; Bergfeld, D.; Clor, L. E.; Spicer, K. R.; Kelly, P. J.; Evans, W. C.; Ingebritsen, S. E.

2018-05-01

From 2009 to 2015 the U.S. Geological Survey (USGS) systematically monitored hydrothermal behavior at selected Cascade Range volcanoes in order to define baseline hydrothermal and geochemical conditions. Gas and water data were collected regularly at 25 sites on 10 of the highest-risk volcanoes in the Cascade Range. These sites include near-summit fumarole groups and springs/streams that show clear evidence of magmatic influence (high 3He/4He ratios and/or large fluxes of magmatic CO2 or heat). Site records consist mainly of hourly temperature and hydrothermal-flux data. Having established baseline conditions during a multiyear quiescent period, the USGS reduced monitoring frequency from 2015 to present. The archived monitoring data are housed at (doi:10.5066/F72N5088). These data (1) are suitable for retrospective comparison with other continuous geophysical monitoring data and (2) will provide context during future episodes of volcanic unrest, such that unrest-related variations at these thoroughly characterized sites will be more clearly recognizable. Relatively high-frequency year-round data are essential to achieve these objectives, because many of the time series reveal significant diurnal, seasonal, and inter-annual variability that would tend to mask unrest signals in the absence of baseline data. Here we characterize normal variability for each site, suggest strategies to detect future volcanic unrest, and explore deviations from background associated with recent unrest.

Site selection and traverse planning to support a lunar polar rover mission: A case study at Haworth Crater

NASA Astrophysics Data System (ADS)

Heldmann, Jennifer L.; Colaprete, Anthony; Elphic, Richard C.; Bussey, Ben; McGovern, Andrew; Beyer, Ross; Lees, David; Deans, Matt

2016-10-01

Studies of lunar polar volatile deposits are of interest for scientific purposes to understand the nature and evolution of the volatiles, and also for exploration reasons as a possible in situ resource to enable long term human exploration and settlement of the Moon. Both theoretical and observational studies have suggested that significant quantities of volatiles exist in the polar regions, although the lateral and horizontal distribution remains unknown at the km scale and finer resolution. A lunar polar rover mission is required to further characterize the distribution, quantity, and character of lunar polar volatile deposits at these higher spatial resolutions. Here we present a case study for NASA's Resource Prospector (RP) mission concept for a lunar polar rover and utilize this mission architecture and associated constraints to evaluate whether a suitable landing site exists to support an RP flight mission. We evaluate the landing site criteria to characterize the Haworth Crater region in terms of expected hydrogen abundance, surface topography, and prevalence of shadowed regions, as well as solar illumination and direct to Earth communications as a function of time to develop a notional rover traverse plan that addresses both science and engineering requirements. We also present lessons-learned regarding lunar traverse path planning focusing on the critical nature of landing site selection, the influence of illumination patterns on traverse planning, the effects of performing shadowed rover operations, the influence of communications coverage on traverse plan development, and strategic planning to maximize rover lifetime and science at end of mission. Here we present a detailed traverse path scenario for a lunar polar volatiles rover mission and find that the particular site north of Haworth Crater studied here is suitable for further characterization of polar volatile deposits.

Site Characterization for Radar Experiments

DTIC Science & Technology

1990-08-01

accomplished waz "New Mine Detection Technologies," Mr. Jack Stoll, Principal Investigator. The Environmental Systems Division (EST) of the Environmental...Mr. Steve Bong of Hilton Systems visiting the proposed study site in M’rch to select specific locations for the test plots. The field data coll in...Technology/Lincoln Laboratory (MIT/LL) described an airborne 35-Ghz radar imaging system . The MIT/LL would employ various kinds of processing on the

Pilot-Scale Demonstration of In-Situ Chemical Oxidation ...

EPA Pesticide Factsheets

A pilot-scale in situ chemical oxidation (ISCO) demonstration, involving subsurface injections of sodium permanganate (NaMnO4), was performed at the US Marine Corp Recruit Depot (MCRD), site 45 (Parris Island (PI), SC). The ground water was originally contaminated with perchloroethylene (PCE) (also known as tetrachloroethylene), a chlorinated solvent used in dry cleaner operations. High resolution site characterization involved multiple iterations of soil core sampling and analysis. Nested micro-wells and conventional wells were also used to sample and analyze ground water for PCE and decomposition products (i.e., trichloroethyelene (TCE), dichloroethylene (c-DCE, t-DCE), and vinyl chloride (VC)), collectively referred to as chlorinated volatile organic compounds (CVOC). This characterization methodology was used to develop and refine the conceptual site model and the ISCO design, not only by identifying CVOC contamination but also by eliminating uncontaminated portions of the aquifer from further ISCO consideration. Direct-push injection was selected as the main method of NaMnO4 delivery due to its flexibility and low initial capital cost. Site impediments to ISCO activities in the source area involved subsurface utilities, including a high pressure water main, a high voltage power line, a communication line, and sanitary and stormwater sewer lines. Utility markings were used in conjunction with careful planning and judicious selection of injection locations. A

Design and methods of the Midwest Stream Quality Assessment (MSQA), 2013

USGS Publications Warehouse

Garrett, Jessica D.; Frey, Jeffrey W.; Van Metre, Peter C.; Journey, Celeste A.; Nakagaki, Naomi; Button, Daniel T.; Nowell, Lisa H.

2017-10-18

During 2013, the U.S. Geological Survey (USGS) National Water-Quality Assessment Project (NAWQA), in collaboration with the USGS Columbia Environmental Research Center, the U.S. Environmental Protection Agency (EPA) National Rivers and Streams Assessment (NRSA), and the EPA Office of Pesticide Programs assessed stream quality across the Midwestern United States. This Midwest Stream Quality Assessment (MSQA) simultaneously characterized watershed and stream-reach water-quality stressors along with instream biological conditions, to better understand regional stressor-effects relations. The MSQA design focused on effects from the widespread agriculture in the region and urban development because of their importance as ecological stressors of particular concern to Midwest region resource managers.A combined random stratified selection and a targeted selection based on land-use data were used to identify and select sites representing gradients in agricultural intensity across the region. During a 14-week period from May through August 2013, 100 sites were selected and sampled 12 times for contaminants, nutrients, and sediment. This 14-week water-quality “index” period culminated with an ecological survey of habitat, periphyton, benthic macroinvertebrates, and fish at all sites. Sediment was collected during the ecological survey for analysis of sediment chemistry and toxicity testing. Of the 100 sites, 50 were selected for the MSQA random stratified group from 154 NRSA sites planned for the region, and the other 50 MSQA sites were selected as targeted sites to more evenly cover agricultural and urban stressor gradients in the study area. Of the 50 targeted sites, 12 were in urbanized watersheds and 21 represented “good” biological conditions or “least disturbed” conditions. The remaining 17 targeted sites were selected to improve coverage of the agricultural intensity gradient or because of historical data collection to provide temporal context for the study.This report provides a detailed description of the MSQA study components, including surveys of ecological conditions, routine water sampling, deployment of passive polar organic compound integrative samplers, and stream sediment sampling at all sites. Component studies that were completed to provide finer scale temporal data or more extensive analysis at selected sites, included continuous water-quality monitoring, daily pesticide sampling, laboratory and in-stream water toxicity testing efforts, and deployment of passive suspended-sediment samplers.

Characterization of a neurokinin B receptor site in rat brain using a highly selective radioligand.

PubMed

Laufer, R; Gilon, C; Chorev, M; Selinger, Z

1986-08-05

We have recently characterized a tachykinin receptor subtype (SP-N) whose preferred ligand is the mammalian neuropeptide, neurokinin B (Laufer, R., Wormser, U., Friedman, Z. Y., Gilon, C., Chorev, M., and Selinger, Z. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 7444-7448). To investigate this novel tachykinin receptor, we have now prepared a radiolabeled peptide, N alpha-[( 125I]desamino-3-iodotyrosyl)-[Asp5,6, N-methyl-Phe8]substance P (5-11) heptapeptide (125I-BH-NH-Senktide), which selectively interacts with the SP-N receptor subtype. The binding of 125I-BH-NH-Senktide to rat cerebral cortex membranes was studied under conditions that minimized nonspecific binding. Unlike other tachykinin receptor probes, this radioligand is not degraded during the binding experiment. Binding of 125I-BH-NH-Senktide is reversible, saturable, and of high affinity (KD = 0.9 nM). The radioligand labels a single class of binding site (122 fmol binding sites/mg of protein), as indicated by a linear Scatchard plot and a Hill coefficient close to unity (nH = 1.05). The pharmacological specificity of this binding site corresponds to that of the neuronal SP-N receptor in guinea pig ileum myenteric plexus, which was determined by a functional bioassay. Among various rat brain regions, the highest binding was observed in the cerebral cortex, olfactory bulb, hypothalamus, and hippocampus. These results suggest the existence and specific distribution of a neurokinin B receptor site of the SP-N type in rat brain. 125I-BH-NH-Senktide is the first selective and potent probe for this receptor and is thus an important tool for further studies of its distribution, regulation, and functional role.

Characterization and design of the FutureGen 2.0 carbon storage site

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

Gilmore, Tyler; Bonneville, Alain; Sullivan, Charlotte

2016-10-01

The objective of the FutureGen 2.0 Project was to demonstrate, at the commercial scale, the technical feasibility of implementing carbon capture and storage (CCS) in a deep saline formation in Illinois, USA. Over approximately 5 years, the FutureGen Alliance conducted a detailed site-selection process and identified a site for carbon sequestration storage in Morgan County, Illinois. The storage site was fully characterized, including the collection of seismic data and the drilling and characterization of a stratigraphic borehole. The characterization data provided critical input for developing a site-specific conceptual model and subsequent numerical modeling simulations. The modeling simulations, coupled with themore » upstream designs of the pipeline and power plant supported the development of a detailed 90 percent design that included the injection wells and associated control and monitoring infrastructure. Collectively, all these data were used by the FutureGen Alliance to develop the required documentation to support the applications for four underground injection control (UIC) permits (one for each proposed well). In August 2014, the U.S. Environmental Protection Agency issued four, first-of-their-kind, Class VI UIC permits for carbon sequestration in the United States to the FutureGen Alliance. The information and data generated under this project have been made publically available through reports and publications, including this journal and others.« less

Strategy for Ranking the Science Value of the Surface of Asteroid 101955 Bennu for Sample Site Selection for Osiris-REx

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Connolly, H. C., Jr.; Lauretta, D. S.

2014-01-01

OSRIS-REx is NASA's New Frontiers 3 sample return mission that will return at least 60 g of pristine surface material from near-Earth asteroid 101955 Bennu in September 2023. The scientific value of the sample increases enormously with the amount of knowledge captured about the geological context from which the sample is collected. The OSIRIS-REx spacecraft is highly maneuverable and capable of investigating the surface of Bennu at scales down to the sub-cm. The OSIRIS-REx instruments will characterize the overall surface geology including spectral properties, microtexture, and geochemistry of the regolith at the sampling site in exquisite detail for up to 505 days after encountering Bennu in August 2018. The mission requires at the very minimum one acceptable location on the asteroid where a touch-and-go (TAG) sample collection maneuver can be successfully per-formed. Sample site selection requires that the follow-ing maps be produced: Safety, Deliverability, Sampleability, and finally Science Value. If areas on the surface are designated as safe, navigation can fly to them, and they have ingestible regolith, then the scientific value of one site over another will guide site selection.

Vadose Zone Transport Field Study: Status Report

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

Gee, Glendon W.; Ward, Anderson L.

2001-11-30

Studies were initiated at the Hanford Site to evaluate the process controlling the transport of fluids in the vadose zone and to develop a reliable database upon which vadose-zone transport models can be calibrated. These models are needed to evaluate contaminant migration through the vadose zone to underlying groundwaters at Hanford. A study site that had previously been extensively characterized using geophysical monitoring techniques was selected in the 200 E Area. Techniques used previously included neutron probe for water content, spectral gamma logging for radionuclide tracers, and gamma scattering for wet bulk density. Building on the characterization efforts of themore » past 20 years, the site was instrumented to facilitate the comparison of nine vadose-zone characterization methods: advanced tensiometers, neutron probe, electrical resistance tomography (ERT), high-resolution resistivity (HRR), electromagnetic induction imaging (EMI), cross-borehole radar (XBR), and cross-borehole seismic (XBS). Soil coring was used to obtain soil samples for analyzing ionic and isotopic tracers.« less

Stability of choice in the honey bee nest-site selection process.

PubMed

Nevai, Andrew L; Passino, Kevin M; Srinivasan, Parthasarathy

2010-03-07

We introduce a pair of compartment models for the honey bee nest-site selection process that lend themselves to analytic methods. The first model represents a swarm of bees deciding whether a site is viable, and the second characterizes its ability to select between two viable sites. We find that the one-site assessment process has two equilibrium states: a disinterested equilibrium (DE) in which the bees show no interest in the site and an interested equilibrium (IE) in which bees show interest. In analogy with epidemic models, we define basic and absolute recruitment numbers (R(0) and B(0)) as measures of the swarm's sensitivity to dancing by a single bee. If R(0) is less than one then the DE is locally stable, and if B(0) is less than one then it is globally stable. If R(0) is greater than one then the DE is unstable and the IE is stable under realistic conditions. In addition, there exists a critical site quality threshold Q(*) above which the site can attract some interest (at equilibrium) and below which it cannot. We also find the existence of a second critical site quality threshold Q(**) above which the site can attract a quorum (at equilibrium) and below which it cannot. The two-site discrimination process, in which we examine a swarm's ability to simultaneously consider two sites differing in both site quality and discovery time, has a stable DE if and only if both sites' individual basic recruitment numbers are less than one. Numerical experiments are performed to study the influences of site quality on quorum time and the outcome of competition between a lower quality site discovered first and a higher quality site discovered second. 2009 Elsevier Ltd. All rights reserved.

[125I]2-(2-chloro-4-iodo-phenylamino)-5-methyl-pyrroline (LNP 911), a high-affinity radioligand selective for I1 imidazoline receptors.

PubMed

Greney, Hugues; Urosevic, Dragan; Schann, Stephan; Dupuy, Laurence; Bruban, Véronique; Ehrhardt, Jean-Daniel; Bousquet, Pascal; Dontenwill, Monique

2002-07-01

The I1 subtype of imidazoline receptors (I1R) is a plasma membrane protein that is involved in diverse physiological functions. Available radioligands used so far to characterize the I(1)R were able to bind with similar affinities to alpha2-adrenergic receptors (alpha2-ARs) and to I1R. This feature was a major drawback for an adequate characterization of this receptor subtype. New imidazoline analogs were therefore synthesized and the present study describes one of these compounds, 2-(2-chloro-4-iodo-phenylamino)-5-methyl-pyrroline (LNP 911), which was of high affinity and selectivity for the I1R. LNP 911 was radioiodinated and its binding properties characterized in different membrane preparations. Saturation experiments with [125I]LNP 911 revealed a single high affinity binding site in PC-12 cell membranes (K(D) = 1.4 nM; B(max) = 398 fmol/mg protein) with low nonspecific binding. [125I]LNP 911 specific binding was inhibited by various imidazolines and analogs but was insensitive to guanosine-5'-O-(3-thio)triphosphate. The rank order of potency of some competing ligands [LNP 911, PIC, rilmenidine, 4-chloro-2-(imidazolin-2-ylamino)-isoindoline (BDF 6143), lofexidine, and clonidine] was consistent with the definition of [125I]LNP 911 binding sites as I1R. However, other high-affinity I1R ligands (moxonidine, efaroxan, and benazoline) exhibited low affinities for these binding sites in standard binding assays. In contrast, when [125I]LNP 911 was preincubated at 4 degrees C, competition curves of moxonidine became biphasic. In this case, moxonidine exhibited similar high affinities on [125I]LNP 911 binding sites as on I1R defined with [125I]PIC. Moxonidine proved also able to accelerate the dissociation of [125I]LNP 911 from its binding sites. These results suggest the existence of an allosteric modulation at the level of the I1R, which seems to be corroborated by the dose-dependent enhancement by LNP 911 of the agonist effects on the adenylate cyclase pathway associated to I1R. Because [125I]LNP 911 was unable to bind to the I2 binding site and alpha2AR, our data indicate that [125I]LNP 911 is the first highly selective radioiodinated probe for I1R with a nanomolar affinity. This new tool should facilitate the molecular characterization of the I1 imidazoline receptor.

Wave Resource Characterization at US Wave Energy Converter (WEC) Test Sites

NASA Astrophysics Data System (ADS)

Dallman, A.; Neary, V. S.

2016-02-01

The US Department of Energy's (DOE) Marine and Hydrokinetic energy (MHK) Program is supporting a diverse research and development portfolio intended to accelerate commercialization of the marine renewable industry by improving technology performance, reducing market barriers, and lowering the cost of energy. Wave resource characterization at potential and existing wave energy converter (WEC) test sites and deployment locations contributes to this DOE goal by providing a catalogue of wave energy resource characteristics, met-ocean data, and site infrastructure information, developed utilizing a consistent methodology. The purpose of the catalogue is to enable the comparison of resource characteristics among sites to facilitate the selection of test sites that are most suitable for a developer's device and that best meet their testing needs and objectives. It also provides inputs for the design of WEC test devices and planning WEC tests, including the planning of deployment and operations and maintenance. The first edition included three sites: the Pacific Marine Energy Center (PMEC) North Energy Test Site (NETS) offshore of Newport, Oregon, the Kaneohe Bay Naval Wave Energy Test Site (WETS) offshore of Oahu, HI, and a potential site offshore of Humboldt Bay, CA (Eureka, CA). The second edition was recently finished, which includes five additional sites: the Jennette's Pier Wave Energy Converter Test Site in North Carolina, the US Army Corps of Engineers (USACE) Field Research Facility (FRF), the PMEC Lake Washington site, the proposed PMEC South Energy Test Site (SETS), and the proposed CalWave Central Coast WEC Test Site. The operational sea states are included according to the IEC Technical Specification on wave energy resource assessment and characterization, with additional information on extreme sea states, weather windows, and representative spectra. The methodology and a summary of results will be discussed.

Characterizing spatial structure of sediment E. coli populations to inform sampling design.

PubMed

Piorkowski, Gregory S; Jamieson, Rob C; Hansen, Lisbeth Truelstrup; Bezanson, Greg S; Yost, Chris K

2014-01-01

Escherichia coli can persist in streambed sediments and influence water quality monitoring programs through their resuspension into overlying waters. This study examined the spatial patterns in E. coli concentration and population structure within streambed morphological features during baseflow and following stormflow to inform sampling strategies for representative characterization of E. coli populations within a stream reach. E. coli concentrations in bed sediments were significantly different (p = 0.002) among monitoring sites during baseflow, and significant interactive effects (p = 0.002) occurred among monitoring sites and morphological features following stormflow. Least absolute shrinkage and selection operator (LASSO) regression revealed that water velocity and effective particle size (D 10) explained E. coli concentration during baseflow, whereas sediment organic carbon, water velocity and median particle diameter (D 50) were important explanatory variables following stormflow. Principle Coordinate Analysis illustrated the site-scale differences in sediment E. coli populations between disconnected stream segments. Also, E. coli populations were similar among depositional features within a reach, but differed in relation to high velocity features (e.g., riffles). Canonical correspondence analysis resolved that E. coli population structure was primarily explained by spatial (26.9–31.7 %) over environmental variables (9.2–13.1 %). Spatial autocorrelation existed among monitoring sites and morphological features for both sampling events, and gradients in mean particle diameter and water velocity influenced E. coli population structure for the baseflow and stormflow sampling events, respectively. Representative characterization of streambed E. coli requires sampling of depositional and high velocity environments to accommodate strain selectivity among these features owing to sediment and water velocity heterogeneity.

MX Siting Investigation. Geotechnical Summary. Prime Characterization Sites, Great Basin, Candidate Siting Province.

DTIC Science & Technology

1979-02-15

O0 1? GAN T’ NUIM’--ER(,) rL~y~ ,’~7icrx~ Eri§c CPERFOnM3NG, ORGANIZATION NAME AND ADORFS 10. PROGRAM ELEMENT PRC2ECT. TASA AREAA WORK UN IT NUMBErS...investigation to check aerial photo inter - pretation and to determine physical properties of the surficial units at selected field stations o Shallow and...contour map, and may represent inter - fingering of volcanic units and/or basin-fill deposits or an east-west trending intrusive body. Data in the Ralston

COPPER COMPLEXATION BY NATURAL ORGANIC MATTER IN CONTAMINATED AND UNCOMTAINATED GROUND WATER

EPA Science Inventory

Ground-water samples were collected from an uncontaminated and a contaminated site. Copper complexation was characterized by ion-selective electrode (ISE), fluorescence quenching (FQ), and cathodic stripping voltammetric (CSV) titrations. All of the samples were titrated at their...

A multi-landing pad DNA integration platform for mammalian cell engineering

PubMed Central

Gaidukov, Leonid; Wroblewska, Liliana; Teague, Brian; Nelson, Tom; Zhang, Xin; Liu, Yan; Jagtap, Kalpana; Mamo, Selamawit; Tseng, Wen Allen; Lowe, Alexis; Das, Jishnu; Bandara, Kalpanie; Baijuraj, Swetha; Summers, Nevin M; Zhang, Lin; Weiss, Ron

2018-01-01

Abstract Engineering mammalian cell lines that stably express many transgenes requires the precise insertion of large amounts of heterologous DNA into well-characterized genomic loci, but current methods are limited. To facilitate reliable large-scale engineering of CHO cells, we identified 21 novel genomic sites that supported stable long-term expression of transgenes, and then constructed cell lines containing one, two or three ‘landing pad’ recombination sites at selected loci. By using a highly efficient BxB1 recombinase along with different selection markers at each site, we directed recombinase-mediated insertion of heterologous DNA to selected sites, including targeting all three with a single transfection. We used this method to controllably integrate up to nine copies of a monoclonal antibody, representing about 100 kb of heterologous DNA in 21 transcriptional units. Because the integration was targeted to pre-validated loci, recombinant protein expression remained stable for weeks and additional copies of the antibody cassette in the integrated payload resulted in a linear increase in antibody expression. Overall, this multi-copy site-specific integration platform allows for controllable and reproducible insertion of large amounts of DNA into stable genomic sites, which has broad applications for mammalian synthetic biology, recombinant protein production and biomanufacturing. PMID:29617873

Selection and Characterization of Landing Sites for Chandrayaan-2 Lander

NASA Astrophysics Data System (ADS)

Gopala Krishna, Barla; Amitabh, Amitabh; Srinivasan, T. P.; Karidhal, Ritu; Nagesh, G.; Manjusha, N.

2016-07-01

Indian Space Research Organisation has planned the second mission to moon known as Chandrayaan-2, which consists of an Orbiter, a Lander and a Rover. This will be the first soft landing mission of India on lunar surface. The Orbiter, Lander and Rover individually will carry scientific payloads that enhance the scientific objectives of Chandrayaan-2. The Lander soft lands on the lunar surface and subsequently Lander & Rover will carry on with the payload activities on the moon surface. Landing Site identification based on the scientific and engineering constrains of lander plays an important role in success of a mission. The Lander poses some constraints because of its engineering design for the selection of the landing site and on the other hand the landing site / region imparts some constrain on the Lander. The various constraints that have to be considered for the study of the landing site are Local slope, Sun illumination during mission life, Radio communication with the Earth, Global slope towards equator, Boulders size, Crater density and boulder distribution. This paper describes the characterization activities of the different landing locations which have been studied for Chandrayaan-2 Lander. The sites have been studied both in the South Polar and North Polar regions of the moon on the near side. The Engineering Constraints at the sites due to the Lander, Factors that affect mission life (i.e. illumination at the location), Factors influencing communication to earth (i.e. RF visibility) & Shadow movements have been studied at these locations and zones that are favourable for landing have been short listed. This paper gives methodology of these studies along with the results of the characteristics of all the sites and the recommendations for further action in finalizing the landing area.

Adaptation of A-to-I RNA editing in Drosophila

PubMed Central

Zhang, Hong

2017-01-01

Adenosine-to-inosine (A-to-I) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. In this study, we systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly half of these sites had events evolutionarily conserved across Drosophila species. We detected strong signatures of positive selection on the nonsynonymous editing sites in Drosophila brains, and the beneficial editing sites were significantly enriched in genes related to chemical and electrical neurotransmission. The signal of adaptation was even more pronounced for the editing sites located in X chromosome or for those commonly observed across Drosophila species. We identified a set of gene candidates (termed “PSEB” genes) that had nonsynonymous editing events favored by natural selection. We presented evidence that editing preferentially increased mutation sequence space of evolutionarily conserved genes, which supported the adaptive evolution hypothesis of editing. We found prevalent nonsynonymous editing sites that were favored by natural selection in female and male adults from five strains of D. melanogaster. We showed that temperature played a more important role than gender effect in shaping the editing levels, although the effect of temperature is relatively weaker compared to that of species effect. We also explored the relevant factors that shape the selective patterns of the global editomes. Altogether we demonstrated that abundant nonsynonymous editing sites in Drosophila brains were adaptive and maintained by natural selection during evolution. Our results shed new light on the evolutionary principles and functional consequences of RNA editing. PMID:28282384

Integrated ground-water monitoring strategy for NRC-licensed facilities and sites: Case study applications

USGS Publications Warehouse

Price, V.; Temples, T.; Hodges, R.; Dai, Z.; Watkins, D.; Imrich, J.

2007-01-01

This document discusses results of applying the Integrated Ground-Water Monitoring Strategy (the Strategy) to actual waste sites using existing field characterization and monitoring data. The Strategy is a systematic approach to dealing with complex sites. Application of such a systematic approach will reduce uncertainty associated with site analysis, and therefore uncertainty associated with management decisions about a site. The Strategy can be used to guide the development of a ground-water monitoring program or to review an existing one. The sites selected for study fall within a wide range of geologic and climatic settings, waste compositions, and site design characteristics and represent realistic cases that might be encountered by the NRC. No one case study illustrates a comprehensive application of the Strategy using all available site data. Rather, within each case study we focus on certain aspects of the Strategy, to illustrate concepts that can be applied generically to all sites. The test sites selected include:Charleston, South Carolina, Naval Weapons Station,Brookhaven National Laboratory on Long Island, New York,The USGS Amargosa Desert Research Site in Nevada,Rocky Flats in Colorado,C-Area at the Savannah River Site in South Carolina, andThe Hanford 300 Area.A Data Analysis section provides examples of detailed data analysis of monitoring data.

Near surface geotechnical and geophysical data cross validated for site characterization applications. The cases of selected accelerometric stations in Crete island (Greece)

NASA Astrophysics Data System (ADS)

Loupasakis, Constantinos; Tsangaratos, Paraskevas; Rozos, Dimitrios; Rondoyianni, Theodora; Vafidis, Antonis; Steiakakis, Emanouil; Agioutantis, Zacharias; Savvaidis, Alexandros; Soupios, Pantelis; Papadopoulos, Ioannis; Papadopoulos, Nikos; Sarris, Apostolos; Mangriotis, Maria-Dafni; Dikmen, Unal

2015-04-01

The near surface ground conditions are highly important for the design of civil constructions. These conditions determine primarily the ability of the foundation formations to bear loads, the stress - strain relations and the corresponding deformations, as well as the soil amplification and corresponding peak ground motion in case of dynamic loading. The static and dynamic geotechnical parameters as well as the ground-type/soil-category can be determined by combining geotechnical and geophysical methods, such as engineering geological surface mapping, geotechnical drilling, in situ and laboratory testing and geophysical investigations. The above mentioned methods were combined for the site characterization in selected sites of the Hellenic Accelerometric Network (HAN) in the area of Crete Island. The combination of the geotechnical and geophysical methods in thirteen (13) sites provided sufficient information about their limitations, setting up the minimum tests requirements in relation to the type of the geological formations. The reduced accuracy of the surface mapping in urban sites, the uncertainties introduced by the geophysical survey in sites with complex geology and the 1-D data provided by the geotechnical drills are some of the causes affecting the right order and the quantity of the necessary investigation methods. Through this study the gradual improvement on the accuracy of the site characterization data in regards to the applied investigation techniques is presented by providing characteristic examples from the total number of thirteen sites. As an example of the gradual improvement of the knowledge about the ground conditions the case of AGN1 strong motion station, located at Agios Nikolaos city (Eastern Crete), is briefly presented. According to the medium scale geological map of IGME the station was supposed to be founded over limestone. The detailed geological mapping reveled that a few meters of loose alluvial deposits occupy the area, expected to lay over the Neogene marly formations and the Mesozoic limestone, identified at the surrounding area. This changes the ground type to E instead of A, based on the EC8 classification. According the geophysical survey the Neogene formations extend down several meters and the mean Vs30 is 476m/s, increasing the rank of the ground type to B. Finally, the geotechnical drill reviled that the loose alluvial deposits extend down 13m containing two clearly identified layers of liquefiable loose sand. Below the alluvial deposits a thin layer (1,5m thick) of Neogene marly formations and the karstified limestone was located, as expected. So finally it was proved that the ground type category at the site is S2, setting up the geotechnical drills as the determinant investigation technique for this site. Besides the above described case, all selected examples present sufficiently the ability, the limitations and the right order of the investigation methods aiming to the site characterization. This research has been co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: THALES. Investing in knowledge society through the European Social Fund.

A cross-site comparison of methods used for hydrogeologic characterization of the Galena-Platteville aquifer in Illinois and Wisconsin, with examples from selected Superfund sites

USGS Publications Warehouse

Kay, Robert T.; Mills, Patrick C.; Dunning, Charles P.; Yeskis, Douglas J.; Ursic, James R.; Vendl, Mark

2004-01-01

The effectiveness of 28 methods used to characterize the fractured Galena-Platteville aquifer at eight sites in northern Illinois and Wisconsin is evaluated. Analysis of government databases, previous investigations, topographic maps, aerial photographs, and outcrops was essential to understanding the hydrogeology in the area to be investigated. The effectiveness of surface-geophysical methods depended on site geology. Lithologic logging provided essential information for site characterization. Cores were used for stratigraphy and geotechnical analysis. Natural-gamma logging helped identify the effect of lithology on the location of secondary- permeability features. Caliper logging identified large secondary-permeability features. Neutron logs identified trends in matrix porosity. Acoustic-televiewer logs identified numerous secondary-permeability features and their orientation. Borehole-camera logs also identified a number of secondary-permeability features. Borehole ground-penetrating radar identified lithologic and secondary-permeability features. However, the accuracy and completeness of this method is uncertain. Single-point-resistance, density, and normal resistivity logs were of limited use. Water-level and water-quality data identified flow directions and indicated the horizontal and vertical distribution of aquifer permeability and the depth of the permeable features. Temperature, spontaneous potential, and fluid-resistivity logging identified few secondary-permeability features at some sites and several features at others. Flowmeter logging was the most effective geophysical method for characterizing secondary-permeability features. Aquifer tests provided insight into the permeability distribution, identified hydraulically interconnected features, the presence of heterogeneity and anisotropy, and determined effective porosity. Aquifer heterogeneity prevented calculation of accurate hydraulic properties from some tests. Different methods, such as flowmeter logging and slug testing, occasionally produced different interpretations. Aquifer characterization improved with an increase in the number of data points, the period of data collection, and the number of methods used.

Habitat selection of a declining white-tailed deer herd in the central Black Hills, South Dakota and Wyoming

NASA Astrophysics Data System (ADS)

Deperno, Christopher Shannon

Habitat selection, survival rates, the Black Hills National Forest Habitat Capability Model (HABCAP), and the USDA Forest Service Geographic Information System (GIS) data base were evaluated for a declining white-tailed deer (Odocoileus virginianus dacotensis) herd in the central Black Hills of South Dakota and Wyoming. From July 1993 through July 1996, 73 adult and yearling female and 12 adult and yearling male white-tailed deer were radiocollared and visually monitored. Habitat information was collected at 4,662 white-tailed deer locations and 1,087 random locations. Natural mortality (71%) was the primary cause of female mortality, followed by harvest (22.5%) and accidental causes (6.5%). More females died in spring (53.2%) than in fall (22.6%), winter (14.5%), or summer (9.7%). Male mortality resulted from hunting in fall (66.7%) and natural causes in spring (33.3%). Survival rates for all deer by year were 62.1% in 1993, 51.1% in 1994, 56.4% in 1995, and 53.9% in 1996 and were similar (P = 0.691) across years. During winter, white-tailed deer selected ponderosa pine- (Pinus ponderosa ) deciduous and burned pine cover types. Overstory-understory habitats selected included pine/grass-forb, pine/bearberry (Arctostaphylos uva-ursi), pine/snowberry (Symphoricarpos albus), burned pine/grass-forb, and pine/shrub habitats. Structural stages selected included sapling-pole pine stands with >70% canopy cover, burned pine sapling-pole and saw-timber stands with <40% canopy cover. Bedding locations were represented by saw-timber pine structural stages with >40% canopy cover and all sapling-pole pine structural stages; sapling-pole stands with >70% canopy cover received the greatest use. White-tailed deer primarily fed in pine saw-timber structural stage with less than 40% canopy cover. Overall, selected habitats contained lower amounts of grass/forb, shrubs, and litter than random locations. Male and female deer generally bedded in areas that were characterized by greater horizontal cover than feeding and random sites. When feeding and bedding sites were combined males selected areas that were characterized by greater levels of horizontal cover than females. During summer, white-tailed deer selected pine-deciduous, aspen (Populus tremuloides), aspen-coniferous, spruce (Picea glauca), and spruce-deciduous cover types. Overstory-understory habitats selected included pine/juniper (Juniperus communis), aspen/shrubs, spruce/juniper, and spruce/shrub habitats. Structural stages selected included pine, aspen, and spruce sapling pole stands with all levels (0--40%, 41--70%, 71--100%) of canopy cover. All habitat types (i.e., pine, aspen, and spruce) were used as bedding locations with pine sapling-pole structural stages with >70% canopy cover used most, whereas pine saw-timber structural stage with less than 40% canopy cover was primarily used for feeding. Females bedded in areas that were characterized by greater horizontal cover than feeding and random sites, whereas male feeding sites had greater horizontal cover characteristics than bedding or random locations.

SITE CHARACTERIZATION USING BIRD SPECIES COMPOSITION IN EASTERN OREGON, USA

EPA Science Inventory

We conducted riparian bird surveys at 25 randomly selected stream reaches in the John Day River Basin of eastern Oregon as part of the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP). At each reach along a kilometer-length transect, ...

MEASUREMENT OF FUGITIVE EMISSIONS AT REGION I LANDFILL

EPA Science Inventory

This report discusses a new measurement technology for characterizing emissions from large area sources. This work was funded by EPA's Monitoring and Measurement for the 21st Century Initiative, or 21M2. The site selected for demonstrating this technology is a superfund landfil...

SPATIAL PATTERNS AND ECOLOGICAL DETERMINANTS OF BENTHIC ALGAL ASSEMBLAGES IN MID-ATLANTIC STREAMS, USA

EPA Science Inventory

We attempted to identify spatial patterns and determinants for benthic algal assemblages in Mid-Atlantic streams. Periphyton, water chemistry, stream physical habitat, riparian conditions, and land cover/use in watersheds were characterized at 89 randomly selected stream sites i...

Geologic and geophysical characterization studies of Yucca Mountain, Nevada, a potential high-level radioactive-waste repository

USGS Publications Warehouse

Whitney, J.W.; Keefer, W.R.

2000-01-01

In recognition of a critical national need for permanent radioactive-waste storage, Yucca Mountain in southwestern Nevada has been investigated by Federal agencies since the 1970's, as a potential geologic disposal site. In 1987, Congress selected Yucca Mountain for an expanded and more detailed site characterization effort. As an integral part of this program, the U.S. Geological Survey began a series of detailed geologic, geophysical, and related investigations designed to characterize the tectonic setting, fault behavior, and seismicity of the Yucca Mountain area. This document presents the results of 13 studies of the tectonic environment of Yucca Mountain, in support of a broad goal to assess the effects of future seismic and fault activity in the area on design, long-term performance, and safe operation of the potential surface and subsurface repository facilities.

Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species

PubMed Central

Gao, Ziyue; Przeworski, Molly; Sella, Guy

2015-01-01

When long-lasting, balancing selection can lead to “trans-species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient balancing selection and derive approximations for summaries of the polymorphism data from two species. Specifically, we characterize the length of the segment that carries most of the footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the patterns of allelic associations among them. We confirm the accuracy of our approximations by coalescent simulations. We further show that for humans and chimpanzees—more generally, for pairs of species with low genetic diversity levels—these patterns are highly unlikely to be generated by neutral recurrent mutations. We discuss the implications for the design and interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa. PMID:25403856

Evolutionary Analysis of Structural Protein Gene VP1 of Foot-and-Mouth Disease Virus Serotype Asia 1

PubMed Central

Zhang, Qingxun; Liu, Xinsheng; Fang, Yuzhen; Pan, Li; Lv, Jianliang; Zhang, Zhongwang; Zhou, Peng; Ding, Yaozhong; Chen, Haotai; Shao, Junjun; Zhao, Furong; Lin, Tong; Chang, Huiyun; Zhang, Jie; Wang, Yonglu; Zhang, Yongguang

2015-01-01

Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare. In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains. Maximum likelihood analysis suggested that the strains circulating in Asia were classified into 8 different groups (groups I–VIII) or were unclassified (viruses collected before 2000). On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago. The result suggested that the virus had a high mutation rate (5.745 × 10−3 substitutions/site/year) in comparison to the other serotypes of FMDV VP1 gene. Furthermore, the structural protein VP1 was under lower selection pressure and the positive selection occurred at many sites, and four codons (positions 141, 146, 151, and 169) were located in known critical antigenic residues. The remaining sites were not located in known functional regions and were moderately conserved, and the reason for supporting all sites under positive selection remains to be elucidated because the power of these analyses was largely unknown. PMID:25793223

Hummingbird Comet Nucleus Analysis Mission

NASA Technical Reports Server (NTRS)

Kojiro, Daniel; Carle, Glenn C.; Lasher, Larry E.

2000-01-01

Hummingbird is a highly focused scientific mission, proposed to NASA s Discovery Program, designed to address the highest priority questions in cometary science-that of the chemical composition of the cometary nucleus. After rendezvous with the comet, Hummingbird would first methodically image and map the comet, then collect and analyze dust, ice and gases from the cometary atmosphere to enrich characterization of the comet and support landing site selection. Then, like its namesake, Hummingbird would carefully descend to a pre-selected surface site obtaining a high-resolution image, gather a surface material sample, acquire surface temperature and then immediately return to orbit for detailed chemical and elemental analyses followed by a high resolution post-sampling image of the site. Hummingbird s analytical laboratory contains instrumentation for a comprehensive molecular and elemental analysis of the cometary nucleus as well as an innovative surface sample acquisition device.

Genomic signatures of selection at linked sites: unifying the disparity among species

PubMed Central

Cutter, Asher D.; Payseur, Bret A.

2014-01-01

Population genetics theory supplies powerful predictions about how natural selection interacts with genetic linkage to sculpt the genomic landscape of nucleotide polymorphism. Both the spread of beneficial mutations and removal of deleterious mutations act to depress polymorphism levels, especially in low-recombination regions. However, empiricists have documented extreme disparities among species. Here we characterize the dominant features that could drive variation in linked selection among species, including roles for selective sweeps being ‘hard’ or ‘soft’, and concealing by demography and genomic confounds. We advocate targeted studies of close relatives to unify our understanding of how selection and linkage interact to shape genome evolution. PMID:23478346

Migration and site selection of Ornithodiplostomum ptychocheilus (Trematoda: Digenea) metacercariae in the brain of fathead minnows ( Pimephales promelas).

PubMed

Matisz, Chelsea E; Goater, Cameron P; Bray, Douglas

2010-04-01

The migration of subadult parasites to preferred sites within final hosts is well characterized. In contrast, the migration of larval stages of trematodes to specific sites within their second intermediate hosts is poorly understood. We used a serial necropsy approach to characterize the migration of Ornithodiplostomum ptychocheilus diplostomules from the point of cercarial penetration, to encystment within the outermost tissues of the brain of fathead minnows. Diplostomules utilized peripheral nerves to access the central nerve cord, or they used specific cranial nerves to directly access the brain. Within 3 h of exposure to cercariae, 46% of all diplostomules were observed within the medulla of the brain. Diplostomules subsequently utilized specific neural tracts to reach lateral regions of the outermost tissue layer of the optic lobes, the stratum marginale. Diplostomules remained in this layer during their 4-week growth phase, then shifted site to the adjacent meninges for encystment. Characterization of a habitat shift for developing versus encysted metacercariae helps explain the results of previous ecological studies that document transient changes in the effects of metacercariae on the surivival, behaviour, and anti-parasite defences of infected fish.

Geoscientific Characterization of the Bruce Site, Tiverton, Ontario

NASA Astrophysics Data System (ADS)

Raven, K.; Jackson, R.; Avis, J.; Clark, I.; Jensen, M.

2009-05-01

Ontario Power Generation is proposing a Deep Geologic Repository (DGR) for the long-term management of its Low and Intermediate Level Radioactive Waste (L&ILW) within a Paleozoic-age sedimentary sequence beneath the Bruce site near Tiverton, Ontario, Canada. The concept envisions that the DGR would be excavated at a depth of approximately 680 m within the Ordovician Cobourg Formation, a massive, dense, low- permeability, argillaceous limestone. Characterization of the Bruce site for waste disposal is being conducted in accordance with a four year multi-phase Geoscientific Site Characterization Plan (GSCP). The GSCP, initially developed in 2006 and later revised in 2008 to account for acquired site knowledge based on successful completion of Phase I investigations, describes the tools and methods selected for geological, hydrogeological and geomechanical site characterization. The GSCP was developed, in part, on an assessment of geoscience data needs and collection methods, review of the results of detailed geoscientific studies completed in the same bedrock formations found off the Bruce site, and recent international experience in geoscientific characterization of similar sedimentary rocks for long-term radioactive waste management purposes. Field and laboratory work related to Phase 1 and Phase 2A are nearing completion and have focused on the drilling, testing and monitoring of four continuously cored vertical boreholes through Devonian, Silurian, Ordovician and Cambrian bedrock to depths of about 860 mBGS. Work in 2009 will focus on drilling and testing of inclined boreholes to assess presence of vertical structure. The available geological, hydrogeological and hydrogeochemical data indicate the presence of remarkably uniform and predictable geology, physical hydrogeologic and geochemical properties over well separation distances exceeding 1 km. The current data set including 2-D seismic reflection surveys, field and lab hydraulic testing, lab petrophysical and diffusion testing, lab porewater and field groundwater characterization, and field head monitoring confirm the anticipated favourable characteristics of the Bruce site for long-term waste management. These favourable characteristics include a tight geomechanically stable host formation that is overlain and underlain by thick, massive, very low permeability shale and argillaceous limestone formations where radionuclide transport appears to be very limited and dominated by diffusion.

Objective sampling design in a highly heterogeneous landscape - characterizing environmental determinants of malaria vector distribution in French Guiana, in the Amazonian region.

PubMed

Roux, Emmanuel; Gaborit, Pascal; Romaña, Christine A; Girod, Romain; Dessay, Nadine; Dusfour, Isabelle

2013-12-01

Sampling design is a key issue when establishing species inventories and characterizing habitats within highly heterogeneous landscapes. Sampling efforts in such environments may be constrained and many field studies only rely on subjective and/or qualitative approaches to design collection strategy. The region of Cacao, in French Guiana, provides an excellent study site to understand the presence and abundance of Anopheles mosquitoes, their species dynamics and the transmission risk of malaria across various environments. We propose an objective methodology to define a stratified sampling design. Following thorough environmental characterization, a factorial analysis of mixed groups allows the data to be reduced and non-collinear principal components to be identified while balancing the influences of the different environmental factors. Such components defined new variables which could then be used in a robust k-means clustering procedure. Then, we identified five clusters that corresponded to our sampling strata and selected sampling sites in each stratum. We validated our method by comparing the species overlap of entomological collections from selected sites and the environmental similarities of the same sites. The Morisita index was significantly correlated (Pearson linear correlation) with environmental similarity based on i) the balanced environmental variable groups considered jointly (p = 0.001) and ii) land cover/use (p-value < 0.001). The Jaccard index was significantly correlated with land cover/use-based environmental similarity (p-value = 0.001). The results validate our sampling approach. Land cover/use maps (based on high spatial resolution satellite images) were shown to be particularly useful when studying the presence, density and diversity of Anopheles mosquitoes at local scales and in very heterogeneous landscapes.

Objective sampling design in a highly heterogeneous landscape - characterizing environmental determinants of malaria vector distribution in French Guiana, in the Amazonian region

PubMed Central

2013-01-01

Background Sampling design is a key issue when establishing species inventories and characterizing habitats within highly heterogeneous landscapes. Sampling efforts in such environments may be constrained and many field studies only rely on subjective and/or qualitative approaches to design collection strategy. The region of Cacao, in French Guiana, provides an excellent study site to understand the presence and abundance of Anopheles mosquitoes, their species dynamics and the transmission risk of malaria across various environments. We propose an objective methodology to define a stratified sampling design. Following thorough environmental characterization, a factorial analysis of mixed groups allows the data to be reduced and non-collinear principal components to be identified while balancing the influences of the different environmental factors. Such components defined new variables which could then be used in a robust k-means clustering procedure. Then, we identified five clusters that corresponded to our sampling strata and selected sampling sites in each stratum. Results We validated our method by comparing the species overlap of entomological collections from selected sites and the environmental similarities of the same sites. The Morisita index was significantly correlated (Pearson linear correlation) with environmental similarity based on i) the balanced environmental variable groups considered jointly (p = 0.001) and ii) land cover/use (p-value << 0.001). The Jaccard index was significantly correlated with land cover/use-based environmental similarity (p-value = 0.001). Conclusions The results validate our sampling approach. Land cover/use maps (based on high spatial resolution satellite images) were shown to be particularly useful when studying the presence, density and diversity of Anopheles mosquitoes at local scales and in very heterogeneous landscapes. PMID:24289184

Silica-supported isolated gallium sites as highly active, selective and stable propane dehydrogenation catalysts† †Electronic supplementary information (ESI) available: Experimental details, material characterization data, catalytic measurement details and crystallographic details. CCDC 1499756. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05178b Click here for additional data file. Click here for additional data file.

PubMed Central

Searles, Keith; Siddiqi, Georges; Safonova, Olga V.

2017-01-01

Single-site gallium centers on the surface of silica are prepared via grafting of [Ga(OSi(OtBu)3)3(THF)] on SiO2–700 followed by a thermolysis step. The resulting surface species corresponds to well-defined tetra-coordinate gallium single-sites, [( 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 SiO)3Ga(XOSi)] (X = –H or Si) according to IR, X-ray absorption near-edge structure and extended X-ray absorption fine structure analysis. These gallium sites show high activity, selectivity and stability for propane dehydrogenation with an initial turnover frequency of 20 per h per gallium center, propylene selectivity of ≥93% and remarkable stability over 20 h. The stability of the catalyst probably results from site-isolation of the active site on a non-reducible support such as silica, diminishing facile reduction typical of Ga2O3-based catalysts. PMID:28553501

Watershed Regressions for Pesticides (WARP) for Predicting Annual Maximum and Annual Maximum Moving-Average Concentrations of Atrazine in Streams

USGS Publications Warehouse

Stone, Wesley W.; Gilliom, Robert J.; Crawford, Charles G.

2008-01-01

Regression models were developed for predicting annual maximum and selected annual maximum moving-average concentrations of atrazine in streams using the Watershed Regressions for Pesticides (WARP) methodology developed by the National Water-Quality Assessment Program (NAWQA) of the U.S. Geological Survey (USGS). The current effort builds on the original WARP models, which were based on the annual mean and selected percentiles of the annual frequency distribution of atrazine concentrations. Estimates of annual maximum and annual maximum moving-average concentrations for selected durations are needed to characterize the levels of atrazine and other pesticides for comparison to specific water-quality benchmarks for evaluation of potential concerns regarding human health or aquatic life. Separate regression models were derived for the annual maximum and annual maximum 21-day, 60-day, and 90-day moving-average concentrations. Development of the regression models used the same explanatory variables, transformations, model development data, model validation data, and regression methods as those used in the original development of WARP. The models accounted for 72 to 75 percent of the variability in the concentration statistics among the 112 sampling sites used for model development. Predicted concentration statistics from the four models were within a factor of 10 of the observed concentration statistics for most of the model development and validation sites. Overall, performance of the models for the development and validation sites supports the application of the WARP models for predicting annual maximum and selected annual maximum moving-average atrazine concentration in streams and provides a framework to interpret the predictions in terms of uncertainty. For streams with inadequate direct measurements of atrazine concentrations, the WARP model predictions for the annual maximum and the annual maximum moving-average atrazine concentrations can be used to characterize the probable levels of atrazine for comparison to specific water-quality benchmarks. Sites with a high probability of exceeding a benchmark for human health or aquatic life can be prioritized for monitoring.

Functional characterization of the 5'-flanking and the promoter region of the human UCP3 (hUCP3) gene.

PubMed

Tu, N; Chen, H; Winnikes, U; Reinert, I; Pirke, K M; Lentes, K U

2000-09-22

Uncoupling protein-3 (UCP3) is considered as an important regulator of energy expenditure and thermogenesis in humans. To get insight into the mechanisms regulating its expression we have cloned and characterized about 5 kb of the 5'-flanking region of the human UCP3 (hUCP3) gene. 5'-RACE analysis suggested a single transcription initiation site 187 bp upstream from the translational start site. The promoter region contains both TATA and CAAT boxes as well as consensus motifs for PPRE, TRE, CRE and muscle-specific factors like MyoD and MEF2 sites. Functional characterization of a 3 kb hUCP3 promoter fragment in multiple cell lines using a CAT-ELISA identified a cis-acting negative regulatory element between -2983 and -982 while the region between -982 and -284 showed greatly increased basal promoter activity suggesting the presence of a strong enhancer element. Promoter activity was particularly enhanced in the murine skeletal muscle cell line C2C12 reflecting the tissue-selective expression pattern of UCP3.

Localization and characterization of (/sup 3/H)desmethylimipramine binding sites in rat brain by quantitative autoradiography

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

Biegon, A.; Rainbow, T.C.

1983-05-01

The high affinity binding sites for the antidepressant desmethlyimipramine (DMI) have been localized in rat brain by quantitative autoradiography. There are high concentrations of binding sites in the locus ceruleus, the anterior ventral thalamus, the ventral portion of the bed nucleus of the stria terminalis, the paraventricular and the dorsomedial nuclei of the hypothalamus. The distribution of DMI binding sites is in striking accord with the distribution of norepinephrine terminals. Pretreatment of rats with the neurotoxin 6-hydroxydopamine, which causes a selective degeneration of catecholamine terminals, results in 60 to 90% decrease in DMI binding. These data support the idea thatmore » high affinity binding sites for DMI are located on presynaptic noradrenergic terminals.« less

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

Bidlack, J.M.; Frey, D.K.; Seyed-Mozaffari, A.

The binding properties of 14{beta}-(bromoacetamido)morphine (BAM) and the ability of BAM to irreversibly inhibit opioid binding to rat brain membranes were examined to characterize the affinity and selectivity of BAM as an irreversible affinity ligand for opioid receptors. BAM had the same receptor selectivity as morphine, with a 3-5-fold decrease in affinity for the different types of opioid receptors. When brain membranes were incubated with BAM, followed by extensive washing, opioid binding was restored to control levels. However, when membranes were incubated with dithiothreitol (DTT), followed by BAM, and subsequently washed, 90% of the 0.25 nM ({sup 3}H)(D-Ala{sup 2},(Me)Phe{sup 4},Gly(ol){supmore » 5})enkephalin (DAGO) binding was irreversibly inhibited as a result of the specific alkylation of a sulfhydryl group at the {mu} binding site. This inhibition was dependent on the concentrations of both DTT and BAM. The {mu} receptor specificity of BAM alkylation was demonstrated by the ability of BAM alkylated membranes to still bind the {delta}-selective peptide ({sup 3}H)(D-penicillamine{sup 2},D-penicillamine{sup 5})enkephalin (DPDPE) and (-)-({sup 3}H)bremazocine in the presence of {mu} and {delta} blockers, selective for {kappa} binding sites. Morphine and naloxone partially protected the binding site from alkylation with BAM, while ligands that did not bind to the {mu}s site did not afford protection. These studies have demonstrated that when a disulfide bond at or near {mu} opioid binding sites was reduced, BAM could then alkylate this site, resulting in the specific irreversible labeling of {mu} opioid receptors.« less

Characterization of the Solution Structure of Human Serum Albumin Loaded with a Metal Porphyrin and Fatty Acids

PubMed Central

Junk, Matthias J.N.; Spiess, Hans W.; Hinderberger, Dariush

2011-01-01

The structure of human serum albumin loaded with a metal porphyrin and fatty acids in solution is characterized by orientation-selective double electron-electron resonance (DEER) spectroscopy. Human serum albumin, spin-labeled fatty acids, and Cu(II) protoporphyrin IX—a hemin analog—form a fully self-assembled system that allows obtaining distances and mutual orientations between the paramagnetic guest molecules. We report a simplified analysis for the orientation-selective DEER data which can be applied when the orientation selection of one spin in the spin pair dominates the orientation selection of the other spin. The dipolar spectra reveal a dominant distance of 3.85 nm and a dominant orientation of the spin-spin vectors between Cu(II) protoporphyrin IX and 16-doxyl stearic acid, the electron paramagnetic resonance reporter group of the latter being located near the entry points to the fatty acid binding sites. This observation is in contrast to crystallographic data that suggest an asymmetric distribution of the entry points in the protein and hence the occurrence of various distances. In conjunction with the findings of a recent DEER study, the obtained data are indicative of a symmetric distribution of the binding site entries on the protein's surface. The overall anisotropic shape of the protein is reflected by one spin-spin vector orientation dominating the DEER data. PMID:21539799

A New Type of Heterogeneous Catalyst with Isolated FE-RH Diatomic Sites

DTIC Science & Technology

1988-06-01

the logical step was to take advantage of the hoped-for changes in reactivity and selectivity of the new sites. They showed that characterization can...These gases were further purified by passing through Oxy-traps ( Alltech Associates) and molecular sieve traps (Linde 4A) to remove any remainin oxygen or...on a support surface. One of the advantages of the N Mossbauer Effect is that only certain atoms are Mossbauer active and the source used will dictate

Selected Ground-Water Data for Yucca Mountain Region, Southern Nevada and Eastern California, Through December 1998

DTIC Science & Technology

2001-01-01

data; X, un ll-completion report, or Fenix & Scisson, Inc., or Raytheon Services Nevada hole-history data; J, Johnston (19 rs (1988); T, Thordarson ...associated with weapons-testing hydrology programs ( Thordarson and others, 1967; Johnston, 1968) or Yucca Mountain site-characterization studies...MV-1, AD-4a, AD-5, AD-6, AD-8, and AM-4. Thordarson and others (1967) describe the contributing unit at site RV-1. Dudley and Larson (1976

The Application of Computer-Aided Discovery to Spacecraft Site Selection

NASA Astrophysics Data System (ADS)

Pankratius, V.; Blair, D. M.; Gowanlock, M.; Herring, T.

2015-12-01

The selection of landing and exploration sites for interplanetary robotic or human missions is a complex task. Historically it has been labor-intensive, with large groups of scientists manually interpreting a planetary surface across a variety of datasets to identify potential sites based on science and engineering constraints. This search process can be lengthy, and excellent sites may get overlooked when the aggregate value of site selection criteria is non-obvious or non-intuitive. As planetary data collection leads to Big Data repositories and a growing set of selection criteria, scientists will face a combinatorial search space explosion that requires scalable, automated assistance. We are currently exploring more general computer-aided discovery techniques in the context of planetary surface deformation phenomena that can lend themselves to application in the landing site search problem. In particular, we are developing a general software framework that addresses key difficulties: characterizing a given phenomenon or site based on data gathered from multiple instruments (e.g. radar interferometry, gravity, thermal maps, or GPS time series), and examining a variety of possible workflows whose individual configurations are optimized to isolate different features. The framework allows algorithmic pipelines and hypothesized models to be perturbed or permuted automatically within well-defined bounds established by the scientist. For example, even simple choices for outlier and noise handling or data interpolation can drastically affect the detectability of certain features. These techniques aim to automate repetitive tasks that scientists routinely perform in exploratory analysis, and make them more efficient and scalable by executing them in parallel in the cloud. We also explore ways in which machine learning can be combined with human feedback to prune the search space and converge to desirable results. Acknowledgements: We acknowledge support from NASA AIST NNX15AG84G (PI V. Pankratius)

Pseudoexon activation increases phenotype severity in a Becker muscular dystrophy patient.

PubMed

Greer, Kane; Mizzi, Kayla; Rice, Emily; Kuster, Lukas; Barrero, Roberto A; Bellgard, Matthew I; Lynch, Bryan J; Foley, Aileen Reghan; O Rathallaigh, Eoin; Wilton, Steve D; Fletcher, Sue

2015-07-01

We report a dystrophinopathy patient with an in-frame deletion of DMD exons 45-47, and therefore a genetic diagnosis of Becker muscular dystrophy, who presented with a more severe than expected phenotype. Analysis of the patient DMD mRNA revealed an 82 bp pseudoexon, derived from intron 44, that disrupts the reading frame and is expected to yield a nonfunctional dystrophin. Since the sequence of the pseudoexon and canonical splice sites does not differ from the reference sequence, we concluded that the genomic rearrangement promoted recognition of the pseudoexon, causing a severe dystrophic phenotype. We characterized the deletion breakpoints and identified motifs that might influence selection of the pseudoexon. We concluded that the donor splice site was strengthened by juxtaposition of intron 47, and loss of intron 44 silencer elements, normally located downstream of the pseudoexon donor splice site, further enhanced pseudoexon selection and inclusion in the DMD transcript in this patient.

Búsqueda de Sitios para CTA: Análisis de Datos Satelitales

NASA Astrophysics Data System (ADS)

Suárez, A. E.; Medina, M. C.; Romero, G. E.

The CTA Consortium has decided to implement a systematic search for sites for the Observatory. This search will be made in two different steps. The first one consists of a general determination of the possible sites on the basis of some very basic selection criteria, such as geographic latitude, altitude and extension of the flat area needed. For those sites passing these criteria, a more intensive characterization should be made, using available satellite data, together with existing ground or air-based measurements. In this work we compare the behavior of different sites analyzing the aerosol content and the total precipitable water vapor, measured by MODIS instrument. FULL TEXT IN SPANISH

Antagonistic versus non-antagonistic models of balancing selection: Characterizing the relative timescales and hitchhiking effects of partial selective sweeps

PubMed Central

Connallon, Tim; Clark, Andrew G.

2012-01-01

Antagonistically selected alleles -- those with opposing fitness effects between sexes, environments, or fitness components -- represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus non-antagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, non-antagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection. PMID:23461340

Lipid Interaction Sites on Channels, Transporters and Receptors: Recent Insights from Molecular Dynamics Simulations

PubMed Central

Hedger, George; Sansom, Mark S. P.

2017-01-01

Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterisation of these sites is of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. PMID:26946244

Characterization and functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in tilapia.

PubMed

Li, Hong Lian; Gu, Xiao Hui; Li, Bi Jun; Chen, Xiao; Lin, Hao Ran; Xia, Jun Hong

2017-01-01

Hypoxia is a major cause of fish morbidity and mortality in the aquatic environment. Hypoxia-inducible factors are very important modulators in the transcriptional response to hypoxic stress. In this study, we characterized and conducted functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in Nile tilapia (Oreochromis niloticus). By cloning and Sanger sequencing, we obtained the full length cDNA sequences for HIF1α (2686bp) and HIF1αn (1308bp), respectively. The CDS of HIF1α includes 15 exons encoding 768 amino acid residues and the CDS of HIF1αn contains 8 exons encoding 354 amino acid residues. The complete CDS sequences of HIF1α and HIF1αn cloned from tilapia shared very high homology with known genes from other fishes. HIF1α show differentiated expression in different tissues (brain, heart, gill, spleen, liver) and at different hypoxia exposure times (6h, 12h, 24h). HIF1αn expression level under hypoxia is generally increased (6h, 12h, 24h) and shows extremely highly upregulation in brain tissue under hypoxia. A functional determination site analysis in the protein sequences between fish and land animals identified 21 amino acid sites in HIF1α and 2 sites in HIF1αn as significantly associated sites (α = 0.05). Phylogenetic tree-based positive selection analysis suggested 22 sites in HIF1α as positively selected sites with a p-value of at least 95% for fish lineages compared to the land animals. Our study could be important for clarifying the mechanism of fish adaptation to aquatic hypoxia environment.

Characterization and functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in tilapia

PubMed Central

Li, Hong Lian; Gu, Xiao Hui; Li, Bi Jun; Chen, Xiao; Lin, Hao Ran; Xia, Jun Hong

2017-01-01

Hypoxia is a major cause of fish morbidity and mortality in the aquatic environment. Hypoxia-inducible factors are very important modulators in the transcriptional response to hypoxic stress. In this study, we characterized and conducted functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in Nile tilapia (Oreochromis niloticus). By cloning and Sanger sequencing, we obtained the full length cDNA sequences for HIF1α (2686bp) and HIF1αn (1308bp), respectively. The CDS of HIF1α includes 15 exons encoding 768 amino acid residues and the CDS of HIF1αn contains 8 exons encoding 354 amino acid residues. The complete CDS sequences of HIF1α and HIF1αn cloned from tilapia shared very high homology with known genes from other fishes. HIF1α show differentiated expression in different tissues (brain, heart, gill, spleen, liver) and at different hypoxia exposure times (6h, 12h, 24h). HIF1αn expression level under hypoxia is generally increased (6h, 12h, 24h) and shows extremely highly upregulation in brain tissue under hypoxia. A functional determination site analysis in the protein sequences between fish and land animals identified 21 amino acid sites in HIF1α and 2 sites in HIF1αn as significantly associated sites (α = 0.05). Phylogenetic tree-based positive selection analysis suggested 22 sites in HIF1α as positively selected sites with a p-value of at least 95% for fish lineages compared to the land animals. Our study could be important for clarifying the mechanism of fish adaptation to aquatic hypoxia environment. PMID:28278251

Water-quality, bed-sediment, and biological data (October 2015 through September 2016) and statistical summaries of data for streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Turner, Matthew A.

2018-03-30

Water, bed sediment, and biota were sampled in selected streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was led by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, to characterize aquatic resources in the Clark Fork Basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2015 through September 2016. Bed-sediment and biota samples were collected once at 13 sites during August 2016.This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2015 through September 2016. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Samples for analysis of turbidity were collected at 13 sites, whereas samples for analysis of dissolved organic carbon were collected at 10 sites. In addition, samples for analysis of nitrogen (nitrate plus nitrite) were collected at two sites. Daily values of mean suspended-sediment concentration and suspended-sediment discharge were determined for three sites. Seasonal daily values of turbidity were determined for five sites. Bed-sediment data include trace-element concentrations in the fine-grained (less than 0.063 millimeter) fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork Basin are provided for the period of record.

Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites.

PubMed

Thinon, Emmanuelle; Fernandez, Joseph P; Molina, Henrik; Hang, Howard C

2018-05-04

S-Fatty-acylation is the covalent attachment of long chain fatty acids, predominately palmitate (C16:0, S-palmitoylation), to cysteine (Cys) residues via a thioester linkage on proteins. This post-translational and reversible lipid modification regulates protein function and localization in eukaryotes and is important in mammalian physiology and human diseases. While chemical labeling methods have improved the detection and enrichment of S-fatty-acylated proteins, mapping sites of modification and characterizing the endogenously attached fatty acids are still challenging. Here, we describe the integration and optimization of fatty acid chemical reporter labeling with hydroxylamine-mediated enrichment of S-fatty-acylated proteins and direct tagging of modified Cys residues to selectively map lipid modification sites. This afforded improved enrichment and direct identification of many protein S-fatty-acylation sites compared to previously described methods. Notably, we directly identified the S-fatty-acylation sites of IFITM3, an important interferon-stimulated inhibitor of virus entry, and we further demonstrated that the highly conserved Cys residues are primarily modified by palmitic acid. The methods described here should facilitate the direct analysis of protein S-fatty-acylation sites and their endogenously attached fatty acids in diverse cell types and activation states important for mammalian physiology and diseases.

Solubilization and characterization of haloperidol-sensitive (+)-( sup 3 H)SKF-10,047 binding sites (sigma sites) from rat liver membranes

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

McCann, D.J.; Su, T.P.

1991-05-01

The zwitterionic detergent 3-((3-cholamidopropyl)dimethylamino)-1-propanesulfonate (CHAPS) produced optimal solubilization of (+)-({sup 3}H)SKF-10,047 binding sites from rat liver membranes at a concentration of 0.2%, well below the critical micellular concentration of the detergent. The pharmacological selectivity of the liver (+)-({sup 3}H)SKF-10,047 binding sites corresponds to that of sigma sites from rat and guinea pig brain. When the affinities of 18 different drugs at (+)-({sup 3}H)SKF-10,047 binding sites in membranes and solubilized preparations were compared, a correlation coefficient of 0.99 and a slope of 1.03 were obtained, indicating that the pharmacological selectivity of rat liver sigma sites is retained after solubilization. In addition,more » the binding of 20 nM ({sup 3}H)progesterone to solubilized rat liver preparations was found to exhibit a pharmacological selectivity appropriate for sigma sites. A stimulatory effect of phenytoin on (+)-({sup 3}H)SKF-10,047 binding to sigma sites persisted after solubilization. When the solubilized preparation was subjected to molecular sizing chromatography, a single peak exhibiting specific (+)-({sup 3}H)SKF-10,047 binding was obtained. The binding activity of this peak was stimulated symmetrically when assays were performed in the presence of 300 microM phenytoin. The molecular weight of the CHAPS-solubilized sigma site complex was estimated to be 450,000 daltons. After solubilization with CHAPS, rat liver sigma sites were enriched to 12 pmol/mg of protein. The present results demonstrate a successful solubilization of sigma sites from rat liver membranes and provide direct evidence that the gonadal steroid progesterone binds to sigma sites. The results also suggest that the anticonvulsant phenytoin binds to an associated allosteric site on the sigma site complex.« less

Identifying the site of spin trapping in proteins by a combination of liquid chromatography, ELISA, and off-line tandem mass spectrometry.

PubMed

Lardinois, Olivier M; Detweiler, Charles D; Tomer, Kenneth B; Mason, Ronald P; Deterding, Leesa J

2008-03-01

An off-line mass spectrometry method that combines immuno-spin trapping and chromatographic procedures has been developed for selective detection of the nitrone spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) covalently attached to proteins, an attachment which occurs only subsequent to DMPO trapping of free radicals. In this technique, the protein-DMPO nitrone adducts are digested to peptides with proteolytic agents, peptides from the enzymatic digest are separated by HPLC, and enzyme-linked immunosorbent assays (ELISA) using polyclonal anti-DMPO nitrone antiserum are used to detect the eluted HPLC fractions that contain DMPO nitrone adducts. The fractions showing positive ELISA signals are then concentrated and characterized by tandem mass spectrometry (MS/MS). This method, which constitutes the first liquid chromatography-ELISA-mass spectrometry (LC-ELISA-MS)-based strategy for selective identification of DMPO-trapped protein residues in complex peptide mixtures, facilitates location and preparative fractionation of DMPO nitrone adducts for further structural characterization. The strategy is demonstrated for human hemoglobin, horse heart myoglobin, and sperm whale myoglobin, three globin proteins known to form DMPO-trappable protein radicals on treatment with H(2)O(2). The results demonstrate the power of the new experimental strategy to select DMPO-labeled peptides and identify sites of DMPO covalent attachments.

Persistent foot-and-mouth disease virus infection in the nasopharynx of cattle: tissue-specific distribution and local cytokine expression

USDA-ARS?s Scientific Manuscript database

Tissues obtained post-mortem from cattle persistently infected with foot-and-mouth disease virus (FMDV) were analyzed to characterize the tissue-specific localization of FMDV and partial transcriptome profiles for selected immunoregulatory cytokines. Analysis of 28 distinct anatomic sites from 21 st...

High temporal resolution photography for observing riparian area use and grazing behavior

USDA-ARS?s Scientific Manuscript database

In 2014, a 2.4 hectare site within the Apache-Sitgreaves National Forest in northeastern Arizona, USA was selected to characterize temporal and spatial patterns of riparian area use. Three consecutive 30, 8, and 46 day time periods representing 1) unrestricted access, 2) prescribed cattle use, and 3...

Logging utilization in Oregon and Washington, 2011–2015

Treesearch

Eric A. Simmons; Todd A. Morgan; Erik C. Berg; Steven W. Hayes; Glenn A. Christensen

2016-01-01

A study of commercial timber harvesting activities in Oregon and Washington was conducted from 2011 through 2015 to characterize current tree utilization, logging operations, and assist with estimating the amount of woody biomass left onsite after harvesting. Sample logging sites were selected within major geographic regions proportional to regional 5-year timber...

Support effects in catalysis studied by in-situ sum frequency generation vibrational spectroscopy and in-situ x-ray spectroscopies

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

Kennedy, Griffin John

Here, kinetic measurements are paired with in-situ spectroscopic characterization tools to investigate colloidally based, supported Pt catalytic model systems in order to elucidate the mechanisms by which metal and support work in tandem to dictate activity and selectivity. The results demonstrate oxide support materials, while inactive in absence of Pt nanoparticles, possess unique active sites for the selective conversion of gas phase molecules when paired with an active metal catalyst.

Microstructure and inclusion of Ti-6Al-4V fabricated by selective laser melting

NASA Astrophysics Data System (ADS)

Huang, Qianli; Hu, Ningmin; Yang, Xing; Zhang, Ranran; Feng, Qingling

2016-12-01

Selective laser melting (SLM) was used in fabricating the dense part from pre-alloyed Ti-6Al-4V powder. The microstructural evolution and inclusion formation of as-fabricated part were characterized in depth. The microstructure was characterized by features of columnar prior β grains and acicular martensite α'. High density defects such as dislocations and twins can be produced in SLM process. Investigations on the inclusions find out that hard alpha inclusion, amorphous CaO and microcrystalline Al2O3 are three main inclusions formed in SLM. The inclusions formed at some specific sites on melt pool surface. The microstructural evolution and inclusion formation of as-fabricated material are closely related to the SLM process.

Geophysical investigations of well fields to characterize fractured-bedrock aquifers in southern New Hampshire

USGS Publications Warehouse

Degnan, James R.; Moore, Richard Bridge; Mack, Thomas J.

2001-01-01

Bedrock-fracture zones near high-yield bedrock wells in southern New Hampshire well fields were located and characterized using seven surface and six borehole geophysical survey methods. Detailed surveys of six sites with various methods provide an opportunity to integrate and compare survey results. Borehole geophysical surveys were conducted at three of the sites to confirm subsurface features. Hydrogeologic settings, including a variety of bedrock and surface geologic materials, were sought to gain an insight into the usefulness of the methods in varied terrains. Results from 15 survey lines, 8 arrays, and 3 boreholes were processed and interpreted from the 6 sites. The surface geophysical methods used provided physical properties of fractured bedrock. Seismic refraction and ground-penetrating radar (GPR) primarily were used to characterize the overburden materials, but in a few cases indicated bedrock-fracture zones. Magnetometer surveys were used to obtain background information about the bedrock to compare with other results, and to search for magnetic lows, which may result from weathered fractured rock. Electromagnetic terrain conductivity surveys (EM) and very-low-frequency electromagnetic surveys (VLF) were used as rapid reconnaissance techniques with the primary purpose of identifying electrical anomalies, indicating potential fracture zones in bedrock. Direct-current (dc) resistivity methods were used to gather detailed subsurface information about fracture depth and orientation. Two-dimensional (2-D) dc-resistivity surveys using dipole-dipole and Schlumberger arrays located and characterized the overburden, bedrock, and bedrock-fracture zones through analysis of data inversions. Azimuthal square array dc-resistivity survey results indicated orientations of conductive steep-dipping bedrock-fracture zones that were located and characterized by previously applied geophysical methods. Various available data sets were used for site selection, characterizations, and interpretations. Lineament data, developed as a part of a statewide and regional scale investigation of the bedrock aquifer, were available to identify potential near-vertical fracture zones. Geophysical surveys indicated fracture zones coincident with lineaments at 4 of the sites. Geologic data collected as a part of the regional scale investigation provided outcrop fracture measurements, ductile fabric, and contact information. Dominant fracture trends correspond to the trends of geophysical anomalies at 4 of the sites. Water-well drillers? logs from water supply and environmental data sets also were used where available to characterize sites. Regional overburden information was compiled from stratified-drift aquifer maps and surficial-geological maps.

Water-quality assessment of part of the upper Mississippi River basin, Minnesota and Wisconsin: Design and implementation of water-quality studies, 1995-98

USGS Publications Warehouse

Stark, James R.; Fallon, J.D.; Fong, A.L.; Goldstein, R.M.; Hanson, P.E.; Kroening, S.E.; Lee, K.E.

1999-01-01

This report describes the design, site-selection, and implementation of the study. Methods used to collect, process, and analyze samples; characterize sites; and assess habitat are described. A comprehensive list of sample sites is provided. Sample analyses for water-quality studies included chlorophyll a, major inorganic constituents, nutrients, trace elements, tritium, radon, environmental isotopes, organic carbon, pesticides, volatile organic compounds, and other synthetic and naturallyoccurring organic compounds. Aquatic-biological samples included fish, benthic macroinvertebrates, and algal enumeration and identification, as well as synthetic-organic compounds and trace elements in fish tissue.

Dialing in single-site reactivity of a supported calixarene-protected tetrairidium cluster catalyst† †Electronic supplementary information (ESI) available: Detailed characterization of Ir4 clusters, raw kinetic data, time scale analysis, experimental methods, and sample preparation. See DOI: 10.1039/c7sc00686a Click here for additional data file.

PubMed Central

Palermo, Andrew; Solovyov, Andrew; Ertler, Daniel

2017-01-01

A closed Ir4 carbonyl cluster, 1, comprising a tetrahedral metal frame and three sterically bulky tert-butyl-calix[4]arene(OPr)3(OCH2PPh2) (Ph = phenyl; Pr = propyl) ligands at the basal plane, was characterized with variable-temperature 13C NMR spectroscopy, which show the absence of scrambling of the CO ligands at temperatures up to 313 K. This demonstration of distinct sites for the CO ligands was found to extend to the reactivity and catalytic properties, as shown by selective decarbonylation in a reaction with trimethylamine N-oxide (TMAO) as an oxidant, which, reacting in the presence of ethylene, leads to the selective bonding of an ethyl ligand at the apical Ir site. These clusters were supported intact on porous silica and found to catalyze ethylene hydrogenation, and a comparison of the kinetics of the single-hydrogenation reaction and steady-state hydrogenation catalysis demonstrates a unique single-site catalyst—with each site having the same catalytic activity. Reaction orders in the catalytic ethylene hydrogenation reaction of approximately 1/2 and 0 for H2 and C2H4, respectively, nearly match those for conventional noble-metal catalysts. In contrast to oxidative decarbonylation, thermal desorption of CO from silica-supported cluster 1 occurred exclusively at the basal plane, giving rise to sites that do not react with ethylene and are catalytically inactive for ethylene hydrogenation. The evidence of distinctive sites on the cluster catalyst leads to a model that links to hydrogen-transfer catalysis on metals—involving some surface sites that bond to both hydrocarbon and hydrogen and are catalytically engaged (so-called “*” sites) and others, at the basal plane, which bond hydrogen and CO but not hydrocarbon and are reservoir sites (so-called “S” sites). PMID:28959418

Site characterization for LIL radioactive waste disposal in Romania

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

Diaconu, D. R.; Birdsell, K. H.; Witkowski, M. S.

2001-01-01

Recent studies in radioactive waste management in Romania have focussed mainly on the disposal of low and intermediate level waste from the operation of the new nuclear power plant at Cernavoda. Following extensive geological, hydrological, seismological, physical and chemical investigations, a disposal site at Saligny has been selected. This paper presents description of the site at Saligny as well as the most important results of the site characterisation. These are reflected in the three-dimensional, stratigraphical representation of the loess and clay layers and in representative parameter values for the main layers. Based on these data, the simulation of the background,more » unsaturated-zone water flow at the Saligny site, calculated by the FEHM code, is in a good agreement with the measured moisture profile.« less

TSAPA: identification of tissue-specific alternative polyadenylation sites in plants.

PubMed

Ji, Guoli; Chen, Moliang; Ye, Wenbin; Zhu, Sheng; Ye, Congting; Su, Yaru; Peng, Haonan; Wu, Xiaohui

2018-06-15

Alternative polyadenylation (APA) is now emerging as a widespread mechanism modulated tissue-specifically, which highlights the need to define tissue-specific poly(A) sites for profiling APA dynamics across tissues. We have developed an R package called TSAPA based on the machine learning model for identifying tissue-specific poly(A) sites in plants. A feature space including more than 200 features was assembled to specifically characterize poly(A) sites in plants. The classification model in TSAPA can be customized by selecting desirable features or classifiers. TSAPA is also capable of predicting tissue-specific poly(A) sites in unannotated intergenic regions. TSAPA will be a valuable addition to the community for studying dynamics of APA in plants. https://github.com/BMILAB/TSAPA. Supplementary data are available at Bioinformatics online.

Improvement of the Uranium Sequestration Ability of a Chlamydomonas sp. (ChlSP Strain) Isolated From Extreme Uranium Mine Tailings Through Selection for Potential Bioremediation Application.

PubMed

Baselga-Cervera, Beatriz; Romero-López, Julia; García-Balboa, Camino; Costas, Eduardo; López-Rodas, Victoria

2018-01-01

The extraction and processing of uranium (U) have polluted large areas worldwide, rendering anthropogenic extreme environments inhospitable to most species. Noticeably, these sites are of great interest for taxonomical and applied bioprospection of extremotolerant species successfully adapted to U tailings contamination. As an example, in this work we have studied a microalgae species that inhabits extreme U tailings ponds at the Saelices mining site (Salamanca, Spain), characterized as acidic (pH between 3 and 4), radioactive (around 4 μSv h -1 ) and contaminated with metals, mainly U (from 25 to 48 mg L -1 ) and zinc (from 17 to 87 mg L -1 ). After isolation of the extremotolerant ChlSP strain, morphological characterization and internal transcribed spacer (ITS)-5.8S gene sequences placed it in the Chlamydomonadaceae , but BLAST analyses identity values, against the nucleotide datasets at the NCBI database, were very low (<92%). We subjected the ChlSP strain to an artificial selection protocol to increase the U uptake and investigated its response to selection. The ancestral strain ChlSP showed a U-uptake capacity of ≈4.30 mg U g -1 of dry biomass (DB). However, the artificially selected strain ChlSG was able to take up a total of ≈6.34 mg U g -1 DB, close to the theoretical maximum response (≈7.9 mg U g -1 DB). The selected ChlSG strain showed two possible U-uptake mechanisms: the greatest proportion by biosorption onto cell walls (ca. 90%), and only a very small quantity, ~0.46 mg g -1 DB, irreversibly bound by bioaccumulation. Additionally, the kinetics of the U-uptake process were characterized during a microalgae growth curve; ChlSG cells removed close to 4 mg L -1 of U in 24 days. These findings open up promising prospects for sustainable management of U tailings waters based on newly evolved extremotolerants and outline the potential of artificial selection in the improvement of desired features in microalgae by experimental adaptation and selection.

Improvement of the Uranium Sequestration Ability of a Chlamydomonas sp. (ChlSP Strain) Isolated From Extreme Uranium Mine Tailings Through Selection for Potential Bioremediation Application

PubMed Central

Baselga-Cervera, Beatriz; Romero-López, Julia; García-Balboa, Camino; Costas, Eduardo; López-Rodas, Victoria

2018-01-01

The extraction and processing of uranium (U) have polluted large areas worldwide, rendering anthropogenic extreme environments inhospitable to most species. Noticeably, these sites are of great interest for taxonomical and applied bioprospection of extremotolerant species successfully adapted to U tailings contamination. As an example, in this work we have studied a microalgae species that inhabits extreme U tailings ponds at the Saelices mining site (Salamanca, Spain), characterized as acidic (pH between 3 and 4), radioactive (around 4 μSv h−1) and contaminated with metals, mainly U (from 25 to 48 mg L−1) and zinc (from 17 to 87 mg L−1). After isolation of the extremotolerant ChlSP strain, morphological characterization and internal transcribed spacer (ITS)-5.8S gene sequences placed it in the Chlamydomonadaceae, but BLAST analyses identity values, against the nucleotide datasets at the NCBI database, were very low (<92%). We subjected the ChlSP strain to an artificial selection protocol to increase the U uptake and investigated its response to selection. The ancestral strain ChlSP showed a U-uptake capacity of ≈4.30 mg U g−1 of dry biomass (DB). However, the artificially selected strain ChlSG was able to take up a total of ≈6.34 mg U g−1 DB, close to the theoretical maximum response (≈7.9 mg U g−1 DB). The selected ChlSG strain showed two possible U-uptake mechanisms: the greatest proportion by biosorption onto cell walls (ca. 90%), and only a very small quantity, ~0.46 mg g−1 DB, irreversibly bound by bioaccumulation. Additionally, the kinetics of the U-uptake process were characterized during a microalgae growth curve; ChlSG cells removed close to 4 mg L−1 of U in 24 days. These findings open up promising prospects for sustainable management of U tailings waters based on newly evolved extremotolerants and outline the potential of artificial selection in the improvement of desired features in microalgae by experimental adaptation and selection. PMID:29662476

Water-quality, bed-sediment, and biological data (October 2014 through September 2015) and statistical summaries of data for streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Turner, Matthew A.

2017-01-19

Water, bed sediment, and biota were sampled in selected streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was led by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, to characterize aquatic resources in the Clark Fork Basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2014 through September 2015. Bed-sediment and biota samples were collected once at 13 sites during August 2015.This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2014 through September 2015. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. At 12 sites, samples for analysis of dissolved organic carbon and turbidity were collected. In addition, samples for analysis of nitrogen (nitrate plus nitrite) were collected at two sites. Daily values of mean suspended-sediment concentration and suspended-sediment discharge were determined for three sites. Seasonal daily values of turbidity were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork Basin are provided for the period of record.

Geologic, hydrologic, and water-quality data from multiple-well monitoring sites in the Central and West Coast basins, Los Angeles County, California, 1995-2000

USGS Publications Warehouse

Land, Michael; Everett, R.R.; Crawford, S.M.

2002-01-01

In 1995, the U.S. Geological Survey (USGS), in cooperation with the HYPERLINK 'http://wrd.org' Water Replenishment District of Southern California (WRDSC), began a study to examine ground-water resources in the Central and West Coast Basins in Los Angeles County, California. The study characterizes the geohydrology and geochemistry of the regional ground-water flow system and provides extensive data for evaluating ground-water management issues. This report is a compilation of geologic, hydrologic, and water-quality data collected from 24 recently constructed multiple-well monitoring sites for the period 1995?2000. Descriptions of the collected drill cuttings were compiled into lithologic logs, which are summarized along with geophysical logs?including gamma-ray, spontaneous potential, resistivity, electromagnetic induction, and temperature tool logs?for each monitoring site. At selected sites, cores were analyzed for magnetic orientation, physical and thermal properties, and mineralogy. Field and laboratory estimates of hydraulic conductivity are presented for most multiple-well monitoring sites. Periodic water-level measurements are also reported. Water-quality information for major ions, nutrients, trace elements, deuterium and oxygen-18, and tritium is presented for the multiple-well monitoring locations, and for selected existing production and observation wells. In addition, boron-11, carbon-13, carbon-14, sulfur-34, and strontium-87/86 data are presented for selected wells.

Geological and technological assessment of artificial reef sites, Louisiana outer continental shelf

USGS Publications Warehouse

Pope, D.L.; Moslow, T.F.; Wagner, J.B.

1993-01-01

This paper describes the general procedures used to select sites for obsolete oil and gas platforms as artificial reefs on the Louisiana outer continental shelf (OCS). The methods employed incorporate six basic steps designed to resolve multiple-use conflicts that might otherwise arise with daily industry and commercial fishery operations, and to identify and assess both geological and technological constraints that could affect placement of the structures. These steps include: (1) exclusion mapping; (2) establishment of artificial reef planning areas; (3) database compilation; (4) assessment and interpretation of database; (5) mapping of geological and man-made features within each proposed reef site; and (6) site selection. Nautical charts, bathymetric maps, and offshore oil and gas maps were used for exclusion mapping, and to select nine regional planning areas. Pipeline maps were acquired from federal agencies and private industry to determine their general locations within each planning area, and to establish exclusion fairways along each pipeline route. Approximately 1600 line kilometers of high-resolution geophysical data collected by federal agencies and private industry was acquired for the nine planning areas. These data were interpreted to determine the nature and extent of near-surface geologic features that could affect placement of the structures. Seismic reflection patterns were also characterized to evaluate near-bottom sedimentation processes in the vicinity of each reef site. Geotechnical borings were used to determine the lithological and physical properties of the sediment, and for correlation with the geophysical data. Since 1987, five sites containing 10 obsolete production platforms have been selected on the Louisiana OCS using these procedures. Industry participants have realized a total savings of approximately US $1 500 000 in salvaging costs by converting these structures into artificial reefs. ?? 1993.

BRDF Characterization and Calibration Inter-Comparison between Terra MODIS, Aqua MODIS, and S-NPP VIIRS

NASA Technical Reports Server (NTRS)

Chang, Tiejun; Xiong, Xiaoxiong (Jack); Angal, Amit; Wu, Aisheng

2016-01-01

The inter-comparison of reflective solar bands (RSB) between Terra MODIS, Aqua MODIS, and SNPP VIIRS is very important for assessment of each instrument's calibration and to identify calibration improvements. One of the limitations of using their ground observations for the assessment is a lack of the simultaneous nadir overpasses (SNOs) over selected pseudo-invariant targets. In addition, their measurements over a selected Earth view target have significant difference in solar and view angles, and these differences magnify the effects of Bidirectional Reflectance Distribution Function (BRDF). In this work, an inter-comparison technique using a semi-empirical BRDF model is developed for reflectance correction. BRDF characterization requires a broad coverage of solar and view angles in the measurements over selected pseudo-invariant targets. Reflectance measurements over Libya 1, 2, and 4 desert sites from both the Aqua and Terra MODIS are regressed to a BRDF model with an adjustable coefficient accounting for the calibration difference between the two instruments. The BRDF coefficients for three desert sites for MODIS bands 1 to 9 are derived and the wavelength dependencies are presented. The analysis and inter-comparison are for MODIS bands 1 to 9 and VIIRS moderate resolution radiometric bands (M bands) M1, M2, M4, M5, M7, M8, M10 and imaging bands (I bands) I1-I3. Results show that the ratios from different sites are in good agreement. The ratios between Terra and Aqua MODIS from year 2003 to 2014 are presented. The inter-comparison between MODIS and VIIRS are analyzed for year 2014.

General M13 phage display: M13 phage display in identification and characterization of protein-protein interactions.

PubMed

Hertveldt, Kirsten; Beliën, Tim; Volckaert, Guido

2009-01-01

In M13 phage display, proteins and peptides are exposed on one of the surface proteins of filamentous phage particles and become accessible to affinity enrichment against a bait of interest. We describe the construction of fragmented whole genome and gene fragment phage display libraries and interaction selection by panning. This strategy allows the identification and characterization of interacting proteins on a genomic scale by screening the fragmented "proteome" against protein baits. Gene fragment libraries allow a more in depth characterization of the protein-protein interaction site by identification of the protein region involved in the interaction.

Characterization of Two (3H) Ketanserin Recognition Sites in Rat Striatum

DTIC Science & Technology

1987-01-01

autoradiography to be localized to The 5-HT, sites are proposed to activate adenylate layer IV of the cortex and striatum ( Pazos et al., cyclase (Barbaccia et al...Chuang (1987). assumption has not been completely tested. Since its introduction as a selective radioligand for Pazos et al. (1985) recently confirmed...cniorophenylalanine. 1833 B S-3 1834 B. L. ROT!! ET AL. enriched in striatum and cortex. Pazos et al. (1985) mAt Tris-Cl, pH 7.40 at 25°C) at 4C. A crude membrane

Pyrrole based Schiff bases as colorimetric and fluorescent chemosensors for fluoride and hydroxide anions.

PubMed

Velmathi, Sivan; Reena, Vijayaraghavan; Suganya, Sivalingam; Anandan, Sambandam

2012-01-01

An efficient colorimetric sensor with pyrrole-NH moiety as binding site and nitro group as a signaling unit has been synthesized by a one step procedure and characterized by spectroscopic techniques, which displays excellent selectivity and sensitivity for fluoride and hydroxide ions. The hydrogen bonding with these anions provides remarkable colorimetric responses. (1)H NMR and FT IR studies has been carried out to confirm the hydrogen bonding. UV-vis and fluorescence spectral changes can be exploited for real time and on site application.

A meta-analysis of lesser prairie-chicken nesting and brood-rearing habitats: implications for habitat management

USGS Publications Warehouse

Hagen, Christian A.; Grisham, Blake A.; Boal, Clint W.; Haukos, David A.

2013-01-01

The distribution and range of lesser prairie-chicken (Tympanuchus pallidicinctus) has been reduced by >90% since European settlement of the Great Plains of North America. Currently, lesser prairie-chickens occupy 3 general vegetation communities: sand sagebrush (Artemisia filifolia), sand shinnery oak (Quercus havardii), and mixed-grass prairies juxtaposed with Conservation Reserve Program grasslands. As a candidate for protection under the Endangered Species Act, there is a need for a synthesis that characterizes habitat structure rangewide. Thus, we conducted a meta-analysis of vegetation characteristics at nest sites and brood habitats to determine whether there was an overall effect (Hedges' d) of habitat selection and to estimate average (95% CI) habitat characteristics at use sites. We estimated effect sizes (di) from the difference between use (nests and brood sites) and random sampling sites for each study (n = 14), and derived an overall effect size (d++). There was a general effect for habitat selection as evidenced by low levels of variation in effect sizes across studies and regions. There was a small to medium effect (d++) = 0.20-0.82) of selection for greater vertical structure (visual obstruction) by nesting females in both vegetation communities, and selection against bare ground (d++ = 0.20-0.58). Females with broods exhibited less selectivity for habitat components except for vertical structure. The variation of d++ was greater during nesting than brooding periods, signifying a seasonal shift in habitat use, and perhaps a greater range of tolerance for brood-rearing habitat. The overall estimates of vegetation cover were consistent with those provided in management guidelines for the species.

Site Selection for Hvdc Ground Electrodes

NASA Astrophysics Data System (ADS)

Freire, P. F.; Pereira, S. Y.

2014-12-01

High-Voltage Direct Current (HVDC) transmission systems are composed of a bipole transmission line with a converter substation at each end. Each substation may be equipped with a HVDC ground electrode, which is a wide area (up to 1 km Ø) and deep (from 3 to 100m) electrical grounding. When in normal operation, the ground electrode will dissipate in the soil the unbalance of the bipole (~1.5% of the rated current). When in monopolar operation with ground return, the HVDC electrode will inject in the soil the nominal pole continuous current, of about 2000 to 3000 Amperes, continuously for a period up to a few hours. HVDC ground electrodes site selection is a work based on extensive geophysical and geological surveys, in order to attend the desired design requirements established for the electrodes, considering both its operational conditions (maximum soil temperature, working life, local soil voltage gradients etc.) and the interference effects on the installations located up to 50 km away. This poster presents the geophysical investigations conducted primarily for the electrodes site selection, and subsequently for the development of the crust resistivity model, which will be used for the interference studies. A preliminary site selection is conducted, based on general geographical and geological criteria. Subsequently, the geology of each chosen area is surveyed in detail, by means of electromagnetic/electrical geophysical techniques, such as magnetotelluric (deep), TDEM (near-surface) and electroresistivity (shallow). Other complementary geologic and geotechnical surveys are conducted, such as wells drilling (for geotechnical characterization, measurement of the water table depth and water flow, and electromagnetic profiling), and soil and water sampling (for measurement of thermal parameters and evaluation of electrosmosis risk). The site evaluation is a dynamic process along the surveys, and some sites will be discarded. For the two or three final sites, the inversion of the combined deep, near-surface and shallow apparent resistivity curves, results in the layered crust resistivity models. These models will allow for the preliminary interference studies, that will result on the selection of the final electrode site (one for each converter substation).

Radioligand Recognition of Insecticide Targets.

PubMed

Casida, John E

2018-04-04

Insecticide radioligands allow the direct recognition and analysis of the targets and mechanisms of toxic action critical to effective and safe pest control. These radioligands are either the insecticides themselves or analogs that bind at the same or coupled sites. Preferred radioligands and their targets, often in both insects and mammals, are trioxabicyclooctanes for the γ-aminobutyric acid (GABA) receptor, avermectin for the glutamate receptor, imidacloprid for the nicotinic receptor, ryanodine and chlorantraniliprole for the ryanodine receptor, and rotenone or pyridaben for NADH + ubiquinone oxidoreductase. Pyrethroids and other Na + channel modulator insecticides are generally poor radioligands due to lipophilicity and high nonspecific binding. For target site validation, the structure-activity relationships competing with the radioligand in the binding assays should be the same as that for insecticidal activity or toxicity except for rapidly detoxified or proinsecticide analogs. Once the radioligand assay is validated for relevance, it will often help define target site modifications on selection of resistant pest strains, selectivity between insects and mammals, and interaction with antidotes and other chemicals at modulator sites. Binding assays also serve for receptor isolation and photoaffinity labeling to characterize the interactions involved.

Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers.

PubMed

Rahimi, Amir; Madadkar-Sobhani, Armin; Touserkani, Rouzbeh; Goliaei, Bahram

2013-11-07

Due to the increasing number of protein structures with unknown function originated from structural genomics projects, protein function prediction has become an important subject in bioinformatics. Among diverse function prediction methods, exploring known 3D-motifs, which are associated with functional elements in unknown protein structures is one of the most biologically meaningful methods. Homologous enzymes inherit such motifs in their active sites from common ancestors. However, slight differences in the properties of these motifs, results in variation in the reactions and substrates of the enzymes. In this study, we examined the possibility of discriminating highly related active site patterns according to their EC-numbers by 3D-motifs. For each EC-number, the spatial arrangement of an active site, which has minimum average distance to other active sites with the same function, was selected as a representative 3D-motif. In order to characterize the motifs, various points in active site elements were tested. The results demonstrated the possibility of predicting full EC-number of enzymes by 3D-motifs. However, the discriminating power of 3D-motifs varies among different enzyme families and depends on selecting the appropriate points and features. © 2013 Elsevier Ltd. All rights reserved.

Water-quality, bed-sediment, and biological data (October 2010 through September 2011) and statistical summaries of data for streams in the Clark Fork basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2013-01-01

Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork basin of western Montana; additional water samples were collected from near Galen to near Missoula at select sites as part of a supplemental sampling program. The sampling program was conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2010 through September 2011. Bed-sediment and biota samples were collected once at 14 sites during August 2011. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2010 through September 2011. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

Eccentricity and fluting in young–growth western hemlock in Oregon.

Treesearch

Ryan Singleton; Dean S. DeBell; David D. Marshall; Barbara L. Gartner

2004-01-01

Stem irregularities can influence estimates of tree and stand attributes, efficiency of manufacturing processes, and quality of wood products. Eccentricity and fluting were characterized in young, managed western hemlock stands in the Oregon Coast Range. Sixty-one trees were selected from pure western hemlock stands across a range of age, site, and densities. The trees...

Adsorbate-mediated strong metal–support interactions in oxide-supported Rh catalysts

DOE PAGES

Matsubu, John C.; Zhang, Shuyi; DeRita, Leo; ...

2016-09-19

The optimization of supported metal catalysts predominantly focuses on engineering the metal site, for which physical insights based on extensive theoretical and experimental contributions have enabled the rational design of active sites. Although it is well known that supports can influence the catalytic properties of metals, insights into how metal–support interactions can be exploited to optimize metal active-site properties are lacking. Here in this paper, we utilize in situ spectroscopy and microscopy to identify and characterize a support effect in oxide-supported heterogeneous Rh catalysts. This effect is characterized by strongly bound adsorbates (HCO x) on reducible oxide supports (TiO 2more » and Nb 2O 5) that induce oxygen-vacancy formation in the support and cause HCO x-functionalized encapsulation of Rh nanoparticles by the support. The encapsulation layer is permeable to reactants, stable under the reaction conditions and strongly influences the catalytic properties of Rh, which enables rational and dynamic tuning of CO 2-reduction selectivity.« less

Physical, chemical, and biological characteristics of selected headwater streams along the Allegheny Front, Blair County, Pennsylvania, July 2011–September 2013

USGS Publications Warehouse

Low, Dennis J.; Brightbill, Robin A.; Eggleston, Heather L.; Chaplin, Jeffrey J.

2016-02-29

Biotic health was characterized at 10 of 12 stream sites; the two sites excluded were established late in the study period (May 2013) for refinement of water quality in the headwaters of Poplar Run and the location of Marcellus Formation gas wells. On the basis of the Maryland Index of Biotic Integrity (MdIBI) for fish assemblages, 8 of 10 streams can be considered in fair health. Tipton Run had the highest MdIBI score (3.75) and the greatest number of native species. South Poplar Run had the lowest MdIBI score (1.75); pollution tolerant blacknose dace was dominant. On the basis of the Pennsylvania Department of Environmental Protection macroinvertebrate index of biotic integrity, 9 of 10 streams were characterized as attaining, with scores as high as 88.9 at Tipton Run. Only Sugar Run was characterized as impaired, with a score of 40.4.

An Introduction to Using Surface Geophysics to Characterize Sand and Gravel Deposits

USGS Publications Warehouse

Lucius, Jeffrey E.; Langer, William H.; Ellefsen, Karl J.

2006-01-01

This report is an introduction to surface geophysical techniques that aggregate producers can use to characterize known deposits of sand and gravel. Five well-established and well-tested geophysical methods are presented: seismic refraction and reflection, resistivity, ground penetrating radar, time-domain electromagnetism, and frequency-domain electromagnetism. Depending on site conditions and the selected method(s), geophysical surveys can provide information concerning aerial extent and thickness of the deposit, thickness of overburden, depth to the water table, critical geologic contacts, and location and correlation of geologic features. In addition, geophysical surveys can be conducted prior to intensive drilling to help locate auger or drill holes, reduce the number of drill holes required, calculate stripping ratios to help manage mining costs, and provide continuity between sampling sites to upgrade the confidence of reserve calculations from probable reserves to proved reserves. Perhaps the greatest value of geophysics to aggregate producers may be the speed of data acquisition, reduced overall costs, and improved subsurface characterization.

An Introduction to Using Surface Geophysics to Characterize Sand and Gravel Deposits

USGS Publications Warehouse

Lucius, Jeffrey E.; Langer, William H.; Ellefsen, Karl J.

2007-01-01

This report is an introduction to surface geophysical techniques that aggregate producers can use to characterize known deposits of sand and gravel. Five well-established and well-tested geophysical methods are presented: seismic refraction and reflection, resistivity, ground penetrating radar, time-domain electromagnetism, and frequency-domain electromagnetism. Depending on site conditions and the selected method(s), geophysical surveys can provide information concerning areal extent and thickness of the deposit, thickness of overburden, depth to the water table, critical geologic contacts, and location and correlation of geologic features. In addition, geophysical surveys can be conducted prior to intensive drilling to help locate auger or drill holes, reduce the number of drill holes required, calculate stripping ratios to help manage mining costs, and provide continuity between sampling sites to upgrade the confidence of reserve calculations from probable reserves to proved reserves. Perhaps the greatest value of geophysics to aggregate producers may be the speed of data acquisition, reduced overall costs, and improved subsurface characterization.

Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

PubMed Central

Zimanyi, Christina M; Chen, Percival Yang-Ting; Kang, Gyunghoon; Funk, Michael A; Drennan, Catherine L

2016-01-01

Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR ‘reads’ the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell. DOI: http://dx.doi.org/10.7554/eLife.07141.001 PMID:26754917

Mineralogy Considerations for 2003 MER Site Selection and the Importance for Astrobiology

NASA Technical Reports Server (NTRS)

Bishop, J. L.

2001-01-01

Much of the discussion of site selection on Mars is based on interesting images of the surface combined with safety issues. I argue that the two rovers should be sent to mineralogically distinct regions. Compositional information is still poorly constrained on Mars; however, the instruments on the 2003 Mars Exploration Rovers (MERs) will provide a unique opportunity for detailed characterization including mineral identification. There is strong motivation for sending one rover to a "typical" region on Mars to be used as a ground truth for the Thermal Emission Spectrometer (TES), while the other rover should be sent to a site where water and chemical alteration are likely to have occurred. Determining the mineralogy of the Martian surface material provides information about the past and present environments on Mars which are an integral aspect of whether or not Mars was suitable for the origin of life. Understanding the mineralogy of terrestrial samples from potentially Mars-like environments is essential to this effort.

A Monofunctional Platinum Complex Coordinated to a Rhodium Metalloinsertor Selectively Binds Mismatched DNA in the Minor Groove

PubMed Central

Weidmann, Alyson G.; Barton, Jacqueline K.

2015-01-01

We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh—O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA non-classically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors. PMID:26397309

How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.

PubMed

Hur, Sun; Stroud, Robert M

2007-04-27

Translational accuracy and efficiency depend upon modification of uridines in the tRNA anticodon stem loop (ASL) by a highly conserved pseudouridine synthase TruA. TruA specifically modifies uridines at positions 38, 39, and/or 40 of tRNAs with highly divergent sequences and structures through a poorly characterized mechanism that differs from previously studied RNA-modifying enzymes. The molecular basis for the site and substrate "promiscuity" was studied by determining the crystal structures of E. coli TruA in complex with two different leucyl tRNAs in conjunction with functional assays and computer simulation. The structures capture three stages of the TruA*tRNA reaction, revealing the mechanism by which TruA selects the target site. We propose that TruA utilizes the intrinsic flexibility of the ASL for site promiscuity and also to select against intrinsically stable tRNAs to avoid their overstabilization through pseudouridylation, thereby maintaining the balance between the flexibility and stability required for its biological function.

A monofunctional platinum complex coordinated to a rhodium metalloinsertor selectively binds mismatched DNA in the minor groove.

PubMed

Weidmann, Alyson G; Barton, Jacqueline K

2015-10-05

We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh-O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA nonclassically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and it triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors.

Light-driven, proton-controlled, catalytic aerobic C-H oxidation mediated by a Mn(III) porphyrinoid complex.

PubMed

Neu, Heather M; Jung, Jieun; Baglia, Regina A; Siegler, Maxime A; Ohkubo, Kei; Fukuzumi, Shunichi; Goldberg, David P

2015-04-15

The visible light-driven, catalytic aerobic oxidation of benzylic C-H bonds was mediated by a Mn(III) corrolazine complex. To achieve catalytic turnovers, a strict selective requirement for the addition of protons was established. The resting state of the catalyst was unambiguously characterized by X-ray diffraction as [Mn(III)(H2O)(TBP8Cz(H))](+), in which a single, remote site on the ligand is protonated. If two remote sites are protonated, however, reactivity with O2 is shut down. Spectroscopic methods revealed that the related Mn(V)(O) complex is also protonated at the same remote site at -60 °C, but undergoes valence tautomerization upon warming.

Assessment of general health of fishes collected at selected sites in the Great Lakes Basin In 2012

USGS Publications Warehouse

Mazik, Patricia M.; Braham, Ryan P.; Hahn, Cassidy M.; Blazer, Vicki

2015-01-01

The U. S. Fish and Wildlife Service received funding through the Great Lakes Restoration Initiative (GLRI) for an Early Warning Program to detect and identify emerging contaminants and to evaluate the effects of these contaminants on fish and wildlife. The U.S. Geological Survey (WV Cooperative Fish and Wildlife Research Unit and National Fish Health Research Laboratory, Leetown Science Center) developed and implemented a biological effects monitoring protocol to assist in this program. Fish collections and measurements of biomarkers of exposure in Fall 2010 and Spring 2011 occurred at individual sites within select Areas of Concern (AOCs). They provided an assessment of the utility of the suite of biomarkers and also identified sites for more in-depth analyses. Selected areas are characterized as areas with known emerging contaminants, sensitive or listed species, areas downstream from municipal wastewater discharges or receiving waters for industrial facilities, and/or areas susceptible to agricultural or urban contamination, or harbors or ports. The results of the 2010- 2011 studies were summarized in Blazer et al. 2014 a, b, c; Braham et al. in review and Blazer et al. in review.

Preparation and evaluation of molecularly imprinted polymer for selective recognition and adsorption of gossypol.

PubMed

Zhi, Keke; Wang, Lulu; Zhang, Yagang; Zhang, Xuemin; Zhang, Letao; Liu, Li; Yao, Jun; Xiang, Wei

2018-03-01

Molecularly imprinted polymers (MIPs) were designed and prepared via bulk thermal polymerization with gossypol as the template molecule and dimethylaminoethyl methacrylate as the functional monomer. The morphology and microstructures of MIPs were characterized by scanning electron microscope and Brunauer-Emmett-Teller surface areas. Static adsorption tests were performed to evaluate adsorption behavior of gossypol by the MIPs. It was found that adsorption kinetics and adsorption isotherms data of MIPs for gossypol were fit well with the pseudo-second-order model and Freundlich model, respectively. Scatchard analysis showed that heterogeneous binding sites were formed in the MIPs, including lower-affinity binding sites with the maximum adsorption of 252 mg/g and higher-affinity binding sites with the maximum adsorption of 632 mg/g. Binding studies also revealed that MIPs had favorable selectivity towards gossypol compared with non-imprinted polymers. Furthermore, adsorption capacity of MIPs maintained above 90% after 5 regeneration cycles, indicating MIPs were recyclable and could be used multiple times. These results demonstrated that prepared MIPs could be a promising functional material for selective adsorption of gossypol. Copyright © 2017 John Wiley & Sons, Ltd.

Deltorphins: a family of naturally occurring peptides with high affinity and selectivity for delta opioid binding sites.

PubMed

Erspamer, V; Melchiorri, P; Falconieri-Erspamer, G; Negri, L; Corsi, R; Severini, C; Barra, D; Simmaco, M; Kreil, G

1989-07-01

Deltorphins are endogenous linear heptapeptides, isolated from skin extracts of frogs belonging to the genus Phyllomedusa, that have a higher affinity and selectivity for delta opioid binding sites than any other natural compound known. Two deltorphins with the sequence Tyr-Ala-Phe-Asp(or Glu)-Val-Val-Gly-NH2 have been isolated from skin extracts of Phyllomedusa bicolor. The alanine in position 2 is in the D configuration. These peptides, [D-Ala2]deltorphins I and II, show an even higher affinity for delta receptors than the previously characterized deltorphin, which contains D-methionine as the second amino acid. These peptides show some similarity to another constituent of Phyllomedusa skin, dermorphin, which is highly selective for mu-opioid receptors. These peptides all have the N-terminal sequence Tyr-D-Xaa-Phe, where D-Xaa is either D-alanine or D-methionine. While this structure seems to be capable of activating both mu and delta opioid receptors, differences in the C-terminal regions of these peptides are probably responsible for the observed high receptor selectivity of dermorphin and deltorphin.

Deltorphins: a family of naturally occurring peptides with high affinity and selectivity for delta opioid binding sites.

PubMed Central

Erspamer, V; Melchiorri, P; Falconieri-Erspamer, G; Negri, L; Corsi, R; Severini, C; Barra, D; Simmaco, M; Kreil, G

1989-01-01

Deltorphins are endogenous linear heptapeptides, isolated from skin extracts of frogs belonging to the genus Phyllomedusa, that have a higher affinity and selectivity for delta opioid binding sites than any other natural compound known. Two deltorphins with the sequence Tyr-Ala-Phe-Asp(or Glu)-Val-Val-Gly-NH2 have been isolated from skin extracts of Phyllomedusa bicolor. The alanine in position 2 is in the D configuration. These peptides, [D-Ala2]deltorphins I and II, show an even higher affinity for delta receptors than the previously characterized deltorphin, which contains D-methionine as the second amino acid. These peptides show some similarity to another constituent of Phyllomedusa skin, dermorphin, which is highly selective for mu-opioid receptors. These peptides all have the N-terminal sequence Tyr-D-Xaa-Phe, where D-Xaa is either D-alanine or D-methionine. While this structure seems to be capable of activating both mu and delta opioid receptors, differences in the C-terminal regions of these peptides are probably responsible for the observed high receptor selectivity of dermorphin and deltorphin. PMID:2544892

Bipartite functions of the CREB co-activators selectively direct alternative splicing or transcriptional activation

PubMed Central

Amelio, Antonio L; Caputi, Massimo; Conkright, Michael D

2009-01-01

The CREB regulated transcription co-activators (CRTCs) regulate many biological processes by integrating and converting environmental inputs into transcriptional responses. Although the mechanisms by which CRTCs sense cellular signals are characterized, little is known regarding how CRTCs contribute to the regulation of cAMP inducible genes. Here we show that these dynamic regulators, unlike other co-activators, independently direct either pre-mRNA splice-site selection or transcriptional activation depending on the cell type or promoter context. Moreover, in other scenarios, the CRTC co-activators coordinately regulate transcription and splicing. Mutational analyses showed that CRTCs possess distinct functional domains responsible for regulating either pre-mRNA splicing or transcriptional activation. Interestingly, the CRTC1–MAML2 oncoprotein lacks the splicing domain and is incapable of altering splice-site selection despite robustly activating transcription. The differential usage of these distinct domains allows CRTCs to selectively mediate multiple facets of gene regulation, indicating that co-activators are not solely restricted to coordinating alternative splicing with increase in transcriptional activity. PMID:19644446

Identification and characterization of regulatory elements in the promoter of ACVR1, the gene mutated in Fibrodysplasia Ossificans Progressiva

PubMed Central

2013-01-01

Background The ACVR1 gene encodes a type I receptor for bone morphogenetic proteins (BMPs). Mutations in the ACVR1 gene are associated with Fibrodysplasia Ossificans Progressiva (FOP), a rare and extremely disabling disorder characterized by congenital malformation of the great toes and progressive heterotopic endochondral ossification in muscles and other non-skeletal tissues. Several aspects of FOP pathophysiology are still poorly understood, including mechanisms regulating ACVR1 expression. This work aimed to identify regulatory elements that control ACVR1 gene transcription. Methods and results We first characterized the structure and composition of human ACVR1 gene transcripts by identifying the transcription start site, and then characterized a 2.9 kb upstream region. This region showed strong activating activity when tested by reporter gene assays in transfected cells. We identified specific elements within the 2.9 kb region that are important for transcription factor binding using deletion constructs, co-transfection experiments with plasmids expressing selected transcription factors, site-directed mutagenesis of consensus binding-site sequences, and by protein/DNA binding assays. We also characterized a GC-rich minimal promoter region containing binding sites for the Sp1 transcription factor. Conclusions Our results showed that several transcription factors such as Egr-1, Egr-2, ZBTB7A/LRF, and Hey1, regulate the ACVR1 promoter by binding to the -762/-308 region, which is essential to confer maximal transcriptional activity. The Sp1 transcription factor acts at the most proximal promoter segment upstream of the transcription start site. We observed significant differences in different cell types suggesting tissue specificity of transcriptional regulation. These findings provide novel insights into the molecular mechanisms that regulate expression of the ACVR1 gene and that could be targets of new strategies for future therapeutic treatments. PMID:24047559

New developments in measurements technology relevant to the studies of deep geological repositories in bedded salt

NASA Astrophysics Data System (ADS)

Mao, N. H.; Ramirez, A. L.

1980-10-01

Developments in measurement technology are presented which are relevant to the studies of deep geological repositories for nuclear waste disposal during all phases of development, i.e., site selection, site characterization, construction, operation, and decommission. Emphasis was placed on geophysics and geotechnics with special attention to those techniques applicable to bedded salt. The techniques are grouped into sections as follows: tectonic environment, state of stress, subsurface structures, fractures, stress changes, deformation, thermal properties, fluid transport properties, and other approaches. Several areas that merit further research and developments are identified. These areas are: in situ thermal measurement techniques, fracture detection and characterization, in situ stress measurements, and creep behavior. The available instrumentations should generally be improved to have better resolution and accuracy, enhanced instrument survivability, and reliability for extended time periods in a hostile environment.

Characterization of Terrain in the Mars Surveyor 2001 Landing Site Latitude and Elevation Region Using Mapping Phase Mars Global Surveyor MOC Images

NASA Technical Reports Server (NTRS)

Malin, M. C.; Edgett, K. S.; Parker, T. J.

1999-01-01

One of the original objectives of the Mars Orbiter Camera (MOC), as proposed in 1985, was to acquire observations to be used in assessing future spacecraft landing sites. Images obtained by the Mars Global Surveyor MOC since March 1999 provide the highest resolution views (1.5-4.5 m/pixel) of the planet ever seen. We have been examining these new data to develop a general view of what Mars is like at meter-scale within the latitudes and elevations that are accessible to the Mars Surveyor 2001 lander. Our goal is to provide guidance to the 2001 landing site selection process, rather than to use MOC images to recommend a specific landing site.

Characterization of selected bed-sediment-bound organic and inorganic contaminants and toxicity, Barnegat Bay and major tributaries, New Jersey, 2012

USGS Publications Warehouse

Romanok, Kristin M.; Reilly, Timothy J.; Lopez, Anthony R.; Trainor, John J.; Hladik, Michelle; Stanley, Jacob K.; Farrar, Daniel

2014-01-01

A study of bed-sediment toxicity and organic and inorganic contaminants was conducted by the U.S. Geological Survey (USGS) in cooperation with the New Jersey Department of Environmental Protection (NJDEP). Bed-sediment samples were collected once from 22 sites in Barnegat Bay and selected major tributaries during August–September 2012 and analyzed for toxicity and a suite of organic and inorganic contaminants by the USGS and the U.S. Army Corps of Engineers. Sampling sites were selected to coincide with an existing water-quality monitoring network used by the NJDEP and others in order to evaluate water-quality conditions in Barnegat Bay and the surrounding watershed. Two of the 22 sites are reference sites and are within or adjacent to the study area; bed-sediment samples from reference sites allow for comparisons of results for the Barnegat Bay watershed to results from less affected settings within the region. Toxicity testing was conducted by exposing the estuarine amphipod Leptocheirus plumulosus and the freshwater amphipod Hyalella azteca to sediments for 28 days, and the percent survival, difference in biomass, and individual dry weights were measured. Reproductive effects also were evaluated for estuarine samples. Bed-sediment samples from four sites within Barnegat Bay were subjected to a toxicity identification evaluation to determine probable causes of toxicity. Samples were analyzed for a suite of 94 currently-used pesticides, 21 legacy pesticides, 24 trace elements, 40 polycyclic aromatic hydrocarbons, 7 polychlorinated biphenyls (PCBs) as Arochlor mixtures, and 145 individual PCB congeners. Concentrations of detected compounds were compared to sediment-quality guidelines, where appropriate.

Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

USGS Publications Warehouse

Leenheer, J.A.; Brown, G.K.; MacCarthy, P.; Cabaniss, S.E.

1998-01-01

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The 'metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-1R spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short- chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The `metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.

Discovery of the 3-Imino-1,2,4-thiadiazinane 1,1-Dioxide Derivative Verubecestat (MK-8931)–A β-Site Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor for the Treatment of Alzheimer’s Disease

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

Scott, Jack D.; Li, Sarah W.; Brunskill, Andrew P. J.

Verubecestat 3 (MK-8931), a diaryl amide-substituted 3-imino-1,2,4-thiadiazinane 1,1-dioxide derivative, is a high-affinity β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor currently undergoing Phase 3 clinical evaluation for the treatment of mild to moderate and prodromal Alzheimer’s disease. Although not selective over the closely related aspartyl protease BACE2, verubecestat has high selectivity for BACE1 over other key aspartyl proteases, notably cathepsin D, and profoundly lowers CSF and brain Aβ levels in rats and nonhuman primates and CSF Aβ levels in humans. In this annotation, we describe the discovery of 3, including design, validation, and selected SAR around the novel iminothiadiazinanemore » dioxide core as well as aspects of its preclinical and Phase 1 clinical characterization.« less

Canada's Deep Geological Repository For Used Nuclear Fuel -The Geoscientific Site Evaluation Process

NASA Astrophysics Data System (ADS)

Hirschorn, S.; Ben Belfadhel, M.; Blyth, A.; DesRoches, A. J.; McKelvie, J. R. M.; Parmenter, A.; Sanchez-Rico Castejon, M.; Urrutia-Bustos, A.; Vorauer, A.

2014-12-01

The Nuclear Waste Management Organization (NWMO) is responsible for implementing Adaptive Phased Management, the approach selected by the Government of Canada for long-term management of used nuclear fuel generated by Canadian nuclear reactors. In May 2010, the NWMO published and initiated a nine-step site selection process to find an informed and willing community to host a deep geological repository for Canada's used nuclear fuel. The site selection process is designed to address a broad range of technical and social, economic and cultural factors. The suitability of candidate areas will be assessed in a stepwise manner over a period of many years and include three main steps: Initial Screenings; Preliminary Assessments; and Detailed Site Characterizations. The Preliminary Assessment is conducted in two phases. NWMO has completed Phase 1 preliminary assessments for the first eight communities that entered into this step. While the Phase 1 desktop geoscientific assessments showed that each of the eight communities contains general areas that have the potential to satisfy the geoscientific safety requirements for hosting a deep geological repository, the assessment identified varying degrees of geoscientific complexity and uncertainty between communities, reflecting their different geological settings and structural histories. Phase 2 activities will include a sequence of high-resolution airborne geophysical surveys and focused geological field mapping to ground-truth lithology and structural features, followed by limited deep borehole drilling and testing. These activities will further evaluate the site's ability to meet the safety functions that a site would need to ultimately satisfy in order to be considered suitable. This paper provides an update on the site evaluation process and describes the approach, methods and criteria that are being used to conduct the geoscientific Preliminary Assessments.

Mass Wasting on the Moon: Implications for Seismicity

NASA Technical Reports Server (NTRS)

Weber, Renee; Nahm, Amanda; Schmerr, Nick; Yanites, Brian

2016-01-01

Seismicity estimates play an important role in creating regional geological characterizations, which are useful for understanding a planet's formation and evolution, and are of key importance to site selection for landed missions. Here we investigate the regional effects of seismicity in planetary environments with the goal of determining whether such surface features on the Moon, could be triggered by fault motion.

Mass Wasting on the Moon: Implications for Seismicity

NASA Technical Reports Server (NTRS)

Weber, R. C.; Nahm, A. L.; Yanites, B.; Schmerr, N.

2016-01-01

Introduction: Seismicity estimates play an important role in creating regional geological characterizations, which are useful for understanding a planet's formation and evolution, and of key importance to site selection for landed missions. Here we investigate the regional effects of lunar seismicity with the goal of determining whether surface features such as landslides and boulder trails on the Moon are triggered by fault motion.

Synthesis and optimization of thiadiazole derivatives as a novel class of substrate competitive c-Jun N-terminal kinase inhibitors

PubMed Central

De, Surya K.; Chen, Vida; Stebbins, John L.; Chen, Li-Hsing; Cellitti, Jason F.; Machleidt, Thomas; Barile, Elisa; Riel-Mehan, Megan; Dahl, Russell; Yang, Li; Emdadi, Aras; Murphy, Ria; Pellecchia, Maurizio

2009-01-01

A series of thiadiazole derivatives has been designed as potential allosteric, substrate competitive inhibitors of the protein kinase JNK. We report on the synthesis, characterization and evaluation of a series of compounds that resulted in the identification of potent and selective JNK inhibitors targeting its JIP-1 docking site. PMID:20045647

Aspen succession and nitrogen loading: a case for epiphytic lichens as bioindicators in the Rocky Mountains, USA

Treesearch

Paul C. Rogers; Kori D. Moore; Ronald J. Ryel

2009-01-01

Forty-seven randomly selected mid-elevation aspen stands were sampled for lichens and stand conditions. Plots were characterized according to tree species cover, basal area, stand age, bole scarring, tree damage, and presence of lichen species. We also recorded ammonia emissions with passive sensors at 25 urban and agricultural sites throughout an adjacent populated...

Structure of matrix metalloproteinase-3 with a platinum-based inhibitor.

PubMed

Belviso, Benny Danilo; Caliandro, Rocco; Siliqi, Dritan; Calderone, Vito; Arnesano, Fabio; Natile, Giovanni

2013-06-18

An X-ray investigation has been performed with the aim of characterizing the binding sites of a platinum-based inhibitor (K[PtCl3(DMSO)]) of matrix metalloproteinase-3 (stromelysin-1). The platinum complex targets His224 in the S1' specificity loop, representing the first step in the selective inhibition process (PDB ID code 4JA1).

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.

PubMed

MacManes, Matthew D; Eisen, Michael B

2014-01-01

As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the P. eremicus transcriptome. We assay four tissues (kidney, liver, brain, testes) from a single individual and supplement this with population level renal transcriptome sequencing from 15 additional animals. We identified a set of transcripts undergoing both purifying and balancing selection based on estimates of Tajima's D. In addition, we used the branch-site test to identify a transcript-Slc2a9, likely related to desert osmoregulation-undergoing enhanced selection in P. eremicus relative to a set of related non-desert rodents.

Air Quality and Meteorological Boundary Conditions during the MCMA-2003 Field Campaign

NASA Astrophysics Data System (ADS)

Sosa, G.; Arriaga, J.; Vega, E.; Magaña, V.; Caetano, E.; de Foy, B.; Molina, L. T.; Molina, M. J.; Ramos, R.; Retama, A.; Zaragoza, J.; Martínez, A. P.; Márquez, C.; Cárdenas, B.; Lamb, B.; Velasco, E.; Allwine, E.; Pressley, S.; Westberg, H.; Reyes, R.

2004-12-01

A comprehensive field campaign to characterize photochemical smog in the Mexico City Metropolitan Area (MCMA) was conducted during April 2003. An important number of equipment was deployed all around the urban core and its surroundings to measure gas and particles composition from the various sources and receptor sites. In addition to air quality measurements, meteorology variables were also taken by regular weather meteorological stations, tethered balloons, radiosondes, sodars and lidars. One important issue with regard to the field campaign was the characterization of the boundary conditions in order to feed meteorological and air quality models. Four boundary sites were selected to measure continuously criteria pollutants, VOC and meteorological variables at surface level. Vertical meteorological profiles were measured at three other sites : radiosondes in Tacubaya site were launched every six hours daily; tethered balloons were launched at CENICA and FES-Cuautitlan sites according to the weather conditions, and one sodar was deployed at UNAM site in the south of the city. Additionally to these measurements, two fixed meteorological monitoring networks deployed along the city were available to complement these measurements. In general, we observed that transport of pollutants from the city to the boundary sites changes every day, according to the coupling between synoptic and local winds. This effect were less important at elevated sites such as Cerro de la Catedral and ININ, where synoptic wind were more dominant during the field campaign. Also, local sources nearby boundary sites hide the influence of pollution coming from the city some days, particularly at the La Reforma site.

Transcriptional Profiling of Breast Cancer Metastases Identifies Liver Metastasis-Selective Genes Associated with Adverse Outcome in Luminal A Primary Breast Cancer.

PubMed

Kimbung, Siker; Johansson, Ida; Danielsson, Anna; Veerla, Srinivas; Egyhazi Brage, Suzanne; Frostvik Stolt, Marianne; Skoog, Lambert; Carlsson, Lena; Einbeigi, Zakaria; Lidbrink, Elisabet; Linderholm, Barbro; Loman, Niklas; Malmström, Per-Olof; Söderberg, Martin; Walz, Thomas M; Fernö, Mårten; Hatschek, Thomas; Hedenfalk, Ingrid

2016-01-01

The complete molecular basis of the organ-specificity of metastasis is elusive. This study aimed to provide an independent characterization of the transcriptional landscape of breast cancer metastases with the specific objective to identify liver metastasis-selective genes of prognostic importance following primary tumor diagnosis. A cohort of 304 women with advanced breast cancer was studied. Associations between the site of recurrence and clinicopathologic features were investigated. Fine-needle aspirates of metastases (n = 91) were subjected to whole-genome transcriptional profiling. Liver metastasis-selective genes were identified by significance analysis of microarray (SAM) analyses and independently validated in external datasets. Finally, the prognostic relevance of the liver metastasis-selective genes in primary breast cancer was tested. Liver relapse was associated with estrogen receptor (ER) expression (P = 0.002), luminal B subtype (P = 0.01), and was prognostic for an inferior postrelapse survival (P = 0.01). The major variation in the transcriptional landscape of metastases was also associated with ER expression and molecular subtype. However, liver metastases displayed unique transcriptional fingerprints, characterized by downregulation of extracellular matrix (i.e., stromal) genes. Importantly, we identified a 17-gene liver metastasis-selective signature, which was significantly and independently prognostic for shorter relapse-free (P < 0.001) and overall (P = 0.001) survival in ER-positive tumors. Remarkably, this signature remained independently prognostic for shorter relapse-free survival (P = 0.001) among luminal A tumors. Extracellular matrix (stromal) genes can be used to partition breast cancer by site of relapse and may be used to further refine prognostication in ER positive primary breast cancer. ©2015 American Association for Cancer Research.

Assessment of airborne bacteria in selected occupational environments in Quezon City, Philippines.

PubMed

Rendon, Rhoshela Vi C; Garcia, Bea Clarise B; Vital, Pierangeli G

2017-05-04

Exposure to bioaerosols has been associated with health deterioration among workers in several occupational environments. This highlights the need to study the microbiological quality of air of workplaces as no such study has been conducted yet in the Philippines. To detect and characterize the culturable mesophilic airborne bacteria in selected occupational environments we used passive sedimentation technique. It was observed that the number of colony-forming units was highest in junk shop, followed by the light railway transit station and last the office. By contrast, the bacterial composition was similar in all sites: Gram-positive cocci > Gram-positive bacilli > Gram-negative bacteria. Staphylococcus aureus and Bacillus spp. were also detected in all sites. These findings suggest that the presence of airborne bacteria may be a potential health hazard in urban occupational environments in the Philippines.

CMI Remedy Selection for HE- and Barium-Contaminated Vadose Zone and Alluvium at LANL

NASA Astrophysics Data System (ADS)

Hickmott, D.; Reid, K.; Pietz, J.; Ware, D.

2008-12-01

A high explosives (HE) machining building outfall at Los Alamos National Laboratory's Technical Area 16 discharged millions of gallons of HE- and barium-contaminated water into the Canon de Valle watershed. The effluent contaminated surface soils, the alluvial aquifer, vadose zone waters, and deep-perched and regional groundwaters with HE and barium, frequently at levels greater than regulatory standards. Site characterization studies began in 1995 and included extensive monitoring of surface water, groundwater, soils, and subsurface solid media. Hydrogeologic and geophysical studies were conducted to help understand contaminant transport mechanisms and pathways. Results from the characterization studies were used to develop a site conceptual model. In 2000 the principal source area was removed. The ongoing Corrective Measure Study (CMS) and Corrective Measure Implementation (CMI) focus on residual vadose zone contamination and on the contaminated alluvial system. Regulators recently selected a CMI remedy that combined: 1) augmented source removal; 2) grouting of an HE- contaminated surge bed; 3) deployment of Stormwater Management System (SMS) stormfilters in contaminated springs; and 4) permeable reactive barriers (PRBs) in contaminated alluvium. The hydrogeologic conceptual model for the vadose zone and alluvial system as well as the status of the canyon as habitat for the Mexican Spotted Owl were key factors in selection of these minimal-environmental-impact remedies. The heterogeneous vadose zone, characterized by flow and contaminant transport in fractures and in surge beds, requires contaminant treatment at a point of discharge. The canyon PRB is being installed to capture water and contaminants prior to infiltration into the vadose zone. Pilot-scale testing of the SMS and lab-scale batch and column tests of a range of media suggest that granular activated carbon, zeolite, and gypsum may be effective media for removal of HE and/or barium from contaminated waters.

Genetic characterization of an extended-spectrum AmpC cephalosporinase with hydrolysing activity against fourth-generation cephalosporins in a clinical isolate of Enterobacter aerogenes selected in vivo.

PubMed

Rodríguez-Martínez, Jose M; Fernández-Echauri, Pedro; Fernández-Cuenca, Felipe; Diaz de Alba, Paula; Briales, Alejandra; Pascual, Alvaro

2012-01-01

Extended-spectrum AmpC cephalosporinases (ESACs) have been reported in Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii. Here, we characterize a new AmpC variant presenting a broadened substrate activity towards fourth-generation cephalosporins, selected in vivo following cefepime treatment for Enterobacter aerogenes. Two consecutive clonally related isolates of E. aerogenes were evaluated. Screening for ESAC production was performed using plates containing 200 mg/L cloxacillin. MICs were determined by microdilution (CLSI guidelines). bla(AmpC) genes were cloned into a pCR-Blunt II-TOPO vector and expressed in Escherichia coli. The ampC genes were cloned into vector pGEX-6P-1 for protein purification. Isolate Ea595 was resistant to two fourth-generation cephalosporins, cefepime and cefpirome; using plates containing cloxacillin, susceptibility to ceftazidime and cefepime was restored, suggesting overproduction of the ESAC β-lactamase. Sequencing identified a new AmpC β-lactamase variant presenting one amino acid substitution, Val291Gly, inside the H-10 helix. Recombinant plasmids harbouring this ESAC β-lactamase conferred a broadened resistance profile to cefepime and cefpirome, with resistance levels increasing from 16- to 32-fold in E. coli. AmpC-Ea595 hydrolysed ceftazidime, cefepime and cefpirome at high levels, presenting a lower K(m) and enabling us to classify the enzyme as an ESAC. Homology modelling suggested that the size of the active site could have increased. We characterized an ESAC β-lactamase selected in vivo and conferring a high level of resistance to fourth-generation cephalosporins in E. aerogenes. The broadened spectrum was caused by a new modification to the H-10 helix, which modified the active site.

Identification of spinal 5-HT sub 3 receptors and their role in the modulation of nociceptive responses in the rat

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

Glaum, S.R.

1988-01-01

The project consisted of two related studies: (1) the characterization of serotonin binding sites in crude and purified synaptic membranes prepared from the rat spinal cord, and (2) the association of serotonin binding sites with functional 5-HT receptor responses in the modulation of nociceptive information at the level of the spinal cord. The first series of experiments involved the preparation of membranes from the dorsal and ventral halves of the rat spinal cord and the demonstration of specific ({sup 3}H)serotonin binding to these membranes. High affinity binding sites which conformed to the 5-HT{sub 3} subtype were identified in dorsal, butmore » not ventral spinal cord synaptic membranes. These experiments also confirmed the presence of high affinity ({sup 3}H)5-HT binding sites in dorsal spinal cord synaptic membranes of the 5-HT{sub 1} subtype. The second group of studies demonstrated the ability of selective 5-HT{sub 3} antagonists to inhibit the antinociceptive response to intrathecally administered 5-HT, as measured by a change in tail flick and hot plate latencies. Intrathecal pretreatment with the selective 5-HT{sub 3} antagonists ICS 205-930 or MDL 72222 abolished the antinociceptive effects of 5-HT. Furthermore, the selective 5-HT{sub 3} agonist 2-methyl-5-HT mimicked the antinociceptive effects of 5-HT.« less

Spatial and Temporal Monitoring of Aerosol over Selected Urban Areas in Egypt

NASA Astrophysics Data System (ADS)

Shokr, Mohammed; El-Tahan, Mohammed; Ibrahim, Alaa

2015-04-01

We utilize remote sensing data of atmospheric aerosols from the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Terra and Aqua satellites to explore spatio-temporal patterns over selected urban sites in Egypt during 2000-2015. High resolution (10 x 10 km^2) Level 2, collection 5, quality-controlled product was used. The selected sites are characterized by different human and industrial activities as well as landscape and meteorological attributes. These have impacts on the dominant types and intensity of aerosols. Aerosol robotic network (AERONET) data were used to validate the calculations from MODIS. The suitability of the MODIS product in terms of spatial and temporal coverage as well as accuracy and robustness has been established. Seasonal patterns of aerosol concentration are identified and compared between the sites. Spatial gradient of aerosol is assessed in the vicinity of major aerosol-emission sites (e.g. Cairo) to determine the range of influence of the generated pollution. Peak aerosol concentrations are explained in terms of meteorological events and land cover. The limited trends found in the temporal records of the aerosol measurements will be confirmed using calibrated long-term ground observations. The study has been conducted under the PEER 2-239 research project titled "The Impact of Biogenic and Anthropogenic Atmospheric Aerosols to Climate in Egypt". Project website is CleanAirEgypt.org

Biophysical characterization of OprB, a glucose-inducible porin of Pseudomonas aeruginosa.

PubMed

Wylie, J L; Bernegger-Egli, C; O'Neil, J D; Worobec, E A

1993-10-01

OprB, a glucose-inducible porin of P. aeruginosa, was characterized by black lipid bilayer analysis and circular dichroism spectroscopy. Black lipid bilayer analysis of OprB revealed a single-channel conductance of 25 pS, the presence of a glucose binding site with a Ks for glucose of 380 +/- 40 mM, and the formation of channels with a strong selection for anions. Analysis of P. aeruginosa OprB circular dichroism spectra revealed a high beta sheet content (40%) which is within the range of that determined for other porins. Values obtained from black lipid bilayer analysis were compared to those previously obtained for OprB of P. putida [Saravolac et al. (1991). J. Bacteriol. 173, 4970-4976] and indicated extensive similarities in the single-channel conductance and glucose-binding properties of these two porins. Immunological and amino terminal sequence analysis revealed a high degree of homology. Of the first 14 amino terminal residues, 12 were identical. A major difference between the two porins was found in their ion selectivity. Whereas P. aeruginosa OprB is anion selective, P. putida OprB and other carbohydrate selective porins are known to be cation selective.

Photographic techniques for characterizing streambed particle sizes

USGS Publications Warehouse

Whitman, Matthew S.; Moran, Edward H.; Ourso, Robert T.

2003-01-01

We developed photographic techniques to characterize coarse (>2-mm) and fine (≤2-mm) streambed particle sizes in 12 streams in Anchorage, Alaska. Results were compared with current sampling techniques to assess which provided greater sampling efficiency and accuracy. The streams sampled were wadeable and contained gravel—cobble streambeds. Gradients ranged from about 5% at the upstream sites to about 0.25% at the downstream sites. Mean particle sizes and size-frequency distributions resulting from digitized photographs differed significantly from those resulting from Wolman pebble counts for five sites in the analysis. Wolman counts were biased toward selecting larger particles. Photographic analysis also yielded a greater number of measured particles (mean = 989) than did the Wolman counts (mean = 328). Stream embeddedness ratings assigned from field and photographic observations were significantly different at 5 of the 12 sites, although both types of ratings showed a positive relationship with digitized surface fines. Visual estimates of embeddedness and digitized surface fines may both be useful indicators of benthic conditions, but digitizing surface fines produces quantitative rather than qualitative data. Benefits of the photographic techniques include reduced field time, minimal streambed disturbance, convenience of postfield processing, easy sample archiving, and improved accuracy and replication potential.

Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

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

Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele

Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites onmore » the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in similar fashion to Jnk-1 siRNA and to rosiglitazone treatment. Together, the data suggest that these new ligand series bind to a novel, allosteric, and physiologically relevant site and therefore represent a unique approach to identify kinase inhibitors.« less

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

Harrison, W.; Dravnieks, A.; Zussman, R.

Samples of malodorous air and dredged material were collected at diked disposal sites at the following locations: Buffalo, NY; Milwaukee, WI; Mobile, AL; York Harbor, ME; Houston, TX; Detroit, MI; and Anacortes, WA; during the period July--October, 1975. Odorous compounds in the air samples were identified by gas chromatography/mass spectrometry, while the detection threshold, intensity, and character of the various odors were determined by experienced panelists using a dynamic, forced-choice-triangle olfactometer. Although significant problems with malodors were not observed beyond the disposal-area dikes during site visits, noteworthy odor episodes had occurred at some sites. An odor-abatement strategy is presented formore » handling the expected range of odor conditions at dredged-material disposal sites. Its aim is to reduce to an acceptable level the intensity of malodors in an affected community. The main steps in the strategy cover selection of the disposal site, site preparation, odor characterization of sediments to be dredged, malodor abatement during dredging and disposal operations, malodor abatement after filling of the disposal site, and the handling of malodor complaints.« less

A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of γ-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes.

PubMed

Woll, Kellie A; Murlidaran, Sruthi; Pinch, Benika J; Hénin, Jérôme; Wang, Xiaoshi; Salari, Reza; Covarrubias, Manuel; Dailey, William P; Brannigan, Grace; Garcia, Benjamin A; Eckenhoff, Roderic G

2016-09-23

Propofol, an intravenous anesthetic, is a positive modulator of the GABAA receptor, but the mechanistic details, including the relevant binding sites and alternative targets, remain disputed. Here we undertook an in-depth study of alkylphenol-based anesthetic binding to synaptic membranes. We designed, synthesized, and characterized a chemically active alkylphenol anesthetic (2-((prop-2-yn-1-yloxy)methyl)-5-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenol, AziPm-click (1)), for affinity-based protein profiling (ABPP) of propofol-binding proteins in their native state within mouse synaptosomes. The ABPP strategy captured ∼4% of the synaptosomal proteome, including the unbiased capture of five α or β GABAA receptor subunits. Lack of γ2 subunit capture was not due to low abundance. Consistent with this, independent molecular dynamics simulations with alchemical free energy perturbation calculations predicted selective propofol binding to interfacial sites, with higher affinities for α/β than γ-containing interfaces. The simulations indicated hydrogen bonding is a key component leading to propofol-selective binding within GABAA receptor subunit interfaces, with stable hydrogen bonds observed between propofol and α/β cavity residues but not γ cavity residues. We confirmed this by introducing a hydrogen bond-null propofol analogue as a protecting ligand for targeted-ABPP and observed a lack of GABAA receptor subunit protection. This investigation demonstrates striking interfacial GABAA receptor subunit selectivity in the native milieu, suggesting that asymmetric occupancy of heteropentameric ion channels by alkylphenol-based anesthetics is sufficient to induce modulation of activity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of γ-Aminobutyric Acid, Type A (GABAA), Receptor Subunit Binding Selectivity in Synaptosomes*

PubMed Central

Woll, Kellie A.; Murlidaran, Sruthi; Pinch, Benika J.; Hénin, Jérôme; Wang, Xiaoshi; Salari, Reza; Covarrubias, Manuel; Dailey, William P.; Brannigan, Grace; Garcia, Benjamin A.; Eckenhoff, Roderic G.

2016-01-01

Propofol, an intravenous anesthetic, is a positive modulator of the GABAA receptor, but the mechanistic details, including the relevant binding sites and alternative targets, remain disputed. Here we undertook an in-depth study of alkylphenol-based anesthetic binding to synaptic membranes. We designed, synthesized, and characterized a chemically active alkylphenol anesthetic (2-((prop-2-yn-1-yloxy)methyl)-5-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenol, AziPm-click (1)), for affinity-based protein profiling (ABPP) of propofol-binding proteins in their native state within mouse synaptosomes. The ABPP strategy captured ∼4% of the synaptosomal proteome, including the unbiased capture of five α or β GABAA receptor subunits. Lack of γ2 subunit capture was not due to low abundance. Consistent with this, independent molecular dynamics simulations with alchemical free energy perturbation calculations predicted selective propofol binding to interfacial sites, with higher affinities for α/β than γ-containing interfaces. The simulations indicated hydrogen bonding is a key component leading to propofol-selective binding within GABAA receptor subunit interfaces, with stable hydrogen bonds observed between propofol and α/β cavity residues but not γ cavity residues. We confirmed this by introducing a hydrogen bond-null propofol analogue as a protecting ligand for targeted-ABPP and observed a lack of GABAA receptor subunit protection. This investigation demonstrates striking interfacial GABAA receptor subunit selectivity in the native milieu, suggesting that asymmetric occupancy of heteropentameric ion channels by alkylphenol-based anesthetics is sufficient to induce modulation of activity. PMID:27462076

A Robust Analytical Approach for the Identification of Specific Protein Carbonylation Sites: Metal-Catalyzed Oxidations of Human Serum Albumin

PubMed Central

Ugur, Zafer; Gronert, Scott

2017-01-01

The formation of protein carbonyls in the metal-catalyzed oxidation of human serum albumin (HSA) is characterized using a new analytical approach that involves tagging the modification site with multiple hydrazide reagents. Protein carbonyl formation at lysine and arginine residues was catalyzed with copper and iron ions, and the resulting oxidation patterns in HSA are contrasted. A total of 18 modification sites were identified with iron ion catalysis and 14 with copper ion catalysis. However, with the more stringent requirement of identification with at least two tagging reagents, the number of validated modification sites drops to 10 for iron and 9 for copper. Of the 14 total validated sites, there were only five in common for the two metal ions. The results illustrate the value of using multiple tagging agents and highlight the selective and specific nature of metal-catalyzed protein oxidations. PMID:28303033

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

Dallman, Ann Renee; Neary, Vincent Sinclair

This report presents met - ocean data and wave energy characteristics at three U.S. wave energy converter (WEC) test and potential deployment sites . Its purpose is to enable the compari son of wave resource characteristics among sites as well as the select io n of test sites that are most suitable for a developer's device and that best meet their testing needs and objectives . It also provides essential inputs for the design of WEC test devices and planning WEC tests, including the planning of deployment and op eration s and maintenance. For each site, this report catalogues wavemore » statistics recommended in the (draft) International Electrotechnical Commission Technical Specification (IEC 62600 - 101 TS) on Wave Energy Characterization, as well as the frequency of oc currence of weather windows and extreme sea states, and statistics on wind and ocean currents. It also provides useful information on test site infrastructure and services .« less

An evaluation of traditional and emerging remote sensing technologies for the detection of fugitive contamination at selected Superfund hazardous waste sites

USGS Publications Warehouse

Slonecker, E. Terrence; Fisher, Gary B.

2011-01-01

This report represents a remote sensing research effort conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency (EPA) for the EPA Office of Inspector General. The objective of this investigation was to explore the efficacy of remote sensing as a technology for postclosure monitoring of hazardous waste sites as defined under the Comprehensive Environmental Response Compensation and Liability Act of 1980 (Public Law 96-510, 42 U.S.C. §9601 et seq.), also known as \\"Superfund.\\" Five delisted Superfund sites in Maryland and Virginia were imaged with a hyperspectral sensor and visited for collection of soil, water, and spectral samples and inspection of general site conditions. This report evaluates traditional and hyperspectral imagery and field spectroscopic measurement techniques in the characterization and analysis of fugitive (anthropogenic, uncontrolled) contamination at previously remediated hazardous waste disposal sites.

Deep Borehole Disposal Safety Analysis.

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

Freeze, Geoffrey A.; Stein, Emily; Price, Laura L.

This report presents a preliminary safety analysis for the deep borehole disposal (DBD) concept, using a safety case framework. A safety case is an integrated collection of qualitative and quantitative arguments, evidence, and analyses that substantiate the safety, and the level of confidence in the safety, of a geologic repository. This safety case framework for DBD follows the outline of the elements of a safety case, and identifies the types of information that will be required to satisfy these elements. At this very preliminary phase of development, the DBD safety case focuses on the generic feasibility of the DBD concept.more » It is based on potential system designs, waste forms, engineering, and geologic conditions; however, no specific site or regulatory framework exists. It will progress to a site-specific safety case as the DBD concept advances into a site-specific phase, progressing through consent-based site selection and site investigation and characterization.« less

Milestones for Selection, Characterization, and Analysis of the Performance of a Repository for Spent Nuclear Fuel and High-Level Radioactive Waste at Yucca Mountain.

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

Rechard, Robert P.

This report presents a concise history in tabular form of events leading up to site identification in 1978, site selection in 1987, subsequent characterization, and ongoing analysis through 2009 of the performance of a repository for spent nuclear fuel and high - level radioactive waste at Yucca Mountain in southern Nevada. The tabulated events generally occurred in five periods: (1) commitment to mined geologic disposal and identification of sites; (2) site selection and analysis, based on regional geologic characterization through literature and analogous data; (3) feasibility analysis demonstrating calculation procedures and importance of system components, based on rough measures ofmore » performance using surface exploration, waste process knowledge, and general laboratory experiments; (4) suitability analysis demonstrating viability of disposal system, based on environment - specific laboratory experiments, in - situ experiments, and underground disposal system characterization; and (5) compliance analysis, based on completed site - specific characterization . The current sixth period beyond 2010 represents a new effort to set waste management policy in the United States. Because the relationship is important to understanding the evolution of the Yucca Mountain Project , the tabulation also shows the interaction between the policy realm and technical realm using four broad categories of events : (a) Regulatory requirements and related federal policy in laws and court decisions, (c) Presidential and agency directives, (c) technical milestones of implementing institutions, and (d) critiques of the Yucca Mountain Project and pertinent national and world events related to nuclear energy and radioactive waste. Preface The historical progression of technical milestones for the Yucca Mountain Project was originally developed for 10 journal articles in a special issue of Reliability Engineering System Safety on the performance assessment for the Yucca Mountain license application [1-10]. The listing of mile stones, a distinct feature of those articles, has been collected and tabulated here. A lthough a brief description is presented here (based on the summaries in the 10 journal articles), the emphasis remains on the tabulation because of its usefulness in providing a comprehensive but concise history of the Yucca Mountain Project. The tabulation presented here is more elaborate than originally presented in that many of the interactions that occurred between the technical realm and policy realm can be depicted in separate columns. The usefulness of the milestones table is due in part to L.A. Connolly, for editorial and reference support, and S.K. Best, Raytheon, and L. Mays, Sandia National Laboratories (SNL), for illustration support. Reviewers P.N. Swift, SNL, and K. Gupta, University of Oklahoma, helped improve the discussion. The historical perspective presented is that of the author and is not necessarily held by reviewers, Sandia National Laboratories , and the US Department of Energy. As a historic perspective, the author is reporting on the work of others; however, any interpretative error s of the documentation are those of the author alone. The characterization and modeling of the Yucca Mountain disposal system required numerous participants with expertise in many areas of science and technology, as evident from the extensive reference list. Their diligent efforts are generally acknowledged here and through the many references to their impressive work, but the 10 journal articles acknowledge by name many of the numerous participants that contributed to the Yucca Mountain Project .« less

Regulatory requirements and tools for environmental assessment of hazardous wastes: Understanding tribal and stakeholder concerns using Department of Energy sites

PubMed Central

Burger, Joanna; Powers, Charles; Gochfeld, Michael

2014-01-01

Many US governmental and Tribal Nation agencies, as well as state and local entities, deal with hazardous wastes within regulatory frameworks that require specific environmental assessments. In this paper we use Department of Energy (DOE) sites as examples to examine the relationship between regulatory requirements and environmental assessments for hazardous waste sites and give special attention to how assessment tools differ. We consider federal laws associated with environmental protection include the National Environmental Policy Act (NEPA), the Resource Conservation and Recovery Act (RCRA), the Comprehensive Environmental Response Compensation and Liability Act (CERCLA), as well as regulations promulgated by the Nuclear Regulatory Commission, Tribal Nations and state agencies. These regulatory regimes require different types of environmental assessments and remedial investigations, dose assessments and contaminant pathways. The DOE case studies illustrate the following points: 1) there is often understandable confusion about what regulatory requirements apply to the site resources, and what environmental assessments are required by each, 2) the messages sent on site safety issued by different regulatory agencies are sometimes contradictory or confusing (e.g. Oak Ridge Reservation), 3) the regulatory frameworks being used to examine the same question can be different, leading to different conclusions (e.g. Brookhaven National Laboratory), 4) computer models used in support of groundwater models or risk assessments are not necessarily successful in convincing Native Americans and others that there is no possibility of risk from contaminants (e.g. Amchitka Island), 5) when given the opportunity to choose between relying on a screening risk assessments or waiting for a full site-specific analysis of contaminants in biota, the screening risk assessment option is rarely selected (e.g. Amchitka, Hanford Site), and finally, 6) there needs to be agreement on whether there has been adequate characterization to support the risk assessment (e.g. Hanford). The assessments need to be transparent and to accommodate different opinions about the relationship between characterizations and risk assessments. This paper illustrates how many of the problems at DOE sites, and potentially at other sites in the U.S. and elsewhere, derive from a lack of either understanding of, or consensus about, the regulatory process, including the timing and types of required characterizations and data in support of site characterizations and risk assessments. PMID:20719428

Contractors Road Heavy Equipment Area SWMU 055 Corrective Measures Implementation Progress Report Kennedy Space Center, Florida

NASA Technical Reports Server (NTRS)

Johnson, Jill W. (Compiler)

2015-01-01

This Corrective Measures Implementation (CMI) Progress Report documents: (i) activities conducted as part of supplemental assessment activities completed from June 2009 through November 2014; (ii) Engineering Evaluation (EE) Advanced Data Packages (ADPs); and (iii) recommendations for future activities related to corrective measures at the Site. Applicable meeting minutes are provided as Appendix A. The following EE ADPs for CRHE are included with this CMI Progress Report: center dot Supplemental Site Characterization ADP (Step 1 EE) (Appendix B) center dot Site Characterization ADP (Step 1 EE) for Hot Spot 1 (HS1) (Appendix C) center dot Remedial Alternatives Evaluation (Step 2 EE) ADP for HS1 (Appendix D) center dot Interim Measures Work Plan (Step 3 EE) ADP for HS1 (Appendix E) center dot Site Characterization ADP (Step 1 EE) ADP for Hot Spot 2 (HS2), High Concentration Plume (HCP), and Low Concentration Plume (LCP) (Appendix F) A summary of direct-push technology (DPT) and groundwater monitoring well sampling results are provided in Appendices G and H, respectively. The Interim Land Use Control Implementation Plan (LUCIP) is provided as Appendix I. Monitoring well completion reports, other applicable field forms, survey data, and analytical laboratory reports are provided as Appendices J through M, respectively, in the electronic copy of this document. Selected Site photographs are provided in Appendix N. The interim groundwater monitoring plan and document revision log are included as Appendices O and P, respectively. KSC Electronic Data Deliverable (KEDD) files are provided on the attached compact disk.

Streamflow gains and losses and selected water-quality observations in five subreaches of the Rio Grande/Rio Bravo del Norte from near Presidio to Langtry, Texas, Big Bend area, United States and Mexico, 2006

USGS Publications Warehouse

Raines, Timothy H.; Turco, Michael J.; Connor, Patrick J.; Bennett, Jeffery B.

2012-01-01

Few historical streamflow and water-quality data are available to characterize the segment of the Rio Grande/Rio Bravo del Norte (hereinafter Rio Grande) extending from near Presidio to near Langtry, Texas. The U.S. Geological Survey, in cooperation with the National Park Service and the Texas Commission on Environmental Quality, collected water-quality and streamflow data from the Rio Grande from near Presidio to near Langtry, Texas, to characterize the streamflow gain and loss and selected constituent concentrations in a 336.3-mile reach of the Rio Grande from near Presidio to near Langtry, Texas. Streamflow was measured at 38 sites and water-quality samples were collected at 20 sites along the Rio Grande in February, March, and June 2006. Streamflow gains and losses over the course of the stream were measured indirectly by computing the differences in measured streamflow between sites along the stream. Water-quality data were collected and analyzed for salinity, dissolved solids, major ions, nutrients, trace elements, and stable isotopes. Selected properties and constituents were compared to available Texas Commission on Environmental Quality general use protection criteria or screening levels. Summary statistics of selected water-quality data were computed for each of the five designated subreaches. Streamflow gain and loss and water-quality constituent concentration were compared for each subreach, rather than the entire segment because of the temporal variation in sample collection caused by controlled releases upstream. Subreach A was determined to be a losing reach, and subreaches B, C, D, and E were determined to be gaining reaches. Compared to concentrations measured in upstream subreaches, downstream subreaches exhibited evidence of dilution of selected constituent concentrations. Subreaches A and B had measured total dissolved solids, chloride, and sulfate exceeding the Texas Commission on Environmental Quality general use protection criteria. Subreaches C, D, and E did not exceed the general use protection criteria for any constituent concentration criteria, but dissolved oxygen concentrations did not meet the general use criteria in these subreaches.

Exobiological exploration of Mars.

PubMed

Klein, H P; DeVincenzi, D L

1995-03-01

Of all the other planets in the solar system, Mars remains the most promising for further elucidating concepts about chemical evolution and the origin of life. Strategies were developed to pursue three exobiological objectives for Mars exploration: determining the abundance and distribution of the biogenic elements and organic compounds, detecting evidence of an ancient biota on Mars, and determining whether indigenous organisms exist anywhere on the planet. The three strategies are quite similar and, in fact, share the same sequence of phases. In the first phase, each requires global reconnaissance and remote sensing by orbiters to select sites of interest for detailed in situ analyses. In the second phase, lander missions are conducted to characterize the chemical and physical properties of the selected sites. The third phase involves conducting "critical" experiments at sites whose properties make them particularly attractive for exobiology. These critical experiments would include, for example, identification of organics, detection of fossils, and detection of extant life. The fourth phase is the detailed analysis of samples returned from these sites in Earth-based laboratories to confirm and extend previous discoveries. Finally, in the fifth phase, human exploration is needed to establish the geological settings for the earlier findings or to discover and explore sites that are not accessible to robotic spacecraft.

Characterization of Bleomycin-Mediated Cleavage of a Hairpin DNA Library

PubMed Central

Segerman, Zachary J.; Roy, Basab; Hecht, Sidney M.

2013-01-01

A study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal free BLM. The ability of Fe(II)•BLM to effect cleavage on both the 3' and 5'-arms of the hairpin DNAs was characterized. The strongly bound DNAs were found to be efficient substrates for Fe•BLM A5-mediated hairpin DNA cleavage. Surprisingly, the most prevalent site of BLM-mediated cleavage was found to be the 5′-AT-3′ dinucleotide sequence. This dinucleotide sequence, and other sequences generally not cleaved well by BLM when examined using arbitrarily chosen DNA substrates, were apparent when examining the library of ten hairpin DNAs. In total, 132 sites of DNA cleavage were produced by exposure of the hairpin DNA library to Fe•BLM A5. The existence of multiple sites of cleavage on both the 3′- and 5′-arms of the hairpin DNAs suggested that some of these might be double-strand cleavage events. Accordingly, an assay was developed with which to test the propensity of the hairpin DNAs to undergo double-strand DNA damage. One hairpin DNA was characterized using this method, and gave results consistent with earlier reports of double-strand DNA cleavage, but with a sequence selectivity different from those reported previously. PMID:23834496

Selective adsorption of thiophenic compounds from fuel over TiO2/SiO2 under UV-irradiation.

PubMed

Miao, Guang; Ye, Feiyan; Wu, Luoming; Ren, Xiaoling; Xiao, Jing; Li, Zhong; Wang, Haihui

2015-12-30

This study investigates selective adsorption of thiophenic compounds from fuel over TiO2/SiO2 under UV-irradiation. The TiO2/SiO2 adsorbents were prepared and then characterized by N2 adsorption, X-ray diffraction and X-ray photoelectron spectroscopy. Adsorption isotherms, selectivity and kinetics of TiO2/SiO2 were measured in a UV built-in batch reactor. It was concluded that (a) with the employment of UV-irradiation, high organosulfur uptake of 5.12 mg/g was achieved on the optimized 0.3TiO2/0.7SiO2 adsorbent at low sulfur concentration of 15 ppmw-S, and its adsorption selectivity over naphthalene was up to 325.5; (b) highly dispersed TiO2 served as the photocatalytic sites for DBT oxidation, while SiO2 acted as the selective adsorption sites for the corresponding oxidized DBT using TiO2 as a promoter, the two types of active sites worked cooperatively to achieve the high adsorption selectivity of TiO2/SiO2; (c) The kinetic rate-determining step for the UV photocatalysis-assisted adsorptive desulfurization (PADS) over TiO2/SiO2 was DBT oxidation; (d) consecutive adsorption-regeneration cycles suggested that the 0.3TiO2/0.7SiO2 adsorbent can be regenerated by acetonitrile washing followed with oxidative air treatment. This work demonstrated an effective PADS approach to greatly enhance adsorption capacity and selectivity of thiophenic compounds at low concentrations for deep desulfurization under ambient conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Effect of ZSM-5 acidity on aromatic product selectivity during upgrading of pine pyrolysis vapors

DOE PAGES

Engtrakul, Chaiwat; Mukarakate, Calvin; Starace, Anne K.; ...

2015-11-14

The impact of catalyst acidity on the selectivity of upgraded biomass pyrolysis products was studied by passing pine pyrolysis vapors over five ZSM-5 catalysts of varying acidity at 500 degrees C. The SiO 2-to-Al 2O 3 ratio (SAR) of the ZSM-5 zeolite was varied from 23 to 280 to control the acidity of the catalyst and the composition of upgraded products. The upgraded product stream was analyzed by GCMS. Additionally, catalysts were characterized using temperature programmed desorption, diffuse-reflectance FTIR spectroscopy, N 2 physisorption, and X-ray diffraction. The results showed that the biomass pyrolysis vapors were highly deoxygenated to form amore » slate of aromatic hydrocarbons over all of the tested ZSM-5 catalysts. As the overall acidity of the ZSM-5 increased the selectivity toward alkylated (substituted) aromatics (e.g., xylene, dimethyl-naphthalene, and methyl-anthracene) decreased while the selectivity toward unsubstituted aromatics (e.g., benzene, naphthalene, and anthracene) increased. Additionally, the selectivity toward polycyclic aromatic compounds (2-ring and 3-ring) increased as catalyst acidity increased, corresponding to a decrease in acid site spacing. The increased selectivity toward less substituted polycyclic aromatic compounds with increasing acidity is related to the relative rates of cyclization and alkylation reactions within the zeolite structure. As the acid site concentration increases and sites become closer to each other, the formation of additional cyclization products occurs at a greater rate than alkylated products. The ability to adjust product selectivity within 1-, 2-, and 3-ring aromatic families, as well as the degree of substitution, by varying ZSM-5 acidity could have significant benefits in terms creating a slate of upgraded biomass pyrolysis products to meet specific target market demands.« less

A framework to spatially cluster air pollution monitoring sites in US based on the PM2.5 composition

PubMed Central

Austin, Elena; Coull, Brent A.; Zanobetti, Antonella; Koutrakis, Petros

2013-01-01

Background Heterogeneity in the response to PM2.5 is hypothesized to be related to differences in particle composition across monitoring sites which reflect differences in source types as well as climatic and topographic conditions impacting different geographic locations. Identifying spatial patterns in particle composition is a multivariate problem that requires novel methodologies. Objectives Use cluster analysis methods to identify spatial patterns in PM2.5 composition. Verify that the resulting clusters are distinct and informative. Methods 109 monitoring sites with 75% reported speciation data during the period 2003–2008 were selected. These sites were categorized based on their average PM2.5 composition over the study period using k-means cluster analysis. The obtained clusters were validated and characterized based on their physico-chemical characteristics, geographic locations, emissions profiles, population density and proximity to major emission sources. Results Overall 31 clusters were identified. These include 21 clusters with 2 or more sites which were further grouped into 4 main types using hierarchical clustering. The resulting groupings are chemically meaningful and represent broad differences in emissions. The remaining clusters, encompassing single sites, were characterized based on their particle composition and geographic location. Conclusions The framework presented here provides a novel tool which can be used to identify and further classify sites based on their PM2.5 composition. The solution presented is fairly robust and yielded groupings that were meaningful in the context of air-pollution research. PMID:23850585

Characterization of the geology, geochemistry, and microbiology of the radio frequency heating demonstration site at the Savannah River Site

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

Eddy Dilek, C.A.; Jarosch, T.R.; Fliermans, C.B.

The overall objective of the Integrated Demonstration Project for the Remediation of Organics at Nonarid Sites at the Savannah River Site (SRS) is to evaluate innovative remediation, characterization, and monitoring systems to facilitate restoration of contaminated sites. The first phase of the demonstration focused on the application and development of in situ air stripping technologies to remediate sediments and groundwater contaminated with volatile organic compounds (VOCs). The second phase focused on the enhancement of the in situ air stripping process by adding selected nutrients to stimulate naturally occurring microorganisms that degrade VOCs. The purpose of the third phase was tomore » evaluate the use of heating technologies [radio frequency (rf) and ohmic heating] to enhance the removal of contamination from clay layers where mass transfer is limited. The objective of this report is to document pretest and post-test data collected in support of the rf heating demonstration. The following data are discussed in this report: (1) a general description of the site including piezometers and sensors installed to monitor the remedial process; (2) stratigraphy, lithology, and a detailed geologic cross section of the study site; (3) tabulations of pretest and post-test moisture and VOC content of the sediments; (4) sampling and analysis procedures for sediment samples; (5) microbial abundance and diversity; (6) three-dimensional images of pretest and post-test contaminant distribution; (7) volumetric calculations.« less

HS3D, A Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database

NASA Astrophysics Data System (ADS)

Pollastro, Pasquale; Rampone, Salvatore

The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D - Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT-AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT-AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: http://www.sci.unisannio.it/docenti/rampone/.

NRC TLD Direct Radiation Monitoring Network. Progress report, October--December 1996

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

Struckmeyer, R.

This report presents the results of the NRC Direct Radiation Monitoring Network for the fourth quarter of 1996. It provides the ambient radiation levels measured in the vicinity of 74 sites throughout the United States. In addition, it describes the equipment used, monitoring station selection criteria, characterization of the dosimeter response, calibration procedures, statistical methods, intercomparison, and quality assurance program. 3 figs., 4 tabs.

Vibrational dynamics (IR, Raman, NRVS) and DFT study of new antitumor tetranuclearstannoxanecluster, Sn(IV)$-$oxo$-$${di$$-$o$-$vanillin} dimethyl dichloride

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

Arjmand, F.; Sharma, S.; Usman, M.

2016-06-21

The vibrational dynamics of a newly synthesized tetrastannoxane was characterized with a combination of experimental (Raman, IR and tin-based nuclear resonance vibrational spectroscopy) and computational (DFT/B3LYP) methods, with an emphasis on the vibrations of the tin sites. The cytotoxic activity revealed a significant regression selectively against the human pancreatic cell lines.

Biological diversity in montane riparian ecosystems: The case of the Mexican spotted owl

Treesearch

Angela Hodgson; Peter B. Stacey

1999-01-01

Although usually considered to be a bird of old growth mixed conifer forests, the Mexican spotted owl historically occurred in a wide range of habitats from lowland cottonwood bosques to montane canyon systems. In a recent study of habitat use in central New Mexico, we found that owls roost primarily in canyon bottoms, and that they select sites that are characterized...

Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase With Atypical Selectivity

PubMed Central

Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun-Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

2015-01-01

Quorum-quenching catalysts are of interest for potential application as biochemical tools to interrogate interbacterial communication pathways, as anti-biofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-L-homoserine (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is one of the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M−1s−1 for N-heptanoyl-L-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) than typical AHL lactonases (ca. > 1 mM). X-ray crystal structures of AidC alone, and with the product N-hexanoyl-L-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multi-angle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a ‘kinked’ α-helix that forms part of a closed binding pocket which provides affinity and enforces selectivity for AHL substrates, and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed. PMID:26115006

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology.

PubMed

Tanouchi, Yu; Covert, Markus W

2017-09-19

During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance. Importantly, the new technologies that we developed to enable this study-sequencing secondary sites using next-generation sequencing and then selecting relevant lysogens using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based selection-are broadly applicable to other phage-bacterium systems. IMPORTANCE Bacteriophages play an important role in bacterial evolution through lysogeny, where the phage genome is integrated into the host chromosome. While phage integration generally occurs at a specific site in the host chromosome, it is also known to occur at other, so-called secondary sites. In this study, we developed a new experimental technology to comprehensively study secondary integration sites and discovered that phage can integrate into over 300 unique sites in the host genome, resulting in significant genetic diversity in bacteria. We further developed an assay to examine the phenotypic consequence of such diverse integration events and found that phage integration can cause changes in evolutionarily relevant traits such as bacterial motility and increases in antibiotic resistance. Importantly, our method is readily applicable to other phage-bacterium systems. Copyright © 2017 Tanouchi and Covert.

The Effects of Urbanization and Other Environmental Gradients on Algal Assemblages in Nine Metropolitan Areas across the United States

USGS Publications Warehouse

Coles, James F.; Bell, Amanda H.; Scudder, Barbara C.; Carpenter, Kurt D.

2009-01-01

The U.S. Geological Survey conducted studies from 2000 to 2004 to determine the effects of urbanization on stream ecosystems in nine major metropolitan study areas across the United States. Biological, chemical, and physical components of streams were assessed at 28 to 30 sites in each study area. Benthic algae were sampled to compare the degree to which algal assemblages correlated to urbanization, as characterized by an urban intensity index (UII), relative to other environmental gradients that function at either the watershed or reach scales. Ordination site scores were derived from principal components analyses of the environmental data to define environmental gradients at two spatial scales: (1) watershed-scale gradients that summarized (a) landscape modifications and (b) socioeconomic factors, and (2) reach-scale gradients that characterized (a) physical habitat and (b) water chemistry. Algal response was initially quantified by site scores derived from nonmetric multi-dimensional scaling ordinations of the algal assemblage data. The site scores were then correlated with a set of algal metrics of structure and function to help select specific indicators that would best represent changes in the algal assemblages and would infer ecological condition. The selected metrics were correlated to the UII and other environmental gradients. The results indicated that diatom-taxa in the assemblages were distinctly different across the nine study areas, likely due to physiographic differences across the country, but nevertheless, some algal metrics were applicable to all areas. Overall, the study results indicated that although the UII represented various landscape changes associated with urbanization across the country, the algal response was more strongly related to more specific factors generally associated with water quality measured within the stream reach.

Tanshinones that selectively block the collagenase activity of cathepsin K provide a novel class of ectosteric antiresorptive agents for bone.

PubMed

Panwar, Preety; Law, Simon; Jamroz, Andrew; Azizi, Pouya; Zhang, Dongwei; Ciufolini, Marco; Brömme, Dieter

2018-03-01

Attempts to generate active site-directed cathepsin K (CatK) inhibitors for the treatment of osteoporosis have failed because of side effects. We have previously shown that an ectosteric tanshinone CatK inhibitor isolated from Salvia miltiorrhiza blocked, selectively, the collagenase activity of CatK, without affecting the active site and demonstrated its bone-preserving activity in vivo. Here, we have characterize the antiresorptive potential of other tanshinones, which may provide a scaffold for side effect-free CatK inhibitors. Thirty-one tanshinones were tested for their activity against CatK in enzymic and cell-based assays. The inhibitory potency against triple helical and fibrillar collagen degradation was determined in enzymic assays, by scanning electron microscopy and mechanical strength measurements. Human osteoclast assays were used to determine the effects of the inhibitors on bone resorption, its reversibility and osteoclastogenesis. Binding sites were characterized by molecular docking. Twelve compounds showed highly effective anti-collagenase activity and protected collagen against destruction and mechanical instability without inhibiting the hydrolysis of non-collagenous substrates. Six compounds were highly effective in osteoclast bone resorption assays with IC 50 values of <500 nM. None of these tanshinones had effects on cell viability, reversibility of bone resorption inhibition and osteoclastogenesis. The core pharmacophore of the tanshinones appears to be the three-ring system with either a para- or ortho-quinone entity. Our study identified several potent ectosteric antiresorptive CatK inhibitors from the medicinal plant, S. miltiorrhiza, which may avoid side effects seen with active site-directed inhibitors in clinical trials. © 2017 The British Pharmacological Society.

A well-defined Pd hybrid material for the Z-selective semihydrogenation of alkynes characterized at the molecular level by DNP SENS.

PubMed

Conley, Matthew P; Drost, Ruben M; Baffert, Mathieu; Gajan, David; Elsevier, Cornelis; Franks, W Trent; Oschkinat, Hartmut; Veyre, Laurent; Zagdoun, Alexandre; Rossini, Aaron; Lelli, Moreno; Lesage, Anne; Casano, Gilles; Ouari, Olivier; Tordo, Paul; Emsley, Lyndon; Copéret, Christophe; Thieuleux, Chloé

2013-09-09

Direct evidence of the conformation of a Pd-N heterocyclic carbene (NHC) moiety imbedded in a hybrid material and of the Pd-NHC bond were obtained by dynamic nuclear polarization surface-enhanced NMR spectroscopy (DNP SENS) at natural abundance in short experimental times (hours). Overall, this silica-based hybrid material containing well-defined Pd-NHC sites in a uniform environment displays high activity and selectivity in the semihydrogenation of alkynes into Z-alkenes (see figure). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Composition controllability of InGaAs nanowire arrays in selective area growth with controlled pitches on Si platform

NASA Astrophysics Data System (ADS)

Chiba, Kohei; Tomioka, Katsuhiro; Yoshida, Akinobu; Motohisa, Junichi

2017-12-01

Composition controllability of vertical InGaAs nanowires (NWs) on Si integrated by selective area growth was characterized for Si photonics in the optical telecommunication bands. The pitch of pre-patterned holes (NW sites) changed to an In/Ga alloy-composition in the solid phase during the NW growth. The In composition with a nanometer-scaled pitch differed completely from that with a μm-scaled pitch. Accordingly, the growth morphologies of InGaAs NWs show different behavior with respect to the In/Ga ratio.

Neurophysiological Organization of the Middle Face Patch in Macaque Inferior Temporal Cortex

PubMed Central

Aparicio, Paul L.; Issa, Elias B.

2016-01-01

While early cortical visual areas contain fine scale spatial organization of neuronal properties, such as orientation preference, the spatial organization of higher-level visual areas is less well understood. The fMRI demonstration of face-preferring regions in human ventral cortex and monkey inferior temporal cortex (“face patches”) raises the question of how neural selectivity for faces is organized. Here, we targeted hundreds of spatially registered neural recordings to the largest fMRI-identified face-preferring region in monkeys, the middle face patch (MFP), and show that the MFP contains a graded enrichment of face-preferring neurons. At its center, as much as 93% of the sites we sampled responded twice as strongly to faces than to nonface objects. We estimate the maximum neurophysiological size of the MFP to be ∼6 mm in diameter, consistent with its previously reported size under fMRI. Importantly, face selectivity in the MFP varied strongly even between neighboring sites. Additionally, extremely face-selective sites were ∼40 times more likely to be present inside the MFP than outside. These results provide the first direct quantification of the size and neural composition of the MFP by showing that the cortical tissue localized to the fMRI defined region consists of a very high fraction of face-preferring sites near its center, and a monotonic decrease in that fraction along any radial spatial axis. SIGNIFICANCE STATEMENT The underlying organization of neurons that give rise to the large spatial regions of activity observed with fMRI is not well understood. Neurophysiological studies that have targeted the fMRI identified face patches in monkeys have provided evidence for both large-scale clustering and a heterogeneous spatial organization. Here we used a novel x-ray imaging system to spatially map the responses of hundreds of sites in and around the middle face patch. We observed that face-selective signal localized to the middle face patch was characterized by a gradual spatial enrichment. Furthermore, strongly face-selective sites were ∼40 times more likely to be found inside the patch than outside of the patch. PMID:27810930

Neurophysiological Organization of the Middle Face Patch in Macaque Inferior Temporal Cortex.

PubMed

Aparicio, Paul L; Issa, Elias B; DiCarlo, James J

2016-12-14

While early cortical visual areas contain fine scale spatial organization of neuronal properties, such as orientation preference, the spatial organization of higher-level visual areas is less well understood. The fMRI demonstration of face-preferring regions in human ventral cortex and monkey inferior temporal cortex ("face patches") raises the question of how neural selectivity for faces is organized. Here, we targeted hundreds of spatially registered neural recordings to the largest fMRI-identified face-preferring region in monkeys, the middle face patch (MFP), and show that the MFP contains a graded enrichment of face-preferring neurons. At its center, as much as 93% of the sites we sampled responded twice as strongly to faces than to nonface objects. We estimate the maximum neurophysiological size of the MFP to be ∼6 mm in diameter, consistent with its previously reported size under fMRI. Importantly, face selectivity in the MFP varied strongly even between neighboring sites. Additionally, extremely face-selective sites were ∼40 times more likely to be present inside the MFP than outside. These results provide the first direct quantification of the size and neural composition of the MFP by showing that the cortical tissue localized to the fMRI defined region consists of a very high fraction of face-preferring sites near its center, and a monotonic decrease in that fraction along any radial spatial axis. The underlying organization of neurons that give rise to the large spatial regions of activity observed with fMRI is not well understood. Neurophysiological studies that have targeted the fMRI identified face patches in monkeys have provided evidence for both large-scale clustering and a heterogeneous spatial organization. Here we used a novel x-ray imaging system to spatially map the responses of hundreds of sites in and around the middle face patch. We observed that face-selective signal localized to the middle face patch was characterized by a gradual spatial enrichment. Furthermore, strongly face-selective sites were ∼40 times more likely to be found inside the patch than outside of the patch. Copyright © 2016 the authors 0270-6474/16/3612729-17$15.00/0.

Selective Se-for-S substitution in Cs-bearing uranyl compounds

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

Gurzhiy, Vladislav V., E-mail: vladgeo17@mail.ru; Tyumentseva, Olga S.; Krivovichev, Sergey V.

Phase formation in the mixed sulfate-selenate aqueous system of uranyl nitrate and cesium nitrate has been investigated. Two types of crystalline compounds have been obtained and characterized using a number of experimental (single crystal XRD, FTIR, SEM) and theoretical (information-based complexity calculations, topological analysis) techniques. No miscibility gaps have been observed for Cs{sub 2}[(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}] (T= S, Se), which crystallizes in tetragonal system, P-42{sub 1}m, a =9.616(1)–9.856(2), c =8.105(1)–8.159(1) Å, V =749.6(2)–792.5(3) Å{sup 3}. Nine phases with variable amount of S and Se have been structurally characterized. The structures of the Cs{sub 2}[(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}]more » (T= S, Se) compounds are based upon the [(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}]{sup 2-} layers of corner-sharing uranyl pentagonal bipyramids and TO{sub 4} tetrahedra. The layers contain two types of tetrahedral sites: T1 (3-connected, i.e. having three O atoms shared by adjacent uranyl polyhedra) and T2 (4-connected). The Se-for-S substitution in tetrahedral sites is highly selective with smaller S{sup 6+} cation showing a strong preference for the more tightly bonded T2 site. Crystallization in the pure Se system starts with the formation of Cs{sub 2}[(UO{sub 2})(SeO{sub 4}){sub 2}(H{sub 2}O)](H{sub 2}O) crystals, its subsequent dissolution and formation of Cs{sub 2}[(UO{sub 2}){sub 2}(SeO{sub 4}){sub 3}]. The information-based structural complexity calculations for these two phases support the rule that more topologically complex structures form at the latest stages of crystallization. - Graphical abstract: Nine phases representing the Cs{sub 2}[(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}] (T= S, Se) solid solution series with variable amount of S and Se have been prepared by isothermal evaporation from aqueous solutions and characterized using a number of experimental and theoretical techniques. No immiscibility is observed between the pure sulfate and selenate compounds. The Se-for-S substitution in tetrahedral sites is highly selective with smaller S{sup 6+} cation showing a strong preference for the more tightly bonded 4-connected site. - Highlights: • Single crystals of novel mixed sulfate-selenate uranyl oxysalts were prepared by evaporation method. • Topological analysis and information-based complexity calculations were used for structure description. • The selective Se-for-S substitution was observed. • Evolution of phase formation in the aqueous Cs{sup +}–UO{sub 2}{sup 2+}–SO{sub 4}{sup 2–}–SeO{sub 4}{sup 2–} system was analyzed.« less

Surface chemistry characterization of hydrodesulfurization and methanol synthesis model nanocatalysts

NASA Astrophysics Data System (ADS)

Komarneni, Mallikharjuna Rao

Surface science investigations of model catalysts have contributed significantly to heterogeneous catalysis over the past several decades. The unique properties of nanomaterials are being exploited in catalysis for the development of highly active and selective catalysts. Surface science investigations of model catalysts such as inorganic fullerene-like (IF) nanoparticles (NP), inorganic nanotubes (INT), and the oxide-supported nanoclusters are included in this dissertation. Thermal desorption spectroscopy and molecular beam scattering were respectively utilized to study the adsorption kinetics and dynamics of gas phase molecules on catalyst surfaces. In addition, ambient pressure kinetics experiments were performed to characterize the catalytic activity of hydrodesulfurization (HDS) nanocatalysts. The nanocatalysts were characterized with a variety of techniques, including Auger electron spectroscopy, x-ray photoelectron spectroscopy, electron microscopy, and x-ray diffraction. The adsorption kinetics studies of thiophene on novel HDS catalysts provided the first evidence for the presence of different adsorption sites on INT-WS2. Additionally, the adsorption sites on IF-MoS2 NP and silica-supported Mo clusters (Mo/silica) were characterized. Furthermore, the C-S bond activation energy of thiophene on Mo/silica was determined. These studies finally led to the fabrication of Ni/Co coated INT-WS2, which showed good catalytic activity towards HDS of thiophene. The studies of methanol synthesis catalysts include the adsorption kinetics and dynamics studies of CO and CO2 on Cu/silica and silica-supported EBL-fabricated Cu/CuOx nanoclusters. The adsorption dynamics of CO on Cu/silica are modeled within the frame work of the capture zone model (CZM), and the active sites of the silica-supported Au/Cu catalysts are successfully mapped. Studies on EBL model catalysts identify the rims of the CuOx nanoclusters as catalytically active sites. This observation has implications for new methanol catalyst design.

The integrated contaminant elution and tracer test toolkit, ICET3, for improved characterization of mass transfer, attenuation, and mass removal

NASA Astrophysics Data System (ADS)

Brusseau, Mark L.; Guo, Zhilin

2018-01-01

It is evident based on historical data that groundwater contaminant plumes persist at many sites, requiring costly long-term management. High-resolution site-characterization methods are needed to support accurate risk assessments and to select, design, and operate effective remediation operations. Most subsurface characterization methods are generally limited in their ability to provide unambiguous, real-time delineation of specific processes affecting mass-transfer, transformation, and mass removal, and accurate estimation of associated rates. An integrated contaminant elution and tracer test toolkit, comprising a set of local-scale groundwater extraction-and injection tests, was developed to ameliorate the primary limitations associated with standard characterization methods. The test employs extended groundwater extraction to stress the system and induce hydraulic and concentration gradients. Clean water can be injected, which removes the resident aqueous contaminant mass present in the higher-permeability zones and isolates the test zone from the surrounding plume. This ensures that the concentrations and fluxes measured within the isolated area are directly and predominantly influenced by the local mass-transfer and transformation processes controlling mass removal. A suite of standard and novel tracers can be used to delineate specific mass-transfer and attenuation processes that are active at a given site, and to quantify the associated mass-transfer and transformation rates. The conceptual basis for the test is first presented, followed by an illustrative application based on simulations produced with a 3-D mathematical model and a brief case study application.

SITE CHARACTERIZATION LIBRARY VERSION 3.0

EPA Science Inventory

The Site Characterization Library is a CD that provides a centralized, field-portable source for site characterization information. Version 3 of the Site Characterization Library contains additional (from earlier versions) electronic documents and computer programs related to th...

Molecular Characterization of Epithelial Ovarian Cancer: Implications for Diagnosis and Treatment.

PubMed

Rojas, Veronica; Hirshfield, Kim M; Ganesan, Shridar; Rodriguez-Rodriguez, Lorna

2016-12-15

Epithelial ovarian cancer is a highly heterogeneous disease characterized by multiple histological subtypes. Molecular diversity has been shown to occur within specific histological subtypes of epithelial ovarian cancer, between different tumors of an individual patient, as well as within individual tumors. Recent advances in the molecular characterization of epithelial ovarian cancer tumors have provided the basis for a simplified classification scheme in which these cancers are classified as either type I or type II tumors, and these two categories have implications regarding disease pathogenesis and prognosis. Molecular analyses, primarily based on next-generation sequencing, otherwise known as high-throughput sequencing, are allowing for further refinement of ovarian cancer classification, facilitating the elucidation of the site(s) of precursor lesions of high-grade serous ovarian cancer, and providing insight into the processes of clonal selection and evolution that may be associated with development of chemoresistance. Potential therapeutic targets have been identified from recent molecular profiling studies of these tumors, and the effectiveness and safety of a number of specific targeted therapies have been evaluated or are currently being studied for the treatment of women with this disease.

Molecular Characterization of Epithelial Ovarian Cancer: Implications for Diagnosis and Treatment

PubMed Central

Rojas, Veronica; Hirshfield, Kim M.; Ganesan, Shridar; Rodriguez-Rodriguez, Lorna

2016-01-01

Epithelial ovarian cancer is a highly heterogeneous disease characterized by multiple histological subtypes. Molecular diversity has been shown to occur within specific histological subtypes of epithelial ovarian cancer, between different tumors of an individual patient, as well as within individual tumors. Recent advances in the molecular characterization of epithelial ovarian cancer tumors have provided the basis for a simplified classification scheme in which these cancers are classified as either type I or type II tumors, and these two categories have implications regarding disease pathogenesis and prognosis. Molecular analyses, primarily based on next-generation sequencing, otherwise known as high-throughput sequencing, are allowing for further refinement of ovarian cancer classification, facilitating the elucidation of the site(s) of precursor lesions of high-grade serous ovarian cancer, and providing insight into the processes of clonal selection and evolution that may be associated with development of chemoresistance. Potential therapeutic targets have been identified from recent molecular profiling studies of these tumors, and the effectiveness and safety of a number of specific targeted therapies have been evaluated or are currently being studied for the treatment of women with this disease. PMID:27983698

Use of an analog site near Raymond, California, to develop equipment and methods for characterizing a potential high-level, nuclear waste repository site at Yucca Mountain, Nevada

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

Umari, A.M.J.; Geldon, A.; Patterson, G.

1994-12-31

Yucca Mountain, Nevada, currently is being investigated by the U.S. Geological Survey as a potential site for a high-level nuclear waste repository. Planned hydraulic-stress and tracer tests in fractured, tuffaceous rocks below the water table at Yucca Mountain will require work at depths in excess of 1,300 feet. To facilitate prototype testing of equipment and methods to be used in aquifer tests at Yucca Mountain, an analog site was selected in the foothills of the Sierra Nevada near Raymond, California. Two of nine 250- to 300-feet deep wells drilled into fractured, granitic rocks at the Raymond site have been instrumentedmore » with packers, pressure transducers, and other equipment that will be used at Yucca Mountain. Aquifer tests conducted at the Raymond site to date have demonstrated a need to modify some of the equipment and methods conceived for use at Yucca Mountain.« less

Novel synthesis and structural characterization of a high-affinity paramagnetic kinase probe for the identification of non-ATP site binders by nuclear magnetic resonance.

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

Moy, Franklin J.; Lee, Arthur; Gavrin, Lori Krim

2010-07-23

To aid in the pursuit of selective kinase inhibitors, we have developed a unique ATP site binder tool for the detection of binders outside the ATP site by nuclear magnetic resonance (NMR). We report here the novel synthesis that led to this paramagnetic spin-labeled pyrazolopyrimidine probe (1), which exhibits nanomolar inhibitory activity against multiple kinases. We demonstrate the application of this probe by performing NMR binding experiments with Lck and Src kinases and utilize it to detect the binding of two compounds proximal to the ATP site. The complex structure of the probe with Lck is also presented, revealing howmore » the probe fits in the ATP site and the specific interactions it has with the protein. We believe that this spin-labeled probe is a valuable tool that holds broad applicability in a screen for non-ATP site binders.« less

Methods for collecting benthic invertebrate samples as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Cuffney, Thomas F.; Gurtz, Martin E.; Meador, Michael R.

1993-01-01

Benthic invertebrate communities are evaluated as part of the ecological survey component of the U.S. Geological Survey's National Water-Quality Assessment Program. These biological data are collected along with physical and chemical data to assess water-quality conditions and to develop an understanding of the factors that affect water-quality conditions locally, regionally, and nationally. The objectives of benthic invertebrate community characterizations are to (1) develop for each site a list of tax a within the associated stream reach and (2) determine the structure of benthic invertebrate communities within selected habitats of that reach. A nationally consistent approach is used to achieve these objectives. This approach provides guidance on site, reach, and habitat selection and methods and equipment for qualitative multihabitat sampling and semi-quantitative single habitat sampling. Appropriate quality-assurance and quality-control guidelines are used to maximize the ability to analyze data within and among study units.

The Effect of Surface Site Ensembles on the Activity and Selectivity of Ethanol Electrooxidation by Octahedral PtNiRh Nanoparticles.

PubMed

Erini, Nina; Beermann, Vera; Gocyla, Martin; Gliech, Manuel; Heggen, Marc; Dunin-Borkowski, Rafal E; Strasser, Peter

2017-06-01

Direct ethanol fuel cells are attractive power sources based on a biorenewable, high energy-density fuel. Their efficiency is limited by the lack of active anode materials which catalyze the breaking of the C-C bond coupled to the 12-electron oxidation to CO 2 . We report shape-controlled PtNiRh octahedral ethanol oxidation electrocatalysts with excellent activity and previously unachieved low onset potentials as low as 0.1 V vs. RHE, while being highly selective to complete oxidation to CO 2 . Our comprehensive characterization and in situ electrochemical ATR studies suggest that the formation of a ternary surface site ensemble around the octahedral Pt 3 Ni 1 Rh x nanoparticles plays a crucial mechanistic role for this behavior. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regional comparisons of on-site solar potential in the residential and industrial sectors

NASA Astrophysics Data System (ADS)

Gatzke, A. E.; Skewes-Cox, A. O.

1980-10-01

Regional and subregional differences in the potential development of decentralized solar technologies are studied. Two sectors of the economy were selected for intensive analysis: the residential and industrial sectors. The sequence of analysis follows the same general steps: (1) selection of appropriate prototypes within each land use sector disaggregated by census region; (2) characterization of the end-use energy demand of each prototype in order to match an appropriate decentralized solar technology to the energy demand; (3) assessment of the energy conservation potential within each prototype limited by land use patterns, technology efficiency, and variation in solar insolation; and (4) evaluation of the regional and subregional differences in the land use implications of decentralized energy supply technologies that result from the combination of energy demand, energy supply potential, and the subsequent addition of increasingly more restrictive policies to increase the percent contribution of on-site solar energy.

Deployment Effects of Marine Renewable Energy Technologies: Wave Energy Scenarios

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

Mirko Previsic

2010-06-17

Given proper care in siting, design, deployment, operation and maintenance, wave energy conversion could become one of the more environmentally benign sources of electricity generation. In order to accelerate the adoption of these emerging hydrokinetic and marine energy technologies, navigational and environmental concerns must be identified and addressed. All developing hydrokinetic projects involve a wide variety of stakeholders. One of the key issues that site developers face as they engage with this range of stakeholders is that, due to a lack of technical certainty, many of the possible conflicts (e.g., shipping and fishing) and environmental issues are not well-understood,. Inmore » September 2008, re vision consulting, LLC was selected by the Department of Energy (DoE) to apply a scenario-based assessment to the emerging hydrokinetic technology sector in order to evaluate the potential impact of these technologies on the marine environment and navigation constraints. The project’s scope of work includes the establishment of baseline scenarios for wave and tidal power conversion at potential future deployment sites. The scenarios capture variations in technical approaches and deployment scales to properly identify and characterize environmental effects and navigational effects. The goal of the project is to provide all stakeholders with an improved understanding of the potential range of technical attributes and potential effects of these emerging technologies and focus all stakeholders on the critical issues that need to be addressed. By identifying and addressing navigational and environmental concerns in the early stages of the industry’s development, serious mistakes that could potentially derail industry-wide development can be avoided. This groundwork will also help in streamlining siting and associated permitting processes, which are considered key hurdles for the industry’s development in the U.S. today. Re vision is coordinating its efforts with two other project teams funded by DoE which are focused on regulatory issues (Pacific Energy Ventures) and navigational issues (PCCI). The results of this study are structured into three reports: (1) Wave power scenario description (2) Tidal power scenario description (3) Framework for Identifying Key Environmental Concerns This is the first report in the sequence and describes the results of conceptual feasibility studies of wave power plants deployed in Humboldt County, California and Oahu, Hawaii. These two sites contain many of the same competing stakeholder interactions identified at other wave power sites in the U.S. and serve as representative case studies. Wave power remains at an early stage of development. As such, a wide range of different technologies are being pursued by different manufacturers. In order to properly characterize potential effects, it is useful to characterize the range of technologies that could be deployed at the site of interest. An industry survey informed the process of selecting representative wave power devices. The selection criteria requires that devices are at an advanced stage of development to reduce technical uncertainties, and that enough data are available from the manufacturers to inform the conceptual design process of this study. Further, an attempt is made to cover the range of different technologies under development to capture variations in potential environmental effects. Table 1 summarizes the selected wave power technologies. A number of other developers are also at an advanced stage of development, but are not directly mentioned here. Many environmental effects will largely scale with the size of the wave power plant. In many cases, the effects of a single device may not be measurable, while larger scale device arrays may have cumulative impacts that differ significantly from smaller scale deployments. In order to characterize these effects, scenarios are established at three deployment scales which nominally represent (1) a small pilot deployment, (2) a small commercial deployment, and (3) a large commercial scale plant. It is important to understand that the purpose of this study was to establish baseline scenarios based on basic device data that was provided to use by the manufacturer for illustrative purposes only.« less

Where in the air? Aerial habitat use of nocturnally migrating birds.

PubMed

Horton, Kyle G; Van Doren, Benjamin M; Stepanian, Phillip M; Farnsworth, Andrew; Kelly, Jeffrey F

2016-11-01

The lower atmosphere (i.e. aerosphere) is critical habitat for migrant birds. This habitat is vast and little is known about the spatio-temporal patterns of distribution and abundance of migrants in it. Increased human encroachment into the aerosphere makes understanding where and when migratory birds use this airspace a key to reducing human-wildlife conflicts. We use weather surveillance radar to describe large-scale height distributions of nocturnally migrating birds and interpret these distributions as aggregate habitat selection behaviours of individual birds. As such, we detail wind cues that influence selection of flight heights. Using six radars in the eastern USA during the spring (2013-2015) and autumn (2013 and 2014), we found migrants tended to adjust their heights according to favourable wind profit. We found that migrants' flight altitudes correlated most closely with the altitude of maximum wind profit; however, absolute differences in flight heights and height of maximum wind profit were large. Migrants tended to fly slightly higher at inland sites compared with coastal sites during spring, but not during autumn. Migration activity was greater at coastal sites during autumn, but not during spring. This characterization of bird migration represents a critical advance in our understanding of migrant distributions in flight and a new window into habitat selection behaviours. © 2016 The Author(s).

Mutational jackpot events generate effective frequency-dependent selection in adapting populations

NASA Astrophysics Data System (ADS)

Hallatschek, Oskar

The site-frequency spectrum is one the most easily measurable quantities that characterize the genetic diversity of a population. While most neutral models predict that site frequency spectra should decay with increasing frequency, a high-frequency uptick has been reported in many populations. Anomalies in the high-frequency tail are particularly unsettling because the highest frequencies can be measured with greatest accuracy. Here, we show that an uptick in the spectrum of neutral mutations generally arises when mutant frequencies are dominated by rare jackpot events, mutational events with large descendant numbers. This leads to an effective pattern of frequency-dependent selection (or unstable internal equilibrium at one half frequency) that causes an accumulation of high-frequency polymorphic sites. We reproduce the known uptick occurring for recurrent hitchhiking (genetic draft) as well as rapid adaptation, and (in the future) generalize the shape of the high-frequency tail to other scenarios that are dominated by jackpot events, such as frequent range expansions. We also tackle (in the future) the inverse approach to use the high-frequency uptick for learning about the tail of the offspring number distribution. Positively selected alleles need to surpass, typically, an u NSF Career Award (PoLS), NIH NIGMS R01, Simons Foundation.

Where in the air? Aerial habitat use of nocturnally migrating birds

PubMed Central

Van Doren, Benjamin M.; Stepanian, Phillip M.; Farnsworth, Andrew; Kelly, Jeffrey F.

2016-01-01

The lower atmosphere (i.e. aerosphere) is critical habitat for migrant birds. This habitat is vast and little is known about the spatio-temporal patterns of distribution and abundance of migrants in it. Increased human encroachment into the aerosphere makes understanding where and when migratory birds use this airspace a key to reducing human–wildlife conflicts. We use weather surveillance radar to describe large-scale height distributions of nocturnally migrating birds and interpret these distributions as aggregate habitat selection behaviours of individual birds. As such, we detail wind cues that influence selection of flight heights. Using six radars in the eastern USA during the spring (2013–2015) and autumn (2013 and 2014), we found migrants tended to adjust their heights according to favourable wind profit. We found that migrants' flight altitudes correlated most closely with the altitude of maximum wind profit; however, absolute differences in flight heights and height of maximum wind profit were large. Migrants tended to fly slightly higher at inland sites compared with coastal sites during spring, but not during autumn. Migration activity was greater at coastal sites during autumn, but not during spring. This characterization of bird migration represents a critical advance in our understanding of migrant distributions in flight and a new window into habitat selection behaviours. PMID:27881761

Characterization of the [125I]-neurokinin A binding site in the circular muscle of human colon

PubMed Central

Warner, Fiona J; Comis, Alfio; Miller, Robert C; Burcher, Elizabeth

1999-01-01

Neurokinin A (NKA) is a potent contractile agonist of human colon circular muscle. These responses are mediated predominantly through tachykinin NK2 receptors. In the present study, the NK2 receptor radioligand [125I]-NKA has been used to characterize binding sites in this tissue, using tachykinin agonists and antagonists. 125INKA labelled a single, high affinity binding site. Specific binding (95% of total binding) of [125I]-NKA was saturable (KD 0.47±0.05 nM), of high capacity (Bmax 2.1±0.1 fmol mg−1 wet weight tissue) and reversible (kinetically derived KD 0.36±0.07 nM). The rank order of agonists competing for the [125I]-NKA binding site was neuropeptide γ (NPγ)≥NKA≥[Lys5,MeLeu9,Nle10]NKA (4–10) (NK2 agonist)>>substance P (SP)>neurokinin B (NKB)≥[Pro9]SP (NK1 agonist)>>senktide (NK3 agonist), indicating binding to an NK2 site. The nonpeptide selective NK2 antagonist SR48968 showed higher affinity for the [125I]-NKA site than selective peptide NK2 antagonists. The rank order of potency for NK2 antagonists was SR48968≥MEN11420>GR94800≥MEN10627>MEN10376≥R396. The NK1 antagonist SR140333 was a weak competitor. The competition curve for SP could be resolved into two sites. When experiments were repeated in the presence of SR140333 (0.1 μM), the curve for SP became monophasic and showed a significant shift to the right, whereas curves to NKA and NKB were unaffected. In conclusion, binding of the radioligand [125I]-NKA to membranes from circular muscle is predominantly to the NK2 receptor. There may be a small component of binding to the NK1 receptor. The NK2 receptor mediates circular muscle contraction, whereas the role of the NK1 receptor in circular muscle is unclear. PMID:10455255

Instantaneous polarization analysis of ambient noise recordings in site response investigations

NASA Astrophysics Data System (ADS)

Del Gaudio, Vincenzo

2017-07-01

A new procedure is proposed for analyses of ambient noise aimed at investigating complex cases of site response to seismic shaking. Information on site response characterized by several resonance frequencies and by amplifications varying with direction can be obtained by analysing instantaneous polarization properties of ambient noise recordings. Through this kind of analysis, it is possible to identify Rayleigh wave packets emerging from incoherent background noise for very short intervals. Analysing noise recordings passed through narrow-band filters with different central frequencies, variations of Rayleigh wave properties depending on frequencies can be estimated. In particular, one can calculate: (i) the instantaneous ratios H/V between the amplitudes of horizontal and vertical components of the elliptical particle motion and (ii) the azimuthal direction of the vertical plane containing such a motion. These can be determined on a large number of recording samples, providing the basis for statistical estimates. A preferential concentration of H/V peak values at site-specific frequencies and directions can reveal directional resonance phenomena. Furthermore, peak amplitudes can be related to site amplification factors and provide constraints for subsurface velocity modelling. Some tests, carried out on data acquired at sites with known response properties, gave indications on how to select the parameters of the analysis that optimize its implementation. In particular, preliminary trials, conducted on a limited number of frequencies, allow the selection of the parameters that, while providing a large number of instantaneous H/V estimates for Rayleigh waves, minimize their scattering. The analysis can then be refined and an H/V curve as function of frequency can be obtained with a higher spectral resolution. First tests showed that cases of directional resonance can be more effectively recognized with this technique and more details can be revealed on its properties (e.g. secondary peaks) in comparison to the Nakamura's method currently employed for ordinary noise analysis. For sites characterized by isotropic response or by differently oriented directional maxima, however, the presence of noise sources with an anisotropic spatial distribution, which excite signals with inhomogeneous distribution of energy through the examined spectral band, can make the correct interpretation of data more difficult.

Geological evaluation of Gulf Coast salt domes: overall assessment of the Gulf Interior Region

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

None

1981-10-01

The three major phases in site characterization and selection are regional studies, area studies, and location studies. This report characterizes regional geologic aspects of the Gulf Coast salt dome basins. It includes general information from published sources on the regional geology; the tectonic, domal, and hydrologic stability; and a brief description the salt domes to be investigated. After a screening exercise, eight domes were chosen for further characterization: Keechi, Oakwood, and Palestine Domes in Texas; Vacherie and Rayburn's domes in North Louisiana; and Cypress Creek and Richton domes in Mississippi. A general description of each, maps of the location, propertymore » ownership, and surface geology, and a geologic cross section were presented for each dome.« less

Despotism and risk of infanticide influence grizzly bear den-site selection.

PubMed

Libal, Nathan S; Belant, Jerrold L; Leopold, Bruce D; Wang, Guiming; Owen, Patricia A

2011-01-01

Given documented social dominance and intraspecific predation in bear populations, the ideal despotic distribution model and sex hypothesis of sexual segregation predict adult female grizzly bears (Ursus arctos) will avoid areas occupied by adult males to reduce risk of infanticide. Under ideal despotic distribution, juveniles should similarly avoid adult males to reduce predation risk. Den-site selection and use is an important component of grizzly bear ecology and may be influenced by multiple factors, including risk from conspecifics. To test the role of predation risk and the sex hypothesis of sexual segregation, we compared adult female (n = 142), adult male (n = 36), and juvenile (n = 35) den locations in Denali National Park and Preserve, Alaska, USA. We measured elevation, aspect, slope, and dominant land cover for each den site, and used maximum entropy modeling to determine which variables best predicted den sites. We identified the global model as the best-fitting model for adult female (area under curve (AUC) = 0.926) and elevation as the best predictive variable for adult male (AUC = 0.880) den sites. The model containing land cover and elevation best-predicted juvenile (AUC = 0.841) den sites. Adult females spatially segregated from adult males, with dens characterized by higher elevations (mean= 1,412 m, SE = 52) and steeper slopes (mean = 21.9°, SE = 1.1) than adult male (elevation: mean = 1,209 m, SE = 76; slope: mean = 15.6°, SE = 1.9) den sites. Juveniles used a broad range of landscape attributes but did not avoid adult male denning areas. Observed spatial segregation by adult females supports the sex hypothesis of sexual segregation and we suggest is a mechanism to reduce risk of infanticide. Den site selection of adult males is likely related to distribution of food resources during spring.

TSPA 1991: An initial total-system performance assessment for Yucca Mountain; Yucca Mountain Site Characterization Project

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

Barnard, R.W.; Wilson, M.L.; Dockery, H.A.

1992-07-01

This report describes an assessment of the long-term performance of a repository system that contains deeply buried highly radioactive waste; the system is assumed to be located at the potential site at Yucca Mountain, Nevada. The study includes an identification of features, events, and processes that might affect the potential repository, a construction of scenarios based on this identification, a selection of models describing these scenarios (including abstraction of appropriate models from detailed models), a selection of probability distributions for the parameters in the models, a stochastic calculation of radionuclide releases for the scenarios, and a derivation of complementary cumulativemore » distribution functions (CCDFs) for the releases. Releases and CCDFs are calculated for four categories of scenarios: aqueous flow (modeling primarily the existing conditions at the site, with allowances for climate change), gaseous flow, basaltic igneous activity, and human intrusion. The study shows that models of complex processes can be abstracted into more simplified representations that preserve the understanding of the processes and produce results consistent with those of more complex models.« less

Location and valence state of strontium cations on the framework of a carbon dioxide selective porous silicoaluminophosphate

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

Zhang, Li; Rivera-Ramos, Milton E.; Hernández-Maldonado, Arturo J.

2014-05-28

A Sr{sup 2+}-SAPO-34 material that displays superior CO2 adsorption selectivity and capacity was characterized via XPS and UV-vis spectroscopy to elucidate the valence state of strontium cations and framework silicon environment. Most importantly, the location of the strontium has been estimated from a Rietveld refinement analysis of synchrotron diffraction data. The XPS analysis indicated that the apparent valence state of the strontium is less than 2, an indication of its interaction with the large anionic framework. Furthermore, UV-vis tests pointed to changes in the silicon environment, plausibly related to this valence state or framework faulting. For the refinement, the analysismore » found that strontium occupied two unique sites: a site Sr1 slightly displaced from six-membered rings and a site Sr2 positioned at the top or bottom of the eight-membered rings. The latter position favors the interaction of the alkaline earth metal with CO{sub 2}, probably resulting in an enhanced electric field-quadrupole moment interaction.« less

Selected ground-water data for Yucca Mountain region, southern Nevada and eastern California, through December 1994

USGS Publications Warehouse

Westenburg, C.L.; La Camera, R. J.

1996-01-01

The U.S. Geological Survey, in support of the U.S. Department of Energy, Yucca Mountain Site Characterization Project, collects, compiles, and summarizes hydrologic data in the Yucca Mountain region. The data are collected to allow assessments of ground-water resources during studies to determine the potential suitability of Yucca Mountain for storing high-level nuclear waste. Data on ground-water levels at 36 sites, ground-water discharge at 6 sites, and ground-water withdrawals within Crater Flat, Jackass Flats, Mercury Valley, and the Amargosa Desert are presented for calendar year 1994. Data collected prior to 1994 are graphically presented and data collected by other agencies (or as part of other programs) are included to further indicate variations of ground-water levels, discharges, and withdrawals through time. A statistical summary of ground-water levels at seven wells in Jackass Flats is presented. The statistical summary includes the number of measurements, the maximum, minimum, and median water-level altitudes, and the average deviation of measured water-level altitudes for selected baseline periods and for calendar years 1992-94.

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

PubMed Central

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Pär K.

2016-01-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. PMID:26721855

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Detecting consistent patterns of directional adaptation using differential selection codon models.

PubMed

Parto, Sahar; Lartillot, Nicolas

2017-06-23

Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles. Our differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.

A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450BM3

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

Dietrich, Jeffrey; Yoshikuni, Yasuo; Fisher, Karl

2009-11-30

Production of fine heterologus pathways in microbial hosts is frequently hindered by insufficient knowledge of the native metabolic pathway and its cognate enzymes; often the pathway is unresolved and enzymes lack detailed characterization. An alternative paradigm to using native pathways is de novo pathway design using well-characterized, substrate-promiscuous enzymes. We demonstrate this concept using P450BM3 from Bacillus megaterium. Using a computer model, we illustrate how key P450BM3 activ site mutations enable binding of non-native substrate amorphadiene, incorporating these mutations into P450BM3 enabled the selective oxidation of amorphadiene arteminsinic-11s,12-epoxide, at titers of 250 mg L"1 in E. coli. We also demonstratemore » high-yeilding, selective transformations to dihydroartemisinic acid, the immediate precursor to the high value anti-malarial drug artemisinin.« less

Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing

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

Kim, Jong Seo; Dai, Ziyu; Aryal, Uma K.

2013-06-17

Proteolytic processing is a ubiquitous, irreversible posttranslational modification that plays an important role in cellular regulation in all living organisms. Herein we report a resin-assisted positive selection method for specifically enriching protein N-terminal peptides to facilitate the characterization of proteolytic processing events by liquid chromatography-tandem mass spectrometry. In this approach, proteins are initially reduced and alkylated and their lysine residues are converted to homoarginines. Then, protein N-termini are selectively converted to reactive thiol groups. We demonstrate that these sequential reactions were achieved with nearly quantitative efficiencies. Thiol-containing N-terminal peptides are then captured (>98% efficiency) by a thiol-affinity resin, a significantmore » improvement over the traditional avidin/biotin enrichment. Application to cell lysates of Aspergillus niger, a filamentous fungus of interest for biomass degradation, enabled the identification of 1672 unique protein N-termini and proteolytic cleavage sites from 690 unique proteins.« less

The role of CEUS in characterization of superficial lymph nodes: a single center prospective study

PubMed Central

de Stefano, Giorgio; Scognamiglio, Umberto; Di Martino, Filomena; Parrella, Roberto; Scarano, Francesco; Signoriello, Giuseppe; Farella, Nunzia

2016-01-01

Accurate lymph node characterization is important in a large number of clinical settings. We evaluated the usefulness of Contrast Enhanced Ultrasound (CEUS) in distinguishing between benign and malignant lymph nodes compared with conventional ultrasonography in the differential diagnosis of superficial lymphadenopathy. We present our experience for 111 patients enrolled in a single center. 111 superficial lymph nodes were selected and only 1 lymph node per patient underwent CEUS. A definitive diagnosis for all lymph nodes was obtained by ultrasonographically guided biopsy and/or excision biopsy. The size of the lymph nodes, the site (neck, axilla, inguinal region) being easily accessible for biopsy, and the US and color Doppler US characteristics guided us in selecting the nodes to be evaluated by CEUS. In our study we identified different enhancement patterns in benign and malignant lymph nodes, with a high degree of diagnostic accuracy for superficial lymphadenopathy in comparison with conventional US. PMID:27191746

Characterization of the particle radiation environment at three potential landing sites on Mars using ESA’s MEREM models

NASA Astrophysics Data System (ADS)

McKenna-Lawlor, S.; Gonçalves, P.; Keating, A.; Morgado, B.; Heynderickx, D.; Nieminen, P.; Santin, G.; Truscott, P.; Lei, F.; Foing, B.; Balaz, J.

2012-03-01

The ‘Mars Energetic Radiation Environment Models’ (dMEREM and eMEREM) recently developed for the European Space Agency are herein used to estimate, for the first time, background Galactic Cosmic Ray (GCR) radiation and flare related solar energetic particle (SEP) events at three candidate martian landing sites under conditions where particle arrival occurred at solar minimum (December, 2006) and solar maximum (April, 2002) during Solar Cycle 23. The three landing sites were selected on the basis that they are characterized by significantly different hydrological conditions and soil compositions. Energetic particle data sets recorded on orbit at Mars at the relevant times were incomplete because of gaps in the measurements due to operational constraints. Thus, in the present study, comprehensive near-Earth particle measurements made aboard the GOES spacecraft were used as proxies to estimate the overall particle doses at each perspective landing site, assuming in each case that the fluxes fell off as 1/r2 (where r is the helio-radial distance) and that good magnetic connectivity always prevailed. The results indicate that the particle radiation environment on Mars can vary according to the epoch concerned and the landing site selected. Particle estimations obtained using MEREM are in reasonable agreement, given the inherent differences between the models, with the related NASA Heavy Ion-Nucleon Transport Code for Space Radiation/HZETRN. Both sets of results indicated that, for short (30 days) stays, the atmosphere of Mars, in the cases of the SEPs studied and the then prevailing background galactic cosmic radiation, provided sufficient shielding at the planetary surface to maintain annual skin and blood forming organ/BFO dose levels below currently accepted ionizing radiation exposure limits. The threat of occurrence of a hard spectrum SEP during Cruise-Phase transfers to/from Mars over 400 days, combined with the associated cumulative effect of prolonged GCR exposure, poses an as yet unsolved hazard to prospective onboard personnel.

A Combined Probe-Molecule, Mössbauer, Nuclear Resonance Vibrational Spectroscopy, and Density Functional Theory Approach for Evaluation of Potential Iron Active Sites in an Oxygen Reduction Reaction Catalyst

DOE PAGES

Kneebone, Jared L.; Daifuku, Stephanie L.; Kehl, Jeffrey A.; ...

2017-07-06

While non-precious metal M-N-C (M = Fe or Co) catalysts have been developed that are effective for the oxygen reduction reaction in polymer electrolyte fuel cells, no consensus has yet been reached regarding the nature of the M sites in these heterogeneous catalysts that are responsible for reaction with dioxygen (O 2). While multiple studies have developed correlations between Fe distributions in as-prepared catalysts and ORR activity, the direct identification of sites reactive towards O 2 or O 2-analog molecules remains a significant challenge. In the present study, we demonstrate a new approach to identifying and characterizing potential Fe activemore » sites in complex ORR catalysts that combines an effective probe molecule (NO (g)) Mössbauer spectroscopy and nuclear resonance vibrational spectroscopy (NRVS) with density functional theory (DFT) calculations. Mössbauer spectroscopic studies demonstrate that NO (g) treatment of electrochemically reduced PANI-57Fe-C leads to selective reaction with only a sub-set of the Fe species present. Nuclear resonance vibrational spectroscopic studies identified new Fe-ligand vibrations associated with the site reactive towards NO (g). DFT calculations of vibrational properties of a small selection of previously proposed active site structures suggest that graphene zig-zag edge hosted Fe-N structures may be responsible for the observed vibrational behavior with NO (g) probe molecules. Moreover, such sites are likely also reactive to O 2, possibly serving as the ORR active sites in the synthesized materials.« less

A Combined Probe-Molecule, Mössbauer, Nuclear Resonance Vibrational Spectroscopy, and Density Functional Theory Approach for Evaluation of Potential Iron Active Sites in an Oxygen Reduction Reaction Catalyst

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

Kneebone, Jared L.; Daifuku, Stephanie L.; Kehl, Jeffrey A.

While non-precious metal M-N-C (M = Fe or Co) catalysts have been developed that are effective for the oxygen reduction reaction in polymer electrolyte fuel cells, no consensus has yet been reached regarding the nature of the M sites in these heterogeneous catalysts that are responsible for reaction with dioxygen (O 2). While multiple studies have developed correlations between Fe distributions in as-prepared catalysts and ORR activity, the direct identification of sites reactive towards O 2 or O 2-analog molecules remains a significant challenge. In the present study, we demonstrate a new approach to identifying and characterizing potential Fe activemore » sites in complex ORR catalysts that combines an effective probe molecule (NO (g)) Mössbauer spectroscopy and nuclear resonance vibrational spectroscopy (NRVS) with density functional theory (DFT) calculations. Mössbauer spectroscopic studies demonstrate that NO (g) treatment of electrochemically reduced PANI-57Fe-C leads to selective reaction with only a sub-set of the Fe species present. Nuclear resonance vibrational spectroscopic studies identified new Fe-ligand vibrations associated with the site reactive towards NO (g). DFT calculations of vibrational properties of a small selection of previously proposed active site structures suggest that graphene zig-zag edge hosted Fe-N structures may be responsible for the observed vibrational behavior with NO (g) probe molecules. Moreover, such sites are likely also reactive to O 2, possibly serving as the ORR active sites in the synthesized materials.« less

Selected techniques for monitoring water movement through unsaturated alluvium during managed aquifer recharge

USGS Publications Warehouse

Nawikas, Joseph M.; O'Leary, David R.; Izbicki, John A.; Burgess, Matthew K.

2016-10-21

Managed aquifer recharge is used to augment natural recharge to aquifers. It can be used to replenish aquifers depleted by pumping or to store water during wetter years for withdrawal during drier years. Infiltration from ponds is a commonly used, inexpensive approach for managed aquifer recharge.At some managed aquifer-recharge sites, the time when infiltrated water arrives at the water table is not always clearly shown by water-level data. As part of site characterization and operation, it can be desirable to track downward movement of infiltrated water through the unsaturated zone to identify when it arrives at the water table.

Geochemical studies of rocks from North Ray Crater, Apollo 16

NASA Technical Reports Server (NTRS)

Lindstrom, M. M.; Salpas, P. A.

1982-01-01

The samples included in the study were all collected as individual specimens from Station 11 near the rim of North Ray Crater. Samples were selected to cover the entire range of rock types from anorthosites to subophitic impact melts, giving particular attention to the feldspathic breccias which predominate at the site. The chemical composition of North Ray Crater rocks is discussed along with the compositional variations among North Ray Crater samples, and the relationships between North Ray Crater and other Apollo 16 stations. It is pointed out that the primary objective in sampling the Apollo 16 site was to characterize materials from the Cayley Plains and Descartes Highlands.

NRC TLD Direct Radiation Monitoring Network. Volume 15, No. 4: Quarterly progress report, October--December 1995

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

Struckmeyer, R.

This report presents the results of the NRC Direct Radiation Monitoring Network for the fourth quarter of 1995. It provides the ambient radiation levels measured in the vicinity of 75 sites throughout the United States. In addition, it describes the equipment used, monitoring station selection criteria, characterization of the dosimeter response, calibration procedures, statistical methods, intercomparison, and quality assurance program.

Polyoxyethylene Tallow Amine, a Glyphosate Formulation Adjuvant: Soil Adsorption Characteristics, Degradation Profile, and Occurrence on Selected Soils from Agricultural Fields in Iowa, Illinois, Indiana, Kansas, Mississippi, and Missouri.

PubMed

Tush, Daniel; Meyer, Michael T

2016-06-07

Polyoxyethylene tallow amine (POEA) is an inert ingredient added to formulations of glyphosate, the most widely applied agricultural herbicide. POEA has been shown to have toxic effects to some aquatic organisms making the potential transport of POEA from the application site into the environment an important concern. This study characterized the adsorption of POEA to soils and assessed its occurrence and homologue distribution in agricultural soils from six states. Adsorption experiments of POEA to selected soils showed that POEA adsorbed much stronger than glyphosate; calcium chloride increased the binding of POEA; and the binding of POEA was stronger in low pH conditions. POEA was detected on a soil sample from an agricultural field near Lawrence, Kansas, but with a loss of homologues that contain alkenes. POEA was also detected on soil samples collected between February and early March from corn and soybean fields from ten different sites in five other states (Iowa, Illinois, Indiana, Missouri, Mississippi). This is the first study to characterize the adsorption of POEA to soil, the potential widespread occurrence of POEA on agricultural soils, and the persistence of the POEA homologues on agricultural soils into the following growing season.

Structural characterization and evolutionary analysis of fish-specific TLR27.

PubMed

Wang, Jinlan; Zhang, Zheng; Liu, Jing; Li, Fang; Chang, Fen; Fu, Hui; Zhao, Jing; Yin, Deling

2015-08-01

Toll-like receptors (TLRs) are critical components of the innate immune response of fish. In a phylogenetic analysis, TLR27 from three fish species, which belongs to TLR family 1, clustered with TLR14/18 and TLR25 on the evolutionary tree. The ectodomain of TLR27 is predicted to include 19 leucine-rich repeat (LRR) modules. Structural modeling showed that the TLR27 ectodomain can be divided into three distinctive sections. The lack of conserved asparagines on the concave surface of the central subdomain causes a structural transition in the middle of the ectodomain, forming a distinct hydrophobic pocket at the border between the central subdomain and the C-terminal subdomain. We infer that, like other functionally characterized TLRs in family 1, the hydrophobic pocket located between LRR11 and LRR12 participates in ligand recognition by TLR27. An evolutionary analysis showed that the dN/dS value at the TLR27 locus was very low. Approximately one quarter of the total number of TLR27 sites are under significant negatively selection pressure, whereas only two sites are under positive selection. Consequently, TLR27 is highly evolutionarily conserved and probably plays an extremely important role in the innate immune systems of fishes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Polyoxyethylene tallow amine, a glyphosate formulation adjuvant: Soil adsorption characteristics, degradation profile, and occurrence on selected soils from agricultural fields in Iowa, Illinois, Indiana, Kansas, Mississippi, and Missouri

USGS Publications Warehouse

Tush, Daniel L.; Meyer, Michael T.

2016-01-01

Polyoxyethylene tallow amine (POEA) is an inert ingredient added to formulations of glyphosate, the most widely applied agricultural herbicide. POEA has been shown to have toxic effects to some aquatic organisms making the potential transport of POEA from the application site into the environment an important concern. This study characterized the adsorption of POEA to soils and assessed its occurrence and homologue distribution in agricultural soils from six states. Adsorption experiments of POEA to selected soils showed that POEA adsorbed much stronger than glyphosate; calcium chloride increased the binding of POEA; and the binding of POEA was stronger in low pH conditions. POEA was detected on a soil sample from an agricultural field near Lawrence, Kansas, but with a loss of homologues that contain alkenes. POEA was also detected on soil samples collected between February and early March from corn and soybean fields from ten different sites in five other states (Iowa, Illinois, Indiana, Missouri, Mississippi). This is the first study to characterize the adsorption of POEA to soil, the potential widespread occurrence of POEA on agricultural soils, and the persistence of the POEA homologues on agricultural soils into the following growing season.

Structural basis for receptor activity-modifying protein-dependent selective peptide recognition by a G protein-coupled receptor

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

Booe, Jason M.; Walker, Christopher S.; Barwell, James

Association of receptor activity-modifying proteins (RAMP1-3) with the G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) enables selective recognition of the peptides calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) that have diverse functions in the cardiovascular and lymphatic systems. How peptides selectively bind GPCR:RAMP complexes is unknown. We report crystal structures of CGRP analog-bound CLR:RAMP1 and AM-bound CLR:RAMP2 extracellular domain heterodimers at 2.5 and 1.8 Å resolutions, respectively. The peptides similarly occupy a shared binding site on CLR with conformations characterized by a β-turn structure near their C termini rather than the α-helical structure common to peptides that bind relatedmore » GPCRs. The RAMPs augment the binding site with distinct contacts to the variable C-terminal peptide residues and elicit subtly different CLR conformations. Lastly, the structures and accompanying pharmacology data reveal how a class of accessory membrane proteins modulate ligand binding of a GPCR and may inform drug development targeting CLR:RAMP complexes.« less

Structural basis for receptor activity-modifying protein-dependent selective peptide recognition by a G protein-coupled receptor

DOE PAGES

Booe, Jason M.; Walker, Christopher S.; Barwell, James; ...

2015-05-14

Association of receptor activity-modifying proteins (RAMP1-3) with the G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) enables selective recognition of the peptides calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) that have diverse functions in the cardiovascular and lymphatic systems. How peptides selectively bind GPCR:RAMP complexes is unknown. We report crystal structures of CGRP analog-bound CLR:RAMP1 and AM-bound CLR:RAMP2 extracellular domain heterodimers at 2.5 and 1.8 Å resolutions, respectively. The peptides similarly occupy a shared binding site on CLR with conformations characterized by a β-turn structure near their C termini rather than the α-helical structure common to peptides that bind relatedmore » GPCRs. The RAMPs augment the binding site with distinct contacts to the variable C-terminal peptide residues and elicit subtly different CLR conformations. Lastly, the structures and accompanying pharmacology data reveal how a class of accessory membrane proteins modulate ligand binding of a GPCR and may inform drug development targeting CLR:RAMP complexes.« less

Oxime amides as a novel zinc binding group in histone deacetylase inhibitors: synthesis, biological activity, and computational evaluation.

PubMed

Botta, Cinzia B; Cabri, Walter; Cini, Elena; De Cesare, Lucia; Fattorusso, Caterina; Giannini, Giuseppe; Persico, Marco; Petrella, Antonello; Rondinelli, Francesca; Rodriquez, Manuela; Russo, Adele; Taddei, Maurizio

2011-04-14

Several oxime containing molecules, characterized by a SAHA-like structure, were explored to select a potentially new biasing binding element for the zinc in HDAC catalytic site. All compounds were evaluated for their in vitro inhibitory activity against the 11 human HDACs isoforms. After identification of a "hit" molecule, a programmed variation at the cap group and at the linker was carried out in order to increase HDAC inhibition and/or paralogue selectivity. Some of the new derivatives showed increased activity against a number of HDAC isoforms, even if their overall activity range is still far from the inhibition values reported for SAHA. Moreover, different from what was reported for their hydroxamic acid analogues the new α-oxime amide derivatives do not select between class I and class II HDACs; rather they target specific isoforms in each class. These somehow contradictory results were finally rationalized by a computational assisted SAR, which gave us the chance to understand how the oxime derivatives interact with the catalytic site and justify the observed activity profile.

Characterization of Co(III) EDTA-Reducing Bacteria in Metal- and Radionuclide-Contaminated Groundwater

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

Gao, Weimin; Gentry, Terry J; Mehlhorn, Tonia L

The Waste Area Grouping 5 (WAG5) site at Oak Ridge National Laboratory has a potential to be a field site for evaluating the effectiveness of various bioremediation approaches and strategies. The site has been well studied in terms of its geological and geochemical properties over the past decade. However, despite the importance of microorganisms in bioremediation processes, the microbiological populations at the WAG5 site and their potential in bioremediation have not been similarly evaluated. In this study, we initiated research to characterize the microbial populations in WAG5 groundwater. Approximately 100 isolates from WAG5 groundwater were isolated and selected based onmore » colony morphology. Fifty-five unique isolates were identified by BOX-PCR and subjected to further characterization. 16S rRNA sequences indicated that these isolates belong to seventeen bacterial genera including Alcaligenes (1 isolate), Aquamonas (1), Aquaspirillum (1), Bacillus (10), Brevundimonas (5), Caulobacter (7), Dechloromonas (2), Janibacter (1), Janthinobacterium (2), Lactobacillus (1), Paenibacillus (4), Pseudomonas (9), Rhodoferax (1), Sphingomonas (1), Stenotrophomonas (6), Variovorax (2), and Zoogloea (1). Metal respiration assays identified several isolates, which phylogenically belong or are close to Caulobacter, Stenotrophomonas, Bacillus, Paenibacillus and Pseudomonas, capable of reducing Co(III)EDTA- to Co(II)EDTA{sup 2-} using the defined M1 medium under anaerobic conditions. In addition, using WAG5 groundwater directly as the inoculants, we found that organisms associated with WAG5 groundwater can reduce both Fe(III) and Co(III) under anaerobic conditions. Further assays were then performed to determine the optimal conditions for Co(III) reduction. These assays indicated that addition of various electron donors including ethanol, lactate, methanol, pyruvate, and acetate resulted in metal reduction. These experiments will provide useful background information for future bioremediation field experiments at the WAG5 site.« less

Empirical analysis of web-based user-object bipartite networks

NASA Astrophysics Data System (ADS)

Shang, Ming-Sheng; Lü, Linyuan; Zhang, Yi-Cheng; Zhou, Tao

2010-05-01

Understanding the structure and evolution of web-based user-object networks is a significant task since they play a crucial role in e-commerce nowadays. This letter reports the empirical analysis on two large-scale web sites, audioscrobbler.com and del.icio.us, where users are connected with music groups and bookmarks, respectively. The degree distributions and degree-degree correlations for both users and objects are reported. We propose a new index, named collaborative similarity, to quantify the diversity of tastes based on the collaborative selection. Accordingly, the correlation between degree and selection diversity is investigated. We report some novel phenomena well characterizing the selection mechanism of web users and outline the relevance of these phenomena to the information recommendation problem.

Hydroisomerization of n-Hexane Using Acidified Metal-Organic Framework and Platinum Nanoparticles.

PubMed

Sabyrov, Kairat; Jiang, Juncong; Yaghi, Omar M; Somorjai, Gabor A

2017-09-13

Exceptionally high surface area and ordered nanopores of a metal-organic framework (MOF) are exploited to encapsulate and homogeneously disperse a considerable amount of phosphotungstic acid (PTA). When combined with platinum nanoparticles positioned on the external surface of the MOF, the construct shows a high catalytic activity for hydroisomerization of n-hexane, a reaction requiring hydrogenation/dehydrogenation and moderate to strong Brønsted acid sites. Characterization of the catalytic activity and acidic sites as a function of PTA loading demonstrates that both the concentration and strength of acidic sites are highest for the catalyst with the largest amount of PTA. The MOF construct containing 60% PTA by weight produces isoalkanes with 100% selectivity and 9-fold increased mass activity as compared to a more traditional aluminosilicate catalyst, further demonstrating the capacity of the MOF to contain a high concentration of active sites necessary for the isomerization reaction.

Nutrient, suspended-sediment, and total suspended-solids data for surface water in the Great Salt Lake basins study unit, Utah, Idaho, and Wyoming, 1980-95

USGS Publications Warehouse

Hadley, Heidi K.

2000-01-01

Selected nitrogen and phosphorus (nutrient), suspended-sediment and total suspended-solids surface-water data were compiled from January 1980 through December 1995 within the Great Salt Lake Basins National Water-Quality Assessment study unit, which extends from southeastern Idaho to west-central Utah and from Great Salt Lake to the Wasatch and western Uinta Mountains. The data were retrieved from the U.S. Geological Survey National Water Information System and the State of Utah, Department of Environmental Quality, Division of Water Quality database. The Division of Water Quality database includes data that are submitted to the U.S. Environmental Protection Agency STOrage and RETrieval system. Water-quality data included in this report were selected for surface-water sites (rivers, streams, and canals) that had three or more nutrient, suspended-sediment, or total suspended-solids analyses. Also, 33 percent or more of the measurements at a site had to include discharge, and, for non-U.S. Geological Survey sites, there had to be 2 or more years of data. Ancillary data for parameters such as water temperature, pH, specific conductance, streamflow (discharge), dissolved oxygen, biochemical oxygen demand, alkalinity, and turbidity also were compiled, as available. The compiled nutrient database contains 13,511 samples from 191 selected sites. The compiled suspended-sediment and total suspended-solids database contains 11,642 samples from 142 selected sites. For the nutrient database, the median (50th percentile) sample period for individual sites is 6 years, and the 75th percentile is 14 years. The median number of samples per site is 52 and the 75th percentile is 110 samples. For the suspended-sediment and total suspended-solids database, the median sample period for individual sites is 9 years, and the 75th percentile is 14 years. The median number of samples per site is 76 and the 75th percentile is 120 samples. The compiled historical data are being used in the basinwide sampling strategy to characterize the broad-scale geographic and seasonal water-quality conditions in relation to major contaminant sources and background conditions. Data for this report are stored on a compact disc.

Free Energy Simulations of Ligand Binding to the Aspartate Transporter GltPh

PubMed Central

Heinzelmann, Germano; Baştuğ, Turgut; Kuyucak, Serdar

2011-01-01

Glutamate/Aspartate transporters cotransport three Na+ and one H+ ions with the substrate and countertransport one K+ ion. The binding sites for the substrate and two Na+ ions have been observed in the crystal structure of the archeal homolog GltPh, while the binding site for the third Na+ ion has been proposed from computational studies and confirmed by experiments. Here we perform detailed free energy simulations of GltPh, giving a comprehensive characterization of the substrate and ion binding sites, and calculating their binding free energies in various configurations. Our results show unequivocally that the substrate binds after the binding of two Na+ ions. They also shed light into Asp/Glu selectivity of GltPh, which is not observed in eukaryotic glutamate transporters. PMID:22098736

Ground-water and surface-water elevations in the Fairbanks International Airport area, Alaska, 1990-96, and selected geohydrologic report references

USGS Publications Warehouse

Claar, David V.; Lilly, Michael R.

1997-01-01

Ground-water and surface-water elevation data were collected at 61 sites from 1990 to 1996 by the U.S. Geological Survey in cooperation with the Alaska Department of Transportation and Public Facilities, Fairbanks International Airport. Water-surface elevations were measured in 41 ground-water observation wells and at 20 surface-water sites to help characterize the geohydrology of the Fairbanks International Airport area. From 1990 to 1993, data were collected in the vicinity of the former fire-training area at the airport. From 1993 to 1996, the data-collection area was expanded to include the entire airport area. The total number of data-collection sites varied each year because of changing project objectives and increased understanding of the geohydrology in the area.

Earthquake ground motion: Chapter 3

USGS Publications Warehouse

Luco, Nicolas; Kircher, Charles A.; Crouse, C. B.; Charney, Finley; Haselton, Curt B.; Baker, Jack W.; Zimmerman, Reid; Hooper, John D.; McVitty, William; Taylor, Andy

2016-01-01

Most of the effort in seismic design of buildings and other structures is focused on structural design. This chapter addresses another key aspect of the design process—characterization of earthquake ground motion into parameters for use in design. Section 3.1 describes the basis of the earthquake ground motion maps in the Provisions and in ASCE 7 (the Standard). Section 3.2 has examples for the determination of ground motion parameters and spectra for use in design. Section 3.3 describes site-specific ground motion requirements and provides example site-specific design and MCER response spectra and example values of site-specific ground motion parameters. Section 3.4 discusses and provides an example for the selection and scaling of ground motion records for use in various types of response history analysis permitted in the Standard.

Investigation of protein selectivity in multimodal chromatography using in silico designed Fab fragment variants.

PubMed

Karkov, Hanne Sophie; Krogh, Berit Olsen; Woo, James; Parimal, Siddharth; Ahmadian, Haleh; Cramer, Steven M

2015-11-01

In this study, a unique set of antibody Fab fragments was designed in silico and produced to examine the relationship between protein surface properties and selectivity in multimodal chromatographic systems. We hypothesized that multimodal ligands containing both hydrophobic and charged moieties would interact strongly with protein surface regions where charged groups and hydrophobic patches were in close spatial proximity. Protein surface property characterization tools were employed to identify the potential multimodal ligand binding regions on the Fab fragment of a humanized antibody and to evaluate the impact of mutations on surface charge and hydrophobicity. Twenty Fab variants were generated by site-directed mutagenesis, recombinant expression, and affinity purification. Column gradient experiments were carried out with the Fab variants in multimodal, cation-exchange, and hydrophobic interaction chromatographic systems. The results clearly indicated that selectivity in the multimodal system was different from the other chromatographic modes examined. Column retention data for the reduced charge Fab variants identified a binding site comprising light chain CDR1 as the main electrostatic interaction site for the multimodal and cation-exchange ligands. Furthermore, the multimodal ligand binding was enhanced by additional hydrophobic contributions as evident from the results obtained with hydrophobic Fab variants. The use of in silico protein surface property analyses combined with molecular biology techniques, protein expression, and chromatographic evaluations represents a previously undescribed and powerful approach for investigating multimodal selectivity with complex biomolecules. © 2015 Wiley Periodicals, Inc.

Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli.

PubMed Central

Liu, J; Turnbough, C L

1994-01-01

In Escherichia coli, expression of the pyrC gene is regulated primarily by a translational control mechanism based on nucleotide-sensitive selection of transcriptional start sites at the pyrC promoter. When intracellular levels of CTP are high, pyrC transcripts are initiated predominantly with CTP at a site 7 bases downstream of the Pribnow box. These transcripts form a stable hairpin at their 5' ends that blocks ribosome binding. When the CTP level is low and the GTP level is high, conditions found in pyrimidine-limited cells, transcripts are initiated primarily with GTP at a site 9 bases downstream of the Pribnow box. These shorter transcripts are unable to form a hairpin at their 5' ends and are readily translated. In this study, we examined the effects of nucleotide sequence and position on the selection of transcriptional start sites at the pyrC promoter. We characterized promoter mutations that systematically alter the sequence at position 7 or 9 downstream of the Pribnow box or vary the spacing between the Pribnow box and wild-type transcriptional initiation region. The results reveal preferences for particular initiating nucleotides (ATP > or = GTP > UTP >> CTP) and for starting positions downstream of the Pribnow box (7 >> 6 and 8 > 9 > 10). The results indicate that optimal nucleotide-sensitive start site switching at the wild-type pyrC promoter is the result of competition between the preferred start site (position 7) that uses the poorest initiating nucleotide (CTP) and a weak start site (position 9) that uses a good initiating nucleotide (GTP). The sequence of the pyrC promoter also minimizes the synthesis of untranslatable transcripts and provides for maximum stability of the regulatory transcript hairpin. In addition, the results show that the effects of the mutations on pyrC expression and regulation are consistent with the current model for translational control. Possible effects of preferences for initiating nucleotides and start sites on the expression and regulation of other genes are discussed. Images PMID:7910603

Use of 2-(/sup 125/I)iodomelatonin to characterize melatonin binding sites in chicken retina

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

Dubocovich, M.L.; Takahashi, J.S.

2-(/sup 125/I)Iodomelatonin binds with high affinity to a site possessing the pharmacological characteristics of a melatonin receptor in chicken retinal membranes. The specific binding of 2-(/sup 125/I)iodomelatonin is stable, saturable, and reversible. Saturation experiments indicated that 2-(/sup 125/I)iodomelatonin labeled a single class of sites with an affinity constant (Kd) of 434 +/- 56 pM and a total number of binding sites (Bmax) of 74.0 +/- 13.6 fmol/mg of protein. The affinity constant obtained from kinetic analysis was in close agreement with that obtained in saturation experiments. Competition experiments showed a monophasic reduction of 2-(/sup 125/I)iodomelatonin binding with a pharmacological ordermore » of indole amine affinities characteristic of a melatonin receptor: 2-iodomelatonin greater than 6-chloromelatonin greater than or equal to melatonin greater than or equal to 6,7-dichloro-2-methylmelatonin greater than 6-hydroxymelatonin greater than or equal to 6-methoxymelatonin much greater than N-acetyltryptamine greater than N-acetyl-5-hydroxytryptamine greater than 5-methoxytryptamine greater than 5-hydroxytryptamine (inactive). The affinities of these melatonin analogs in competing for 2-(/sup 125/I)iodomelatonin binding sites were correlated closely with their potencies for inhibition of the calcium-dependent release of (3H)dopamine from chicken and rabbit retinas, indicating association of the binding site with a functional response regulated by melatonin. The results indicate that 2-(/sup 125/I)iodomelatonin is a selective, high-affinity radioligand for the identification and characterization of melatonin receptor sites.« less

YUCCA MOUNTAIN SITE DESCRIPTION

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

A.M. Simmons

The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work donemore » at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel.« less

SMARTe Site Characterization Tool. In: SMARTe20ll, EPA/600/C-10/007

EPA Science Inventory

The purpose of the Site Characterization Tool is to: (1) develop a sample design for collecting site characterization data and (2) perform data analysis on uploaded data. The sample design part helps to determine how many samples should be collected to characterize a site with ...

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

PubMed

Wang, Yanan; Song, Jiangning; Marquez-Lago, Tatiana T; Leier, André; Li, Chen; Lithgow, Trevor; Webb, Geoffrey I; Shen, Hong-Bin

2017-07-18

Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8. To fill this gap, we propose a new knowledge-transfer computational framework which effectively utilizes the hidden shared knowledge from some MMP types to enhance predictions of other, distinct target substrate-cleavage sites. Our computational framework uses support vector machines combined with transfer machine learning and feature selection. To demonstrate the value of the model, we extracted a variety of substrate sequence-derived features and compared the performance of our method using both 5-fold cross-validation and independent tests. The results show that our transfer-learning-based method provides a robust performance, which is at least comparable to traditional feature-selection methods for prediction of MMP-2, -3, -7, -8, -9 and -12 substrate-cleavage sites on independent tests. The results also demonstrate that our proposed computational framework provides a useful alternative for the characterization of sequence-level determinants of MMP-substrate specificity.

Signatures of Sex-Antagonistic Selection on Recombining Sex Chromosomes

PubMed Central

Kirkpatrick, Mark; Guerrero, Rafael F.

2014-01-01

Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes. PMID:24578352

Selective extraction and enrichment of multiphosphorylated peptides using polyarginine-coated diamond nanoparticles.

PubMed

Chang, Chia-Kai; Wu, Chih-Che; Wang, Yi-Sheng; Chang, Huan-Cheng

2008-05-15

Despite recent advances in phosphopeptide research, detection and characterization of multiply phosphorylated peptides have been a challenge. This work presents a new strategy that not only can effectively extract phosphorylated peptides from complex samples but also can selectively enrich multiphosphorylated peptides for direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis. Polyarginine-coated diamond nanoparticles are the solid-phase extraction supports used for this purpose. The supports show an exceptionally high affinity for multiphosphorylated peptides due to multiple arginine-phosphate interactions. The efficacy of this method was demonstrated by analyzing a small volume (50 microL) of tryptic digests of proteins such as beta-casein, alpha-casein, and nonfat milk at a concentration as low as 1 x 10 (-9) M. The concentration is markedly lower than that can be achieved by using other currently available technologies. We quantified the enhanced selectivity and detection sensitivity of the method using mixtures composed of mono- and tetraphosphorylated peptide standards. This new affinity-based protocol is expected to find useful applications in characterizing multiple phosphorylation sites on proteins of interest in complex and dilute analytes.

Immobilization of ionophore and surface characterization studies of the titanium(III) ion in a PVC-membrane sensor.

PubMed

Rezayi, Majid; Heng, Lee Yook; Kassim, Anuar; Ahmadzadeh, Saeid; Abdollahi, Yadollah; Jahangirian, Hossein

2012-01-01

Novel ionophores comprising various hydroxide and amine structures were immobilized onto poly(vinyl chloride) (PVC) matrices, and these were examined to determine Ti(III) selectivity. To predict the selectivity of Ti(III), a PVC membrane was used to investigate the binding of Ti(III) to c-methylcalix[4]resorcinarene (CMCR). The study showed that the chelating ligand, CMCR, was coordinated selectively to Ti(III) at eight coordination sites involving the oxygen atoms at the interface of the membrane/solution. The membrane was prepared, based on CMCR as an ionophore, sodium tetrakis(4-fluorophenyl) borate (NaTFPB) as a lipophilic ionic additive, and dioctylphthalate (DOP) as a plasticizer. The immobilization of the ionophore and surface characterization studies revealed that the performance of CMCR-immobilized PVC was equivalent to that of mobile ionophores in supported liquid membranes (SLMs). The strengths of the ion-ionophore (CMCR-Ti(OH)(OH(2))(5) (2+)) interactions and the role of ionophores on membranes were studied via UV-Vis, Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) and and X-ray diffraction (XRD).

Skin impedance is not a factor in transcutaneous electrical nerve stimulation effectiveness

PubMed Central

Vance, Carol GT; Rakel, Barbara A; Dailey, Dana L; Sluka, Kathleen A

2015-01-01

Objective Transcutaneous electrical nerve stimulation (TENS) is a nonpharmacological intervention used to manage pain using skin surface electrodes. Optimal electrode placement is unclear. We hypothesized that better analgesia would occur if electrodes were placed over sites with lower skin impedance. Optimal site selection (OSS) and sham site selection (SSS) electrode sites on the forearm were identified using a standard clinical technique. Methods Experiment 1 measured skin impedance in the forearm at OSS and SSS. Experiment 2 was a crossover design double-blind randomized controlled trial comparing OSS-TENS, SSS-TENS, and placebo TENS (P-TENS) to confirm differences in skin impedance between OSS and SSS, and measure change in pressure pain threshold (PPT) following a 30-minute TENS treatment. Healthy volunteers were recruited (ten for Experiment 1 [five male, five female] and 24 for Experiment 2 [12 male, 12 female]). TENS was applied for 30 minutes at 100 Hz frequency, 100 µs pulse duration, and “strong but nonpainful” amplitude. Results Experiment 1 results demonstrate significantly higher impedance at SSS (17.69±1.24 Ω) compared to OSS (13.53±0.57 Ω) (P=0.007). For Experiment 2, electrode site impedance was significantly higher over SSS, with both the impedance meter (P=0.001) and the TENS unit (P=0.012) compared to OSS. PPT change was significantly greater for both OSS-TENS (P=0.024) and SSS-TENS (P=0.025) when compared to P-TENS. PPT did not differ between the two active TENS treatments (P=0.81). Conclusion Skin impedance is lower at sites characterized as optimal using the described technique of electrode site selection. When TENS is applied at adequate intensities, skin impedance is not a factor in attainment of hypoalgesia of the forearm in healthy subjects. Further investigation should include testing in patients presenting with painful conditions. PMID:26316808

Using the Sonoran Desert test site to monitor the long-term radiometric stability of the Landsat TM/ETM+ and Terra MODIS sensors

USGS Publications Warehouse

Angal, A.; Xiong, X.; Choi, T.; Chander, G.; Wu, A.

2009-01-01

Pseudo-invariant ground targets have been extensively used to monitor the long-term radiometric calibration stability of remote sensing instruments. The NASA MODIS Characterization Support Team (MCST), in collaboration with members from the U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center, has previously demonstrated the use of pseudo-invariant ground sites for the long-term stability monitoring of Terra MODIS and Landsat 7 ETM+ sensors. This paper focuses on the results derived from observations made over the Sonoran Desert. Additionally, Landsat 5 TM data over the Sonoran Desert site were used to evaluate the temporal stability of this site. Top-ofatmosphere (TOA) reflectances were computed for the closely matched TM, ETM+, and MODIS spectral bands over selected regions of interest. The impacts due to different viewing geometries, or the effect of test site Bi-directional Reflectance Distribution Function (BRDF), are also presented. ?? 2009 SPIE.

Site selection for DOE/JIP gas hydrate drilling in the northern Gulf of Mexico

USGS Publications Warehouse

Hutchinson, Deborah; Shelander, Dianna; Dai, J.; McConnell, D.; Shedd, William; Frye, Matthew; Ruppel, Carolyn D.; Boswell, R.; Jones, Emrys; Collett, Timothy S.; Rose, Kelly K.; Dugan, Brandon; Wood, Warren T.

2008-01-01

n the late spring of 2008, the Chevron-led Gulf of Mexico Gas Hydrate Joint Industry Project (JIP) expects to conduct an exploratory drilling and logging campaign to better understand gas hydrate-bearing sands in the deepwater Gulf of Mexico. The JIP Site Selection team selected three areas to test alternative geological models and geophysical interpretations supporting the existence of potential high gas hydrate saturations in reservoir-quality sands. The three sites are near existing drill holes which provide geological and geophysical constraints in Alaminos Canyon (AC) lease block 818, Green Canyon (GC) 955, and Walker Ridge (WR) 313. At the AC818 site, gas hydrate is interpreted to occur within the Oligocene Frio volcaniclastic sand at the crest of a fold that is shallow enough to be in the hydrate stability zone. Drilling at GC955 will sample a faulted, buried Pleistocene channel-levee system in an area characterized by seafloor fluid expulsion features, structural closure associated with uplifted salt, and abundant seismic evidence for upward migration of fluids and gas into the sand-rich parts of the sedimentary section. Drilling at WR313 targets ponded sheet sands and associated channel/levee deposits within a minibasin, making this a non-structural play. The potential for gas hydrate occurrence at WR313 is supported by shingled phase reversals consistent with the transition from gas-charged sand to overlying gas-hydrate saturated sand. Drilling locations have been selected at each site to 1) test geological methods and models used to infer the occurrence of gas hydrate in sand reservoirs in different settings in the northern Gulf of Mexico; 2) calibrate geophysical models used to detect gas hydrate sands, map reservoir thicknesses, and estimate the degree of gas hydrate saturation; and 3) delineate potential locations for subsequent JIP drilling and coring operations that will collect samples for comprehensive physical property, geochemical and other analyses

Aspartic acid 397 in subunit B of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae forms part of a sodium-binding site, is involved in cation selectivity, and affects cation-binding site cooperativity.

PubMed

Shea, Michael E; Juárez, Oscar; Cho, Jonathan; Barquera, Blanca

2013-10-25

The Na(+)-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMNC).

Aspartic Acid 397 in Subunit B of the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae Forms Part of a Sodium-binding Site, Is Involved in Cation Selectivity, and Affects Cation-binding Site Cooperativity

PubMed Central

Shea, Michael E.; Juárez, Oscar; Cho, Jonathan; Barquera, Blanca

2013-01-01

The Na+-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMNC). PMID:24030824

Identifying suitable sanitary landfill locations in the state of Morelos, México, using a Geographic Information System

NASA Astrophysics Data System (ADS)

Marín, Luis E.; Torres, Vicente; Bolongaro, Andrea; Reyna, José A.; Pohle, O.; Hernández-Espriú, A.; Chavarría, Jerónimo; García-Barrios, R.; Tabla, Hugo Francisco Parra

GIS is a powerful tool that may help to better manage natural resources. In this paper, we present a GIS model developed for the state of Morelos as an aid to determine whether a potential site, Loma de Mejia, met the Mexican Federal Guidelines. The Mexican Government has established federal guidelines for sanitary landfill site selection (NOM-083-SERMARNAT-2003). These guidelines were translated into a water-based Geographic Information System and applied to the state of Morelos, Mexico. For these examples, we used the SIGAM® (Sistema de Información Geográfico del Agua en México; a water-based GIS for Mexico) which has at least 60 layers from the National Water Commission (CONAGUA), the national mapping agency (INEGI; Instituto Nacional de Estadística, Geografía e Informática), NASA, and academic institutions. Results show that a GIS is a powerful tool that may allow federal, state and municipal policy makers to conduct an initial regional site reconnaissance rapidly. Once potential sites are selected, further characterization must be carried out in order to determine if proposed locations are suitable or not for a sanitary landfill. Based on the SIGAM© software, the Loma de Mejia would not comply with the Mexican Federal Guidelines.

Viral proteases: an emerging therapeutic target.

PubMed

Korant, B D

1988-01-01

Only a few viral diseases are presently treatable because of our limited knowledge of specific viral target molecules. An attractive class of viral molecules toward which chemotherapeutic agents could be aimed are proteases coded by some virus groups such as retro- or picornaviruses (poliomyelitis, common cold virus). The picornavirus enzymes were discovered first, and they have now been characterized by a combination of molecular-genetic and biochemical approaches. Several laboratories have expressed the picornaviral enzymes in heterologous systems and have reported proteolytic activity, as well as the high cleavage fidelity diagnostic of the viral proteases. After dealing with several technical difficulties often encountered in standard genetic engineering approaches, one viral protease is now available to us in quantity and is amendable to mutagenic procedures. The initial outcome of the mutagenesis studies has been the confirmation of our earlier work with inhibitors, which suggested a cysteine active-site class. There is a clustering of active-site residues which may be unique to these viruses. The requirement for an active-site cysteine-histidine pair in combination with detailed information on the viral cleavage sites has permitted design of selective inhibitors with attractive antiviral properties. Future goals include investigation of the structural basis for selective processing and application of the cleavage specificity to general problems in genetic engineering.

Hot Dry Rock Geothermal Energy Development Program. Annual report, fiscal year 1979

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

Cremer, G.M.; Duffield, R.B.; Smith, M.C.

1980-08-01

The Fenton Hill Project is still the principal center for developing methods, equipment, and instrumentation for creating and utilizing HDR geothermal reservoirs. The search for a second site for a similar experimental system in a different geological environment has been intensified, as have the identification and characterization of other HDR areas that may prove suitable for either experimental or commercial development. The Phase I fracture system was enlarged during FY79. Drilling of the injection well of the Phase II system began at Fenton Hill in April 1979. Environmental monitoring of the Fenton Hill area continued through FY79. The environmental studiesmore » indicate that the hot dry rock operations have caused no significant environmental impact. Other supporting activities included rock physics, rock mechanics, fracture mapping, and instrumentation development. Two closely related activities - evaluation of the potential HDR energy resource of the US and the selection of a site for development of a second experimental heat-extraction system generally similar to that at Fenton Hill - have resulted in the collection of geology, hydrology, and heat-flow data on some level of field activity in 30 states. The resource-evaluation activity included reconnaissance field studies and a listing and preliminary characterization of US geothermal areas in which HDR energy extraction methods may be applicable. The selection of Site 2 has taken into account such legal, institutional, and economic factors as land ownership and use, proximity to possible users, permitting and licensing requirements and procedures, environmental issues, areal extent of the geothermal area, and visibility to and apparent interest by potential industrial developers.« less

Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

DOE PAGES

Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang; ...

2015-06-26

Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a k cat/K M value of approximately 2 × 10 6 M -1 s -1 for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typicalmore » AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. Lastly, the structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. We discuss implications for the catalytic mechanism of AHL lactonases.« less

Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

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

Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang

Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a k cat/K M value of approximately 2 × 10 6 M -1 s -1 for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typicalmore » AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. Lastly, the structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. We discuss implications for the catalytic mechanism of AHL lactonases.« less

Study site characterization. Chapter 2

Treesearch

Chris Potter; Richard Birdsey

2008-01-01

This chapter is an overview of the main site characterization requirements at landscape-scale sampling locations. The overview is organized according to multiple "Site Attribute" headings that require descriptions throughout a given study site area, leading ultimately to a sufficient overall site characterization. Guidance is provided to describe the major...

Target-site resistance to neonicotinoids.

PubMed

Crossthwaite, Andrew J; Rendine, Stefano; Stenta, Marco; Slater, Russell

2014-10-01

Neonicotinoid insecticides selectively target the invertebrate nicotinic acetylcholine receptor and disrupt excitatory cholinergic neurotransmission. First launched over 20 years ago, their broad pest spectrum, variety of application methods and relatively low risk to nontarget organisms have resulted in this class dominating the insecticide market with global annual sales in excess of $3.5 bn. This remarkable commercial success brings with it conditions in the field that favour selection of resistant phenotypes. A number of important pest species have been identified with mutations at the nicotinic acetylcholine receptor associated with insensitivity to neonicotinoids. The detailed characterization of these mutations has facilitated a greater understanding of the invertebrate nicotinic acetylcholine receptor.

A Restoration Suitability Index Model for the Eastern Oyster (Crassostrea virginica) in the Mission-Aransas Estuary, TX, USA

PubMed Central

Beseres Pollack, Jennifer; Cleveland, Andrew; Palmer, Terence A.; Reisinger, Anthony S.; Montagna, Paul A.

2012-01-01

Oyster reefs are one of the most threatened marine habitats on earth, with habitat loss resulting from water quality degradation, coastal development, destructive fishing practices, overfishing, and storm impacts. For successful and sustainable oyster reef restoration efforts, it is necessary to choose sites that support long-term growth and survival of oysters. Selection of suitable sites is critically important as it can greatly influence mortality factors and may largely determine the ultimate success of the restoration project. The application of Geographic Information Systems (GIS) provides an effective methodology for identifying suitable sites for oyster reef restoration and removes much of the uncertainty involved in the sometimes trial and error selection process. This approach also provides an objective and quantitative tool for planning future oyster reef restoration efforts. The aim of this study was to develop a restoration suitability index model and reef quality index model to characterize locations based on their potential for successful reef restoration within the Mission-Aransas Estuary, Texas, USA. The restoration suitability index model focuses on salinity, temperature, turbidity, dissolved oxygen, and depth, while the reef quality index model focuses on abundance of live oysters, dead shell, and spat. Size-specific Perkinsus marinus infection levels were mapped to illustrate general disease trends. This application was effective in identifying suitable sites for oyster reef restoration, is flexible in its use, and provides a mechanism for considering alternative approaches. The end product is a practical decision-support tool that can be used by coastal resource managers to improve oyster restoration efforts. As oyster reef restoration activities continue at small and large-scales, site selection criteria are critical for assisting stakeholders and managers and for maximizing long-term sustainability of oyster resources. PMID:22792410

Hydrologic, water-quality, and meteorologic data from selected sites in the Upper Catawba River Basin, North Carolina, January 1993 through March 1994

USGS Publications Warehouse

Jaynes, M.L.

1994-01-01

Hydrologic, water-quality, and meteorologic data were collected from January 1993 through March 1994 as part of a water-quality investigation of the Upper Catawba River Basin, North Carolina. Specific objectives of the investigation were to characterize the water quality of Rhodhiss Lake, Lake Hickory, and three tributary streams, and to calibrate hydrodynamic water-quality models for the two reservoirs. Sampling locations included 11 sites in Rhodhiss Lake, 14 sites in Lake Hickory, and 3 tributary sites. Tributary sites were located at Lower Creek upstream from Rhodhiss Lake and at Upper Little River and Middle Little River upstream from Lake Hickory. During 21 sampling visits, specific conductance, pH, water temperature, dissolved-oxygen concentration, and water transparency were measured at all sampling locations. Water samples were collected for analysis of biochemical oxygen demand, fecal coliform bacteria, hardness, alkalinity, total and volatile suspended solids, suspended sediment, nutrients, total organic carbon, chlorophyll, iron, calcium, and magnesium from three sites in each reservoir and from the three tributary sites. Chemical and particle-size analyses of bottom material from Rhodhiss Lake and Lake Hickory were performed once during the study. At selected locations, automated instruments recorded water level, streamflow, water temperature, solar radiation, and air temperature at 15-minute intervals throughout the study. Hydrologic data presented in the report include monthly water-level statistics and daily mean values of discharge. Diagrams, tables, and statistical summaries of water-quality data are provided. Meteorologic data in the report include monthly precipitation, and daily mean values of solar radiation and air temperature.

Water-quality, bed-sediment, and biological data (October 2009 through September 2010) and statistical summaries of data for streams in the Clark Fork basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2012-01-01

Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork basin. The sampling program was conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2009 through September 2010. Bed-sediment and biota samples were collected once at 13 sites during August 2010. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2009 through September 2010. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

Water-quality, bed-sediment, and biological data (October 2011 through September 2012) and statistical summaries of data for streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2014-01-01

Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork Basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2011 through September 2012. Bed-sediment and biota samples were collected once at 13 sites during August 2012. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2011 through September 2012. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork Basin are provided for the period of record since 1985.

Characterization of Light at Night Data from Select SkyGlowNet Nodes

NASA Astrophysics Data System (ADS)

Flurchick, K. M.; Deal, S.; Foster, C.

2013-05-01

Internet-enabled sky brightness meters (iSBMs) that continuously record and log sky brightness at the zenith have been installed at the prototype nodes of a network called SkyGlowNet. Also logged are time and weather information. These data are polled at a user-defined frequency, typically about every 45 seconds. Although the SkyGlowNetdata are used for various professional scientific studies, they are also useful for independent student research projects. In this case, the data are uploaded to the SkyGlowNetwebsite, initially to a proprietary area where the data for each institution are embargoed for one or two semesters as students conduct research projects with their data. When released from embargo, the data are moved to another area where they can be accessed by all SkyGlowNet participants. In this paper, we describe a student project in which the data collected at two SkyGlowNet sites are characterized. The data streams are parsed into homogenous segments and statistical tools are employed to describe variations observed in the data values. We demonstrate how to differentiate between natural phenomena and the effects of artificial lighting on the brightness of the night sky. In our poster we show how these effects compare between sites as separate as Arizona and North Carolina. We also have experimented with the development of statistical metrics that are used to help categorize sky brightness on select nights, and can nearly automatically provide a characterization of the quality of the night sky for astronomical purposes.

Environmental Definition Program Cross Sectional Analysis; Summary of Data and Analysis Techniques

DTIC Science & Technology

1975-12-31

selected locations, and to characterize cloud and precipitation systems during certain tests and experiments conducted at Wallops Flight Center and at...values. The LWCA was on- site at Wallops Flight Center assisting the special Elight measurements. Other computer programs developed were designed to...550581 N 37025, E Kiev 50024 N 30027 E Simferopol 45001, N 33059! E Perm 58001, N 56018, E Aktyubinsk 50020, N 570131 E Semipalatinsk 50021! N 80015

Exploration of factors affecting the onset and maturation course of follicular lymphoma through simulations of the germinal center.

PubMed

Fenwick, Michael K; Escobedo, Fernando A

2009-08-01

Genetic mutations frequently observed in human follicular lymphoma (FL) B-cells result in aberrant expression of the anti-apoptotic protein bcl-2 and surface immunoglobulins (Igs) which display one or more novel variable (V) region N-glycosylation motifs. In the present study, we develop a simulation model of the germinal center (GC) to explore how these mutations might influence the emergence and clonal expansion of key mutants which provoke FL development. The simulations employ a stochastic method for calculating the cellular dynamics, which incorporates actual IgV region sequences and a simplified hypermutation scheme. We first bring our simulations into agreement with experimental data for well-characterized normal and bcl-2(+) anti-hapten GC responses in mice to provide a model for understanding how bcl-2 expression leads to permissive selection and memory cell differentiation of weakly competitive B-cells. However, as bcl-2 expression in the GC alone is thought to be insufficient for FL development, we next monitor simulated IgV region mutations to determine the emergence times of key mutants displaying aberrant N-glycosylation motifs recurrently observed in human FL IgV regions. Simulations of 26 germline V(H) gene segments indicate that particular IgV regions have a dynamical selective advantage by virtue of the speed with which one or more of their key sites can generate N-glycosylation motifs upon hypermutation. Separate calculations attribute the high occurrence frequency of such IgV regions in FL to an ability to produce key mutants at a fast enough rate to overcome stochastic processes in the GC that hinder clonal expansion. Altogether, these simulations characterize three pathways for FL maturation through positively selected N-glycosylations, namely, via one of two key sites within germline V(H) region gene segments, or via a site in the third heavy chain complementarity-determining region (CDR-H3) that is generated from VDJ recombination.

Stepwise magnetic-geochemical approach for efficient assessment of heavy metal polluted sites

NASA Astrophysics Data System (ADS)

Appel, E.; Rösler, W.; Ojha, G.

2012-04-01

Previous studies have shown that magnetometry can outline the distribution of fly ash deposition in the surroundings of coal-burning power plants and steel industries. Especially the easy-to-measure magnetic susceptibility (MS) is capable to act as a proxy for heavy metal (HM) pollution caused by such kind of point source pollution. Here we present a demonstration project around the coal-burning power plant complex "Schwarze Pumpe" in eastern Germany. Before reunification of West and East Germany huge amounts of HM pollutants were emitted from the "Schwarze Pumpe" into the environment by both fly ash emission and dumped clinker. The project has been conducted as part of the TASK Centre of Competence which aims at bringing new innovative techniques closer to the market. Our project combines in situ and laboratory MS measurements and HM analyses in order to demonstrate the efficiency of a stepwise approach for site assessment of HM pollution around point sources of fly-ash emission and deposition into soil. The following scenario is played through: We assume that the "true" spatial distribution of HM pollution (given by the pollution load index PLI comprising Fe, Zn, Pb, and Cu) is represented by our entire set of 85 measured samples (XRF analyses) from forest sites around the "Schwarze Pumpe". Surface MS data (collected with a Bartington MS2D) and in situ vertical MS sections (logged by an SM400 instrument) are used to determine a qualitative overview of potentially higher and lower polluted areas. A suite of spatial HM distribution maps obtained by random selections of 30 out of the 85 analysed sites is compared to the HM map obtained from a targeted 30-sites-selection based on pre-information from the MS results. The PLI distribution map obtained from the targeted 30-sites-selection shows all essential details of the "true" pollution map, while the different random 30-sites-selections miss important features. This comparison shows that, for the same cost investment, a stepwise combined magnetic-geochemical site assessment leads to a clearly more significant characterization of soil pollution than by a common approach with exclusively random sampling for geochemical analysis, or alternatively to an equal quality result for lower costs.

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

Burton, J. C.; Environmental Research

The Commodity Credit Corporation (CCC) of the U.S. Department of Agriculture (USDA) has entered into an interagency agreement with the U.S. Department of Energy (DOE) under which Argonne National Laboratory provides technical assistance for hazardous waste site characterization and remediation for the CCC/USDA. Carbon tetrachloride is the contaminant of primary concern at sites in Kansas where former CCC/USDA grain storage facilities were located. Argonne applies its QuickSite(reg sign) Expedited Site Characterization (ESC) approach to these former facilities. The QuickSite environmental site characterization methodology is Argonne's proprietary implementation of the ESC process (ASTM 1998). Argonne has used this approach at severalmore » former CCC/USDA facilities in Kansas, including Agenda, Agra, Everest, and Frankfort. The Argonne ESC approach revolves around a multidisciplinary, team-oriented approach to problem solving. The basic features and steps of the QuickSite methodology are as follows: (1) A team of scientists with diverse expertise and strong field experience is required to make the process work. The Argonne team is composed of geologists, geochemists, geophysicists, hydrogeologists, chemists, biologists, engineers, computer scientists, health and safety personnel, and regulatory staff, as well as technical support staff. Most of the staff scientists are at the Ph.D. level; each has on average, more than 15 years of experience. The technical team works together throughout the process. In other words, the team that plans the program also implements the program in the field and writes the reports. More experienced scientists do not remain in the office while individuals with lesser degrees or experience carry out the field work. (2) The technical team reviews, evaluates, and interprets existing data for the site and the contaminants there to determine which data sets are technically valid and can be used in initially designing the field program. A basic mistake sometimes made in the site characterization process is failure to use technically sound available data to form working hypotheses on hydrogeology, contaminant distribution, etc. for initial testing. (3) After assembling and interpreting existing data for the site, the entire technical team visits the site to identify as a group the site characteristics that might prohibit or enhance any particular technological approach. Logistic and community constraints are also identified at this point. (4) After the field visit, the team selects a suite of technologies appropriate to the problem and completes the design of the field program. No one technique works well at all sites, and a suite of techniques is necessary to delineate site features fully. In addition, multiple technologies are employed to increase confidence in conclusions about site features. Noninvasive and minimally invasive technologies are emphasized to minimize risk to the environment, the community, and the staff. In no case is the traditional approach of installing a massive number of monitoring wells followed. A dynamic work plan that outlines the program is produced for the sponsoring and regulatory agencies. The word ''dynamic'' is emphasized because the work plan is viewed as a guide, subject to modification, for the site characterization activity, rather than a document that is absolute and unchangeable. Therefore, the health and safety plan and the quality assurance/quality control plan must be broad and encompass all possible alterations to the plan. The cooperation of the regulating agency is essential in successful implementation of this process. The sponsoring and regulatory agencies are notified if significant changes to the site-specific work plan are necessary. (5) The entire team participates in the technical field program. Several technical activities are undertaken simultaneously. These may range from different surface geophysics investigations to vegetation sampling. Data from the various activities are reduced and interpreted each day by the technical staff. Various computer programs are used to visualize and integrate the data. However, people do the data interpretation and integration, not the computers, which are just one more tool at the site. At the end of the day, the staff members meet, review results, and modify the next day's program as necessary to optimize activities that are generating overlapping or confirming site details. Data are not arbitrarily discarded -- each finding must be explained and understood. Anomalous readings may be due to equipment malfunctions, laboratory error, or the inability of a technique to work in a given setting. The suite of selected technologies is adjusted in the field if necessary. (6) The end result of this process is the optimization of the field activity to produce a high-quality technical product that is cost and time effective.« less

Water-quality assessment of the Ozark Plateaus study unit, Arkansas, Kansas, Missouri, and Oklahoma- habitat data and characteristics at selected sites, 1993-95

USGS Publications Warehouse

Femmer, Suzanne R.

1997-01-01

The characterization of instream and riparian habitat is part of the multiple lines of evidence used by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program to assess the water quality of streams. In the NAWQA Program, integrated physical, chemical, and biological assessments are used to describe water-quality conditions. The instream and riparian habitat data are collected at sites selected for surface-water chemistry analyses and biological assessment. Instream and riparian habitat data are structured in a nested scheme?at sampling reach, segment, and basin scales. The habitat data were collected in the Ozark Plateaus study unit at 41 sites during 1993-95. Thirteen of these sites, representative of selected combinations of physiography, land use, and basin size, have longitudinal, transverse, and quarter point vegetation plot surveys in addition to the Level I survey measurements (reach length, depth, velocity, dominant substrate, embeddedness, and vegetation quarter points, for example) recommended by the NAWQA Program protocols. These habitat data were from onsite measurements, U.S. Geological Survey topographic maps, and a geographic information system. The analyses of the habitat data indicates substantial differences between sites of differing physiography and basin-scale land-use activities. The basins range from 46.4 to 4,318 square kilometers and have stream orders from 2 to 6. All streams studied are a riffle/pool type, and most have cobble that is less than 50 percent embedded as the dominant streambed substrate. Of the three physiographic sections studied, the Boston Mountains have the largest mean segment and sideslope gradients, basin relief, woody species diversity, and stream depths when compared with sites of similar size. Channel sinuosities, mean velocities, and canopy angles are largest at sites in the Springfield Plateau physiographic section. The sites in the Salem Plateau physiographic section have the largest woody vegetation densities and mean channel widths. Sites in basins with predominantly agricultural land use tend to have more open canopies, steeper segment gradients, and more sinuous stream channels than the forested sites. Sites in predominantly forested basins tend to have deeper and swifter flow, smaller channel widths, and more dense woody riparian vegetation (at small basins) than the agricultural sites.

Water quality in Reedy Fork and Buffalo Creek basins in the Greensboro area, North Carolina, 1986-87

USGS Publications Warehouse

Davenport, M.S.

1989-01-01

Water and bottom-sediment samples were collected from April 1986 through September 1987 at 19 sites in Guilford County and the City of Greensboro, North Carolina. Sampling locations included 13 stream sites, two lakes that supply the City of Greensboro with drinking water, two City of Greensboro finished drinking-water filtration plants, and effluent from the two municipal wastewater plants prior to outfall into receiving streams. Water sampling consisted of six surveys during various stages of steady ground-water flow at all sites and high-flow-event sampling during two storms at six sites. Bottom-sediment samples were collected at three sites during two routine sampling surveys. A summary of nearly 22, 000 separate chemical or physical analyses of water samples or bottom sediment is presented and discussed as individual values, ranges of values, or median values with respect to the locations of sampling sites, streamflow conditions, or other information bearing on water-quality conditions under discussion. The results include discussions of general water-quality indicators; major ion, nutrient, and trace-element concentrations; acid and base/neutral extractable organic compounds; volatile organic compounds; and organochlorine and organophosphorus pesticides detected at each sampling site. Loadings of selected constituents are also estimated on a yearly and daily basis. The quality of the raw and finished water, municipal effluents, and streams in the Greensboro area are characterized by using State and Federal water-quality standards. Inorganic constituents most commonly found in excess of standards were iron, copper, zinc, arsenic, phosphorus, manganese, cyanide, and mercury. Relatively few organic compounds were detected; however, those consistently reported were phthalate, thihalomethane, organophosphorus pesticide, benzol, and phenolic compounds. Selected inorganic, physical, and total organic carbon data are used in a Wilcoxon test for two independent variables to statistically compare water-quality characteristics in selected rural, semideveloped and urban basins. During low-flow sampling, the constituents that differed significantly among all sites were calcium, magnesium, and chloride. During low flows, concentrations of orthophosphate, fluoride, sulfate, and TOC differed at the urban site from the rural and semideveloped and urban sites. There were no significant differences among sites in concentrations of sodium, suspended sediment, nickel, zinc, copper, and mercury during low flows. The Wilcoxon test performed on high-flow data indicated that concentrations of TOC, chloride, sulfate, suspended sediment, and nickel were not significantly different among the sites.

Variation in teenage mothers' experiences of child care and other components of welfare reform: selection processes and developmental consequences.

PubMed

Yoshikawa, H; Rosman, E A; Hsueh, J

2001-01-01

Developmental evaluations of the current wave of welfare reform programs present challenges with regard to (1) assessing child outcomes; (2) accounting for heterogeneity among low-income families in both baseline characteristics and involvement in self-sufficiency activities and supports, and (3) development of alternatives to experimental approaches to causal inference. This study (N = 1,079) addresses these challenges by examining effects on 4- to 6-year-old children of different patterns of child care, self-sufficiency activities, and other service utilization indicators among experimental-group mothers in a 16-site welfare reform program. Outcomes in areas of cognitive ability and behavior problems were investigated. The study identified seven subgroups of participants engaging in different patterns of service utilization and activity involvement. A two-stage simultaneous equation methodology was used to account for selection, and effects on child cognitive ability of participation in specific patterns of services and activities were found. For example, children of mothers characterized by high levels of involvement in center-based child care, education, and job training showed higher levels of cognitive ability than children of mothers in groups characterized by high involvement in center-based care and education, or center-based care and job training. In addition, children of mothers in groups with high levels of involvement in any of these activities showed higher levels of cognitive ability than those with low levels of involvement. The bulk of selection effects occurred through site-level differences, rather than family-level socio-economic status or maternal depression indicators. Implications for welfare reform program and policy concerns are discussed.

Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

2015-06-01

To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

Molecular evolution of the betagamma lens crystallin superfamily: evidence for a retained ancestral function in gamma N crystallins?

PubMed

Weadick, Cameron J; Chang, Belinda S W

2009-05-01

Within the vertebrate eye, betagamma crystallins are extremely stable lens proteins that are uniquely adapted to increase refractory power while maintaining transparency. Unlike alpha crystallins, which are well-characterized, multifunctional proteins that have important functions both in and out of the lens, betagamma lens crystallins are a diverse group of proteins with no clear ancestral or contemporary nonlens role. We carried out phylogenetic and molecular evolutionary analyses of the betagamma-crystallin superfamily in order to study the evolutionary history of the gamma N crystallins, a recently discovered, biochemically atypical family suggested to possess a divergent or ancestral function. By including nonlens, betagamma-motif-containing sequences in our analysis as outgroups, we confirmed the phylogenetic position of the gamma N family as sister to other gamma crystallins. Using maximum likelihood codon models to estimate lineage-specific nonsynonymous-to-synonymous rate ratios revealed strong positive selection in all of the early lineages within the betagamma family, with the striking exception of the lineage leading to the gamma N crystallins which was characterized by strong purifying selection. Branch-site analysis, used to identify candidate sites involved in functional divergence between gamma N crystallins and its sister clade containing all other gamma crystallins, identified several positively selected changes at sites of known functional importance in the betagamma crystallin protein structure. Further analyses of a fish-specific gamma N crystallin gene duplication revealed a more recent episode of positive selection in only one of the two descendant lineages (gamma N2). Finally, from the guppy, Poecilia reticulata, we isolated complete gamma N1 and gamma N2 coding sequence data from cDNA and partial coding sequence data from genomic DNA in order to confirm the presence of a novel gamma N2 intron, discovered through data mining of two pufferfish genomes. We conclude that the function of the gamma N family likely resembles the ancestral vertebrate betagamma crystallin more than other betagamma families. Furthermore, owing to the presence of an additional intron in some fish gamma N2 crystallins, and the inferred action of positive selection following the fish-specific gamma N duplication, we suggest that further study of fish gamma N crystallins will be critical in further elucidating possible ancestral functions of gamma N crystallins and any nonstructural role they may have.

Sorption selectivity of birnessite particle edges: a d-PDF analysis of Cd(ii) and Pb(ii) sorption by δ-MnO2 and ferrihydrite.

PubMed

van Genuchten, Case M; Peña, Jasquelin

2016-08-10

Birnessite minerals (layer-type MnO2), which bear both internal (cation vacancies) and external (particle edges) metal sorption sites, are important sinks of contaminants in soils and sediments. Although the particle edges of birnessite minerals often dominate the total reactive surface area, especially in the case of nanoscale crystallites, the metal sorption reactivity of birnessite particle edges remains elusive. In this study, we investigated the sorption selectivity of birnessite particle edges by combining Cd(ii) and Pb(ii) adsorption isotherms at pH 5.5 with surface structural characterization by differential pair distribution function (d-PDF) analysis. We compared the sorption reactivity of δ-MnO2 to that of the nanomineral, 2-line ferrihydrite, which exhibits only external surface sites. Our results show that, whereas Cd(ii) and Pb(ii) both bind to birnessite layer vacancies, only Pb(ii) binds extensively to birnessite particle edges. For ferrihydrite, significant Pb(ii) adsorption to external sites was observed (roughly 20 mol%), whereas Cd(ii) sorption was negligible. These results are supported by bond valence calculations that show comparable degrees of saturation of oxygen atoms on birnessite and ferrihydrite particle edges. Therefore, we propose that the sorption selectivity of birnessite edges follows the same order of that reported previously for ferrihydrite: Ca(ii) < Cd(ii) < Ni(ii) < Zn(ii) < Cu(ii) < Pb(ii).

Melibiose permease and alpha-galactosidase of Escherichia coli: Identification by selective labeling using a T7 RNA polymerase/promoter expression system

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

Pourcher, T.; Bassilana, M.; Sarkar, H.K.

1990-01-23

Identification and selective labeling of the melibiose permease and alpha-galactosidase in Escherichia coli, which are encoded by the melB and melA genes, respectively, have been accomplished by selectively labeling the two gene products with a T7 RNA polymerase expression system. Following generation of a novel EcoRI restriction site in the intergenic sequence between the two genes of the mel operon by oligonucleotide-directed, site-specific mutagenesis, melA and melB were separately inserted into plasmid pT7-6 of the T7 expression system. Expression of melB was markedly enhanced by placing a strong, synthetic ribosome binding site at an optimal distance upstream from the initiationmore » codon of melB. Expression of cloned gene products was characterized functionally and by performing autoradiographic analysis on total cell, inner membrane, and cytoplasmic proteins from cells pulse labeled with (35S)methionine in the presence of rifampicin and resolved by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The results first confirm that alpha-galactosidase is a cytoplasmic protein with an Mr of 50K; in contrast, the membrane-bound melibiose permease is identified as a protein with an apparent Mr of 39K, a value significantly higher than that of 30K previously suggested.« less

Dynamics of human protein kinase Aurora A linked to drug selectivity

DOE PAGES

Pitsawong, Warintra; Buosi, Vanessa; Otten, Renee; ...

2018-06-14

Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinases Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Auroramore » A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome.« less

Dynamics of human protein kinase Aurora A linked to drug selectivity

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

Pitsawong, Warintra; Buosi, Vanessa; Otten, Renee

Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinases Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Auroramore » A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome.« less

Significance of Graphitic Surfaces in Aurodicyanide Adsorption by Activated Carbon: Experimental and Computational Approach

NASA Astrophysics Data System (ADS)

Bhattacharyya, Dhiman; Depci, Tolga; Prisbrey, Keith; Miller, Jan D.

Despite tremendous developments in industrial use of activated carbon (AC) for gold adsorption, specific aurodicyanide [Au(CN)2-] adsorption sites on the carbon have intrigued researchers. The graphitic structure of AC has been well established. Previously radiochemical and now, XPS and Raman characterizations have demonstrated higher site-specific gold adsorption on graphitic edges. Morphological characterizations have revealed the presence of slit-pores (5-10 Å). Molecular-dynamics-simulation (MDS) performed on graphitic slit-pores illustrated gold-cyanide ion-pair preferentially adsorbs on edges. Ab-initio simulations predicted lower barrier for electron sharing in pores with aurodic yanide, indicating tighter bonding than graphitic surface and was well supported by Gibbs energy calculations too. Interaction energy as function of the separation distance indicated tighter bonding of gold cyanide to the graphite edges than water molecules. Selective adsorption of aurodicyanide ion-pair seems to be related to low polarity of gold complex and its accommodation at graphitic edges.

Properties of Subsurface Soil Cores from Four Geologic Provinces Surrounding Mars Desert Research Station, Utah: Characterizing Analog Martian Soil in a Human Exploration Scenario

NASA Technical Reports Server (NTRS)

Stoker, C. R.; Clarke, J. D. A.; Direito, S.; Foing, B.

2011-01-01

The DOMEX program is a NASA-MMAMA funded project featuring simulations of human crews on Mars focused on science activities that involve collecting samples from the subsurface using both manual and robotic equipment methods and analyzing them in the field and post mission. A crew simulating a human mission to Mars performed activities focused on subsurface science for 2 weeks in November 2009 at Mars Desert Research Station near Hanksville, Utah --an important chemical and morphological Mars analog site. Activities performed included 1) survey of the area to identify geologic provinces, 2) obtaining soil and rock samples from each province and characterizing their mineralogy, chemistry, and biology; 3) site selection and reconnaissance for a future drilling mission; 4) deployment and testing of Mars Underground Mole, a percussive robotic soil sampling device; and 5) recording and analyzing how crew time was used to accomplish these tasks. This paper summarizes results from analysis of soil cores

Water-Quality, Bed-Sediment, and Biological Data (October 2005 through September 2006) and Statistical Summaries of Long-Term Data for Streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2007-01-01

Water, bed sediment, and biota were sampled in streams from Butte to below Milltown Reservoir as part of a long-term monitoring program in the upper Clark Fork basin; additional water-quality samples were collected in the Clark Fork basin from sites near Milltown Reservoir downstream to near the confluence of the Clark Fork and Flathead River as part of a supplemental sampling program. The sampling programs were conducted in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water-quality samples were collected periodically at 22 sites from October 2005 through September 2006. Bed-sediment and biological samples were collected once at 12 sites during August 2006. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at all long-term and supplemental monitoring sites from October 2005 through September 2006. Water-quality data include concentrations of selected major ions, trace ele-ments, and suspended sediment. Nutrients also were analyzed in the supplemental water-quality samples. Daily values of suspended-sed-iment concentration and suspended-sediment discharge were determined for four sites, and seasonal daily values of turbidity were determined for four sites. Bed-sediment data include trace-ele-ment concentrations in the fine-grained fraction. Bio-logical data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of long-term water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

10 CFR 960.3-2-3 - Recommendation of sites for characterization.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Recommendation of sites for characterization. 960.3-2-3... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites... President not less than three candidate sites for such characterization. The recommendation decision shall...

10 CFR 960.3-1-4-3 - Site recommendation for characterization.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Site recommendation for characterization. 960.3-1-4-3... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation for characterization. The evidence required to support the recommendation of a site as a candidate...

In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

PubMed Central

Stoltenburg, Regina; Schubert, Thomas; Strehlitz, Beate

2015-01-01

A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment) is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for monitoring the aptamer selection progress. Structural investigations and sequence truncation experiments of the selected aptamer for Protein A led to the conclusion, that a stem-loop structure at its 5’-end including the 5’-primer binding site is essential for aptamer-target binding. Extensive interaction analyses between aptamer and Protein A were performed by methods like surface plasmon resonance, MicroScale Thermophoresis and bead-based binding assays using fluorescence measurements. The binding of the aptamer to its target was thus investigated in assays with immobilization of one of the binding partners each, and with both binding partners in solution. Affinity constants were determined in the low micromolar to submicromolar range, increasing to the nanomolar range under the assumption of avidity. Protein A provides more than one binding site for the aptamer, which may overlap with the known binding sites for immunoglobulins. The aptamer binds specifically to both native and recombinant Protein A, but not to other immunoglobulin-binding proteins like Protein G and L. Cross specificity to other proteins was not found. The application of the aptamer is directed to Protein A detection or affinity purification. Moreover, whole cells of Staphylococcus aureus, presenting Protein A on the cell surface, could also be bound by the aptamer. PMID:26221730

In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A.

PubMed

Stoltenburg, Regina; Schubert, Thomas; Strehlitz, Beate

2015-01-01

A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment) is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for monitoring the aptamer selection progress. Structural investigations and sequence truncation experiments of the selected aptamer for Protein A led to the conclusion, that a stem-loop structure at its 5'-end including the 5'-primer binding site is essential for aptamer-target binding. Extensive interaction analyses between aptamer and Protein A were performed by methods like surface plasmon resonance, MicroScale Thermophoresis and bead-based binding assays using fluorescence measurements. The binding of the aptamer to its target was thus investigated in assays with immobilization of one of the binding partners each, and with both binding partners in solution. Affinity constants were determined in the low micromolar to submicromolar range, increasing to the nanomolar range under the assumption of avidity. Protein A provides more than one binding site for the aptamer, which may overlap with the known binding sites for immunoglobulins. The aptamer binds specifically to both native and recombinant Protein A, but not to other immunoglobulin-binding proteins like Protein G and L. Cross specificity to other proteins was not found. The application of the aptamer is directed to Protein A detection or affinity purification. Moreover, whole cells of Staphylococcus aureus, presenting Protein A on the cell surface, could also be bound by the aptamer.

Selecting chemical and ecotoxicological test batteries for risk assessment of trace element-contaminated soils (phyto)managed by gentle remediation options (GRO).

PubMed

Kumpiene, Jurate; Bert, Valérie; Dimitriou, Ioannis; Eriksson, Jan; Friesl-Hanl, Wolfgang; Galazka, Rafal; Herzig, Rolf; Janssen, Jolien; Kidd, Petra; Mench, Michel; Müller, Ingo; Neu, Silke; Oustriere, Nadège; Puschenreiter, Markus; Renella, Giancarlo; Roumier, Pierre-Hervé; Siebielec, Grzegorz; Vangronsveld, Jaco; Manier, Nicolas

2014-10-15

During the past decades a number of field trials with gentle remediation options (GRO) have been established on trace element (TE) contaminated sites throughout Europe. Each research group selects different methods to assess the remediation success making it difficult to compare efficacy between various sites and treatments. This study aimed at selecting a minimum risk assessment battery combining chemical and ecotoxicological assays for assessing and comparing the effectiveness of GRO implemented in seven European case studies. Two test batteries were pre-selected; a chemical one for quantifying TE exposure in untreated soils and GRO-managed soils and a biological one for characterizing soil functionality and ecotoxicity. Soil samples from field studies representing one of the main GROs (phytoextraction in Belgium, Sweden, Germany and Switzerland, aided phytoextraction in France, and aided phytostabilization or in situ stabilization/phytoexclusion in Poland, France and Austria) were collected and assessed using the selected test batteries. The best correlations were obtained between NH4NO3-extractable, followed by NaNO3-extractable TE and the ecotoxicological responses. Biometrical parameters and biomarkers of dwarf beans were the most responsive indicators for the soil treatments and changes in soil TE exposures. Plant growth was inhibited at the higher extractable TE concentrations, while plant stress enzyme activities increased with the higher TE extractability. Based on these results, a minimum risk assessment battery to compare/biomonitor the sites phytomanaged by GROs might consist of the NH4NO3 extraction and the bean Plantox test including the stress enzyme activities. Copyright © 2014 Elsevier B.V. All rights reserved.

Uncertainty and the Conceptual Site Model

NASA Astrophysics Data System (ADS)

Price, V.; Nicholson, T. J.

2007-12-01

Our focus is on uncertainties in the underlying conceptual framework upon which all subsequent steps in numerical and/or analytical modeling efforts depend. Experienced environmental modelers recognize the value of selecting an optimal conceptual model from several competing site models, but usually do not formally explore possible alternative models, in part due to incomplete or missing site data, as well as relevant regional data for establishing boundary conditions. The value in and approach for developing alternative conceptual site models (CSM) is demonstrated by analysis of case histories. These studies are based on reported flow or transport modeling in which alternative site models are formulated using data that were not available to, or not used by, the original modelers. An important concept inherent to model abstraction of these alternative conceptual models is that it is "Far better an approximate answer to the right question, which is often vague, than the exact answer to the wrong question, which can always be made precise." (Tukey, 1962) The case histories discussed here illustrate the value of formulating alternative models and evaluating them using site-specific data: (1) Charleston Naval Site where seismic characterization data allowed significant revision of the CSM and subsequent contaminant transport modeling; (2) Hanford 300-Area where surface- and ground-water interactions affecting the unsaturated zone suggested an alternative component to the site model; (3) Savannah River C-Area where a characterization report for a waste site within the modeled area was not available to the modelers, but provided significant new information requiring changes to the underlying geologic and hydrogeologic CSM's used; (4) Amargosa Desert Research Site (ADRS) where re-interpretation of resistivity sounding data and water-level data suggested an alternative geologic model. Simple 2-D spreadsheet modeling of the ADRS with the revised CSM provided an improved match to vapor-phase tritium migration. Site-specific monitoring coupled to these alternative CSM's greatly assists in conducting uncertainty assessments. (Work supported by USNRC contract NRC-04-03-061.)

Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro

PubMed Central

Purohit, Nupur K.; Robu, Mihaela; Shah, Rashmi G.; Geacintov, Nicholas E.; Shah, Girish M.

2016-01-01

The existing methodologies for studying robust responses of poly (ADP-ribose) polymerase-1 (PARP-1) to DNA damage with strand breaks are often not suitable for examining its subtle responses to altered DNA without strand breaks, such as UV-damaged DNA. Here we describe two novel assays with which we characterized the interaction of PARP-1 with UV-damaged DNA in vivo and in vitro. Using an in situ fractionation technique to selectively remove free PARP-1 while retaining the DNA-bound PARP-1, we demonstrate a direct recruitment of the endogenous or exogenous PARP-1 to the UV-lesion site in vivo after local irradiation. In addition, using the model oligonucleotides with single UV lesion surrounded by multiple restriction enzyme sites, we demonstrate in vitro that DDB2 and PARP-1 can simultaneously bind to UV-damaged DNA and that PARP-1 casts a bilateral asymmetric footprint from −12 to +9 nucleotides on either side of the UV-lesion. These techniques will permit characterization of different roles of PARP-1 in the repair of UV-damaged DNA and also allow the study of normal housekeeping roles of PARP-1 with undamaged DNA. PMID:26753915

Geochemical and radiological characterization of soils from former radium processing sites

USGS Publications Warehouse

Landa, E.R.

1984-01-01

Soil samples were collected from former radium processing sites in Denver, CO, and East Orange, NJ. Particle-size separations and radiochemical analyses of selected samples showed that while the greatest contents of both 226Ra and U were generally found in the finest (< 45 ??m) fraction, the pattern was not always of progressive increase in radionuclide content with decreasing particle size. Leaching tests on these samples showed a large portion of the 225Ra and U to be soluble in dilute hydrochloric acid. Radon-emanation coefficients measured for bulk samples of contaminated soil were about 20%. Recovery of residual uranium and vanadium, as an adjunct to any remedial action program, appears unlikely due to economic considerations.

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

PubMed Central

Sousa, Vitor C.; Carneiro, Miguel; Ferrand, Nuno; Hey, Jody

2013-01-01

When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus). PMID:23457232

Monitored natural attenuation of chlorinated solvents—Moving beyond reductive dechlorination

USGS Publications Warehouse

Vangelas, Karen M.; Looney, Brian B.; Early, Tom O.; Gilmore, Tyler; Chapelle, Francis H.; Adams, Karen M.; Sink, Claire H.

2006-01-01

Monitored natural attenuation (MNA), while a remedy of choice for many sites, can be challenging when the contaminants are chlorinated solvents. Even with many high-quality technical guidance references available, there continue to be challenges implementing MNA at some chlorinated solvent sites. The U.S. Department of Energy, as one organization facing such challenges, is leading a project that will incorporate developing concepts and tools into the existing toolbox for selecting and implementing MNA as a remediation option at sites with chlorinated solvent contamination. The structure and goals of this project were introduced in an article in the Winter 2004 issue of Remediation (Sink et al., 2004). This article is a summary of the three technical areas being developed through the project: mass balance, enhanced attenuation, and characterization and monitoring supporting the first two areas.

Efficient synthesis of molecularly imprinted polymers with bio-recognition sites for the selective separation of bovine hemoglobin.

PubMed

Zhang, Zulei; Li, Lei

2018-06-01

We developed a facile approach to the construction of bio-recognition sites in silica nanoparticles for efficient separation of bovine hemoglobin based on amino-functionalized silica nanoparticles grafting by 3-aminopropyltriethoxylsilane providing hydrogen bonds with bovine hemoglobin through surface molecularly imprinting technology. The resulting amino-functionalized silica surface molecularly imprinted polymers were characterized using scanning electron microscope, transmission electronic microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and thermogravimetric analysis. Results showed that the as-synthesized imprinted polymers exhibited spherical morphology and favorable thermal stability. The binding adsorption experiments showed that the imprinted polymers can reach equilibrium within 1 h. The Langmuir isotherm and pseudo-second-order kinetic model fitted the adsorption data well. Meanwhile, the imprinted polymers possessed a maximum binding capacity up to 90.3 mg/g and highly selectivity for the recognition of bovine hemoglobin. Moreover, such high binding capacity and selectivity retained after eight cycles, indicating the good stability and reusability of the imprinted polymers. Finally, successful application in the selective recognition of bovine hemoglobin from a real bovine blood sample indicated that the imprinted polymers displayed great potentials in efficient purification and separation of target proteins. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Microanatomic Segregation of Selection by Apoptosis in the Germinal Center

PubMed Central

Mayer, Christian T.; Gazumyan, Anna; Kara, Ervin E.; Gitlin, Alexander D.; Golijanin, Jovana; Viant, Charlotte; Pai, Joy; Oliveira, Thiago Y.; Wang, Qiao; Escolano, Amelia; Medina-Ramirez, Max; Sanders, Rogier W.; Nussenzweig, Michel C.

2018-01-01

B cells undergo rapid cell division and affinity maturation in anatomically distinct sites in lymphoid organs called germinal centers (GCs). Homeostasis is maintained in part by B-cell apoptosis. However, the precise contribution of apoptosis to GC biology and selection is not well defined. We developed apoptosis-indicator mice and used them to visualize, purify, and characterize dying GC B cells. Apoptosis is prevalent in the GC with up to half of all GC B cells dying every 6h. Moreover, programmed cell death is differentially regulated in the light zone (LZ) and the dark zone (DZ): LZ B cells die by default if they are not positively selected, whereas DZ cells die when their antigen receptors are damaged by activation-induced cytidine deaminase (AID). PMID:28935768

Phenotypic evaluation and characterization of 21 industrial Saccharomyces cerevisiae yeast strains.

PubMed

Kong, In Iok; Turner, Timothy Lee; Kim, Heejin; Kim, Soo Rin; Jin, Yong-Su

2018-02-01

Microorganisms have been studied and used extensively to produce value-added fuels and chemicals. Yeasts, specifically Saccharomyces cerevisiae, receive industrial attention because of their well-known ability to ferment glucose and produce ethanol. Thousands of natural or genetically modified S. cerevisiae have been found in industrial environments for various purposes. These industrial strains are isolated from industrial fermentation sites, and they are considered as potential host strains for superior fermentation processes. In many cases, industrial yeast strains have higher thermotolerance, increased resistances towards fermentation inhibitors and increased glucose fermentation rates under anaerobic conditions when compared with laboratory yeast strains. Despite the advantages of industrial strains, they are often not well characterized. Through screening and phenotypic characterization of commercially available industrial yeast strains, industrial fermentation processes requiring specific environmental conditions may be able to select an ideal starting yeast strain to be further engineered. Here, we have characterized and compared 21 industrial S. cerevisiae strains under multiple conditions, including their tolerance to varying pH conditions, resistance to fermentation inhibitors, sporulation efficiency and ability to ferment lignocellulosic sugars. These data may be useful for the selection of a parental strain for specific biotechnological applications of engineered yeast. © FEMS 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Hydrologic and geologic characteristics of the Yucca Mountain site relevant to the performance of a potential repository: Day 1, Las Vegas, Nevada to Pahrump, Nevada: Stop 6A. Keane Wonder Spring and regional groundwater flow in the Death Valley region

USGS Publications Warehouse

Steinkampf, W.C.

2000-01-01

Yucca Mountain, located ~100 mi northwest of Las Vegas, Nevada, has been designated by Congress as a site to be characterized for a potential mined geologic repository for high-level radioactive waste. This field trip will examine the regional geologic and hydrologic setting for Yucca Mountain, as well as specific results of the site characterization program, The first day focuses on the regional seeing with emphasis on current and paleo hydrology, which are both of critical concern for predicting future performance of a potential repository. Morning stops will be in southern Nevada and afternoon stops will be in Death Valley. The second day will be spent at Yucca Mountain. The filed trip will visit the underground testing sites in the "Exploratory Studies Facility" and the "Busted Butte Unsaturated Zone Transport Field Test" plus several surface-based testing sites. Much of the work at the site has concentrated on studies of the unsaturated zone, and element of the hydrologic system that historically has received little attention. Discussions during the second day will comprise selected topics of Yucca Mountain geology, mic hazard in the Yucca Mountain area. Evening discussions will address modeling of regional groundwater flow, the geology and hydrology of Yucca Mountain to the performance of a potential repository. Day 3 will examine the geologic framework and hydrology of the Pahute Mesa-Oasis Valley Groundwater Basin and then will continue to Reno via Hawthorne, Nevada and the Walker Lake area.

Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design

NASA Astrophysics Data System (ADS)

Sheng, Chunquan; Ji, Haitao; Miao, Zhenyuan; Che, Xiaoyin; Yao, Jianzhong; Wang, Wenya; Dong, Guoqiang; Guo, Wei; Lü, Jiaguo; Zhang, Wannian

2009-06-01

Myristoyl-CoA:protein N-myristoyltransferase (NMT) is a cytosolic monomeric enzyme that catalyzes the transfer of the myristoyl group from myristoyl-CoA to the N-terminal glycine of a number of eukaryotic cellular and viral proteins. Recent experimental data suggest NMT from parasites could be a promising new target for the design of novel antiparasitic agents with new mode of action. However, the active site topology and inhibitor specificity of these enzymes remain unclear. In this study, three-dimensional models of NMT from Plasmodium falciparum (PfNMT), Leishmania major (LmNMT) and Trypanosoma brucei (TbNMT) were constructed on the basis of the crystal structures of fungal NMTs using homology modeling method. The models were further refined by energy minimization and molecular dynamics simulations. The active sites of PfNMT, LmNMT and TbNMT were characterized by multiple copy simultaneous search (MCSS). MCSS functional maps reveal that PfNMT, LmNMT and TbNMT share a similar active site topology, which is defined by two hydrophobic pockets, a hydrogen-bonding (HB) pocket, a negatively-charged HB pocket and a positively-charged HB pocket. Flexible docking approaches were then employed to dock known inhibitors into the active site of PfNMT. The binding mode, structure-activity relationships and selectivity of inhibitors were investigated in detail. From the results of molecular modeling, the active site architecture and certain key residues responsible for inhibitor binding were identified, which provided insights for the design of novel inhibitors of parasitic NMTs.

Exploring the site-selective binding of jatrorrhizine to human serum albumin: spectroscopic and molecular modeling approaches.

PubMed

Mi, Ran; Hu, Yan-Jun; Fan, Xiao-Yang; Ouyang, Yu; Bai, Ai-Min

2014-01-03

This paper exploring the site-selective binding of jatrorrhizine to human serum albumin (HSA) under physiological conditions (pH=7.4). The investigation was carried out using fluorescence spectroscopy, UV-vis spectroscopy, and molecular modeling. The results of fluorescence quenching and UV-vis absorption spectra experiments indicated the formation of the complex of HSA-jatrorrhizine. Binding parameters calculating from Stern-Volmer method and Scatchard method were calculated at 298, 304 and 310 K, with the corresponding thermodynamic parameters ΔG, ΔH and ΔS as well. Binding parameters calculating from Stern-Volmer method and Scatchard method showed that jatrorrhizine bind to HSA with the binding affinities of the order 10(4) L mol(-1). The thermodynamic parameters studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the electrostatic interactions play a major role for jatrorrhizine-HSA association. Site marker competitive displacement experiments and molecular modeling calculation demonstrating that jatrorrhizine is mainly located within the hydrophobic pocket of the subdomain IIIA of HSA. Furthermore, the synchronous fluorescence spectra suggested that the association between jatrorrhizine and HSA changed molecular conformation of HSA. Copyright © 2013. Published by Elsevier B.V.

The School Site Planner. Land for Learning. Site Selection, Site Planning, Playgrounds, Recreation, and Athletic Fields.

ERIC Educational Resources Information Center

North Carolina State Dept. of Public Instruction, Raleigh. Div. of School Support.

The selection and planning of sites for school facilities can be critical and difficult due to the varied and complex demands schools must satisfy. This publication addresses the many factors that need consideration during the process of site selection, planning, development, and use. The report examines not only the site selection and planning…

Reconnaissance of chemical and physical characteristics of selected bottom sediments of the Caloosahatchee River and estuary, tributaries, and contiguous bays, Lee County, Florida, July 20-30, 1998

USGS Publications Warehouse

Fernandez, Mario; Marot, M.E.; Holmes, C.W.

1999-01-01

This report summarizes a reconnaissance study, conducted July 20-30, 1998, of chemical and physical characteristics of recently deposited bottom sediments in the Caloosahatchee River and Estuary. Recently deposited sediments were identified using an isotopic chronometer, Beryllium-7 (7Be), a short-lived radioisotope. Fifty-nine sites were sampled in an area that encompasses the Caloosahatchee River (River) about three miles upstream from the Franklin Lock (S-79), the entire tidally affected length of the river (estuary), and the contiguous water bodies of Matlacha Pass, San Carlos Bay, Estero Bay, Tarpon Bay, and Pine Island Sound in Lee County, Florida. Bottom sediments were sampled for 7Be at 59 sites. From the results of the 7Be analysis, 30 sites were selected for physical and chemical analysis. Sediments were analyzed for particle size, total organic carbon (TOC), trace elements, and toxic organic compounds, using semiquantitative methods for trace elements and organic compounds. The semiquantitative scans of trace elements indicated that cadmium, copper, lead, and zinc concentrations, when normalized to aluminum, were above the natural background range at 24 of 30 sites. Particle size and TOC were used to characterize sediment deposition patterns and organic content. Pesticides, polychlorinated biphenyls (PCBs), and carcinogenic polycyclic aromatic hydrocarbons (CaPAHs) were determined at 30 sites using immunoassay analysis. The semiquantitative immunoassay analyses of toxic organic compounds indicated that all of the samples contained DDT, cyclodienes as chlordane (pesticides), and CaPAHs. PCBs were not detected. Based on analyses of the 30 sites, sediments at 10 of these sites were analyzed for selected trace elements and toxic organic compounds, including pesticides, PCBs, and PAHs, using quantitative laboratory procedures. No arsenic or cadmium was detected. Zinc was detected at two sites with concentrations greater than the lower limit of the range of sediment contaminant concentrations that are usually or always associated with adverse effects (Florida Department of Environmental Protection's Sediment Quality Assessment Guidelines). Organochlorine pesticides were detected at four sites at concentrations below the reporting limits; there were no organophosphorus pesticides or PCBs detected. PAHs were detected at eight sites; however, only four sites had concentrations above the reporting limit.

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

PubMed Central

Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

2013-01-01

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

Evolutionary dynamics of Newcastle disease virus

USGS Publications Warehouse

Miller, P.J.; Kim, L.M.; Ip, Hon S.; Afonso, C.L.

2009-01-01

A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an increase in virulence may accelerate the rate of NDV evolution. ?? 2009 Elsevier Inc.

OSIRIS-REx Touch-And-Go (TAG) Navigation Performance

NASA Technical Reports Server (NTRS)

Berry, Kevin; Antreasian, Peter; Moreau, Michael C.; May, Alex; Sutter, Brian

2015-01-01

The Origins Spectral Interpretation Resource identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in 2016 to rendezvous with the near-Earth asteroid (101955) Bennu in late 2018. Following an extensive campaign of proximity operations activities to characterize the properties of Bennu and select a suitable sample site, OSIRIES-REx will fly a Touch-And-Go (TAG) trajectory to the asteroid's surface to obtain a regolith sample. The paper summarizes the mission design of the TAG sequence, the propulsive required to achieve the trajectory, and the sequence of events leading up to the TAG event. The paper will summarize the Monte-Carlo simulation of the TAG sequence and present analysis results that demonstrate the ability to conduct the TAG within 25 meters of the selected sample site and +-2 cms of the targeted contact velocity. The paper will describe some of the challenges associated with conducting precision navigation operations and ultimately contacting a very small asteroid.

OSIRI-REx Touch and Go (TAG) Navigation Performance

NASA Technical Reports Server (NTRS)

Berry, Kevin; Antreasian, Peter; Moreau, Michael C.; May, Alex; Sutter, Brian

2015-01-01

The Origins Spectral Interpretation Resource Identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in 2016 to rendezvous with the near-Earth asteroid (101955) Bennu in late 2018. Following an extensive campaign of proximity operations activities to characterize the properties of Bennu and select a suitable sample site, OSIRIS-REx will fly a Touch-And-Go (TAG) trajectory to the asteroid's surface to obtain a regolith sample. The paper summarizes the mission design of the TAG sequence, the propulsive maneuvers required to achieve the trajectory, and the sequence of events leading up to the TAG event. The paper also summarizes the Monte-Carlo simulation of the TAG sequence and presents analysis results that demonstrate the ability to conduct the TAG within 25 meters of the selected sample site and 2 cm/s of the targeted contact velocity. The paper describes some of the challenges associated with conducting precision navigation operations and ultimately contacting a very small asteroid.

Identification of fecal input sites in spring water by selection and genotyping of multiresistant Escherichia coli.

PubMed

Wicki, Melanie; Karabulut, Fatma; Auckenthaler, Adrian; Felleisen, Richard; Tanner, Marcel; Baumgartner, Andreas

2011-12-01

The localization of fecal input sites is important for water quality management. For this purpose, we have developed a new approach based on a three-step procedure, including a preparatory phase, the screening of multiresistant bacteria using selective agar plates, and a typing phase where selected Escherichia coli isolates are characterized by antibiotic resistance profiles and molecular fingerprinting techniques (pulsed-field gel electrophoresis [PFGE]). These two well-known source tracking methods were combined in order to reduce cost and effort. This approach was successfully applied under field conditions in a study area located in the north-western part of Switzerland. E. coli isolates from spring water and surface water samples collected in this area were screened with selective agar plates. In this way, 21 different groups, each consisting of strains with the same pattern of antibiotic resistance, were found. Of these, four groups were further analyzed using PFGE. Strains with identical PFGE profiles were detected repeatedly, demonstrating the suitability of this method for the localization of fecal input sites over an extended period of time. Identical PFGE patterns of strains detected in water from two different springs were also found in the stream flowing through the study area. These results demonstrated the applicability of the new approach for the examination of incidents of fecal contamination in drinking water. The advantages of the described approach over genotyping methods currently being used to identify sources of fecal contaminants are a reduction in time, costs, and the effort required. Identical isolates could be identified without the construction of large libraries.

Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints

PubMed Central

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

“Trojan” is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules. PMID:25803627

Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints.

PubMed

Petrov, Petar; Syrjänen, Riikka; Smith, Jacqueline; Gutowska, Maria Weronika; Uchida, Tatsuya; Vainio, Olli; Burt, David W

2015-01-01

"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.

Improving Site Characterization for Rock Dredging using a Drilling Parameter Recorder and the Point Load Test

DTIC Science & Technology

1994-09-01

materials. Also, available data from drilling rates in the mining and tunneling industries (Howarth and Rowlands 1987, Somerton 1959) indicate a...selected uniform natural rock materials and several man -made rock simulants were used to obtain drilling parameter records for materials of known...Dredging Seminar, Atlantic City, NJ, May 1993. Western Dredging Association (WEDA) and Texas A&M University. Somerton , W. H. (1959). "A laboratory study of

Incorporation of High Energy Materials Into High Density Polymers

DTIC Science & Technology

1987-09-21

and the pure graft copolymer was isolated by selective solvent extraction. 5 f. Isolation of pure Qraft copolymers. The isolation of pure EPDM -g-PS...characterized, such as EPDM -g-PST and EPDM -g-PMST. Two methods of synthesis were successful: a macromonomer (a polymer containing a polymerizab head group) was...copolymerized with ethylene and propylene to lead to the final product, and chlorination of a commercial EPDM allowed the chlorinated sites to serve as

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... developed, and on the progress of waste form and waste package research and development. The semiannual... of site characterization will be established. Other topics related to site characterization shall...

Parmodulins inhibit thrombus formation without inducing endothelial injury caused by vorapaxar.

PubMed

Aisiku, Omozuanvbo; Peters, Christian G; De Ceunynck, Karen; Ghosh, Chandra C; Dilks, James R; Fustolo-Gunnink, Susanna F; Huang, Mingdong; Dockendorff, Chris; Parikh, Samir M; Flaumenhaft, Robert

2015-03-19

Protease-activated receptor-1 (PAR1) couples the coagulation cascade to platelet activation during myocardial infarction and to endothelial inflammation during sepsis. This receptor demonstrates marked signaling bias. Its activation by thrombin stimulates prothrombotic and proinflammatory signaling, whereas its activation by activated protein C (APC) stimulates cytoprotective and antiinflammatory signaling. A challenge in developing PAR1-targeted therapies is to inhibit detrimental signaling while sparing beneficial pathways. We now characterize a novel class of structurally unrelated small-molecule PAR1 antagonists, termed parmodulins, and compare the activity of these compounds to previously characterized compounds that act at the PAR1 ligand-binding site. We find that parmodulins target the cytoplasmic face of PAR1 without modifying the ligand-binding site, blocking signaling through Gαq but not Gα13 in vitro and thrombus formation in vivo. In endothelium, parmodulins inhibit prothrombotic and proinflammatory signaling without blocking APC-mediated pathways or inducing endothelial injury. In contrast, orthosteric PAR1 antagonists such as vorapaxar inhibit all signaling downstream of PAR1. Furthermore, exposure of endothelial cells to nanomolar concentrations of vorapaxar induces endothelial cell barrier dysfunction and apoptosis. These studies demonstrate how functionally selective antagonism can be achieved by targeting the cytoplasmic face of a G-protein-coupled receptor to selectively block pathologic signaling while preserving cytoprotective pathways. © 2015 by The American Society of Hematology.

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease

PubMed Central

Romero-Garmendia, Irati; Jauregi-Miguel, Amaia; Plaza-Izurieta, Leticia; Cros, Marie-Pierre; Legarda, Maria; Irastorza, Iñaki; Herceg, Zdenko; Fernandez-Jimenez, Nora

2018-01-01

The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models. PMID:29748492

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease.

PubMed

Romero-Garmendia, Irati; Garcia-Etxebarria, Koldo; Hernandez-Vargas, Hector; Santin, Izortze; Jauregi-Miguel, Amaia; Plaza-Izurieta, Leticia; Cros, Marie-Pierre; Legarda, Maria; Irastorza, Iñaki; Herceg, Zdenko; Fernandez-Jimenez, Nora; Bilbao, Jose Ramon

2018-05-10

The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.

Morpho-chemical characterization and surface properties of carcinogenic zeolite fibers.

PubMed

Mattioli, Michele; Giordani, Matteo; Dogan, Meral; Cangiotti, Michela; Avella, Giuseppe; Giorgi, Rodorico; Dogan, A Umran; Ottaviani, Maria Francesca

2016-04-05

Erionite belonging to the zeolite family is a human health-hazard, since it was demonstrated to be carcinogenic. Conversely, offretite family zeolites were suspected carcinogenic. Mineralogical, morphological, chemical, and surface characterizations were performed on two erionites (GF1, MD8) and one offretite (BV12) fibrous samples and, for comparison, one scolecite (SC1) sample. The specific surface area analysis indicated a larger availability of surface sites for the adsorption onto GF1, while SC1 shows the lowest one and the presence of large pores in the poorly fibrous zeolite aggregates. Selected spin probes revealed a high adsorption capacity of GF1 compared to the other zeolites, but the polar/charged interacting sites were well distributed, intercalated by less polar sites (Si-O-Si). MD8 surface is less homogeneous and the polar/charged sites are more interacting and closer to each other compared to GF1. The interacting ability of BV12 surface is much lower than that found for GF1 and MD8 and the probes are trapped in small pores into the fibrous aggregates. In comparison with the other zeolites, the non-carcinogenic SC1 shows a poor interacting ability and a lower surface polarity. These results helped to clarify the chemical properties and the surface interacting ability of these zeolite fibers which may be related to their carcinogenicity. Copyright © 2015 Elsevier B.V. All rights reserved.

Reconnaissance Strategy for Seep Chemosynthetic Communities in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

MacDonald, I. R.; Roberts, H. H.; Fisher, C. R.; Bernard, B. B.; Joye, S.; Carney, R.; Hunt, J.; Shedd, W.

2007-05-01

The Continental Slope of the Gulf of Mexico hosts diverse chemosynthetic communities at oil and gas seeps. Exploration is needed to extend knowledge of the Gulf of Mexico chemosynthetic ecosystem in the zones anticipated to receive energy exploration and production activities over the coming decades. A nested survey approach can be used to identify representative sampling sites within this vast offshore area. Potential sites where chemosynthetic community could occur are selected on the basis geophysical, geochemical, and satellite remote-sensing indicators. Photo-reconnaissance using cost-effective camera systems is then used to confirm the presences or absence of chemosynthetic communities at high-probability sites. Follow-up sampling can then proceed with submersibles or ROVs to acquire tissue and or geochemical samples. However, because access is limited, submersible dives may not be possible at all sites. Two examples of this approach have recently been applied in the northern and southern Gulf of Mexico, respectively. We compared community characterizations obtained from the initial reconnaissance with more detailed characterizations forthcoming from submersible sampling. Our results show that major differences in community type and geochemical substrata are evident from preliminary reconnaissance, while details of animal densities and species compositions require targeted sampling with submersibles. However, given the limited access to submersibles, cost-effective surveys with deep-sea camera systems would greatly expand understanding of the zoogeography of chemosynthetic fauna in the Gulf of Mexico and Caribbean Sea.

SMARTE'S SITE CHARACTERIZATION TOOL

EPA Science Inventory

Site Characterization involves collecting environmental data to evaluate the nature and extent of contamination. Environmental data could consist of chemical analyses of soil, sediment, water or air samples. Typically site characterization data are statistically evaluated for thr...

40 CFR 761.247 - Sample site selection for pipe segment removal.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Natural Gas Pipeline: Selecting Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.247 Sample site selection for pipe segment removal. (a) General. (1) Select the pipe... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Sample site selection for pipe segment...

School Site Selection and Approval Guide.

ERIC Educational Resources Information Center

California State Dept. of Education, Sacramento. Div. of School Facilities Planning.

This guide is designed to assist school districts in selecting school sites that provide both a safe and supportive environment for the instructional program and the learning process, and gain state approval for the selected sites. The guide includes a set of selection criteria that have proven helpful to site selection teams, information about…

40 CFR 761.247 - Sample site selection for pipe segment removal.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Sample site selection for pipe segment... Natural Gas Pipeline: Selecting Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.247 Sample site selection for pipe segment removal. (a) General. (1) Select the pipe...

Predominant-period site classification for response spectra prediction equations in Italy

USGS Publications Warehouse

Di Alessandro, Carola; Bonilla, Luis Fabian; Boore, David M.; Rovelli, Antonio; Scotti, Oona

2012-01-01

We propose a site‐classification scheme based on the predominant period of the site, as determined from the average horizontal‐to‐vertical (H/V) spectral ratios of ground motion. Our scheme extends Zhao et al. (2006) classifications by adding two classes, the most important of which is defined by flat H/V ratios with amplitudes less than 2. The proposed classification is investigated by using 5%‐damped response spectra from Italian earthquake records. We select a dataset of 602 three‐component analog and digital recordings from 120 earthquakes recorded at 214 seismic stations within a hypocentral distance of 200 km. Selected events are in the moment‐magnitude range 4.0≤Mw≤6.8 and focal depths from a few kilometers to 46 km. We computed H/V ratios for these data and used them to classify each site into one of six classes. We then investigate the impact of this classification scheme on empirical ground‐motion prediction equations (GMPEs) by comparing its performance with that of the conventional rock/soil classification. Although the adopted approach results in only a small reduction of the overall standard deviation, the use of H/V spectral ratios in site classification does capture the signature of sites with flat frequency‐response, as well as deep and shallow‐soil profiles, characterized by long‐ and short‐period resonance, respectively; in addition, the classification scheme is relatively quick and inexpensive, which is an advantage over schemes based on measurements of shear‐wave velocity.

Selected Ground-Water Data for Yucca Mountain Region, Southern Nevada and Eastern California, Through December 1992

USGS Publications Warehouse

La Camera, Richard J.; Westenburg, Craig L.

1994-01-01

Tne U.S. Geological Survey. in support of the U.S. Department of Energy, Yucca Mountain Site- Characterization Project, collects, compiles, and summarizes water-resource data in the Yucca Mountain region. The data are collected to document the historical and current condition of ground-water resources, to detect and document changes in those resources through time, and to allow assessments of ground-water resources during investigations to determine the potential suitability of Yucca Mountain for storing high-level nuclear waste. Data on ground-water levels at 36 sites, ground- water discharge at 6 sites, ground-water quality at 19 sites, and ground-water withdrawals within Crater Fiat, Jackass Flats, Mercury Valley, and the Amargosa Desert are presented. Data on ground-water levels, discharges, and withdrawals collected by other agencies or as part of other programs are included to further indicate variations through time. A statistical summary of ground-water levels and median annual ground-water withdrawals in Jackass Flats is presented. The statistical summary includes the number of measurements, the maximum, minimum, and median water-level altitudes, and the average deviation of a11 water-level altitudes for selected baseline periods and for calendar year 1992. Data on ground-water quality are compared to established, proposed, or tentative primary and secondary drinking-water standards, and measures which exceeded those standards are listed for 18 sites. Detected organic compounds for which established, proposed, or tentative drinking-water standards exist also are listed.

Landscape characteristics of fragmented shrubsteppe habitats and breeding passerine birds

USGS Publications Warehouse

Knick, Steven T.; Rotenberry, J.T.

1995-01-01

We examined the influence of local and landscape-level attributes of fragmented habitats in shrubsteppe habitats on the breeding distributions of Sage (Amphispiza belli) and Brewer's (Spizella breweri) Sparrows, Sage Thrashers (Oreoscoptes montanus), Horned Larks (Eremophila alpestris), and Western Meadowlarks (Sturnella neglecta) in the Snake River Plains of southwestern Idaho. We developed habitat (resource) selection models for each species by combining bird counts conducted from 1991 through 1933 with local vegetation characteristics and landscape attributes derived from satellite imagery. Site selection by shrubsteppe species (Sage and Brewer's Sparrows, and Sage Thrashers) depended on local vegetation cover and landscape features, such as the patch size of shrub habitats or the spatial similarity of sites. Marginal sites for these species (with species present in one of three years) were intermediate between unoccupied (never present) and occupied sites along environmental gradients characterized by increasing size of shrub habitat patches and total shrub cover and by decreasing disturbance. Horned Larks and Western Meadowlarks, typical grassland species, were not sensitive to landscape features, and their occupancy depended on the amount of grassland or shrub cover. In contrast to shrubsteppe species, sites that varied by occupancy rates of Western Meadowlarks did not significantly differ in vegetation or landscape components. Our results demonstrate that fragmentation of shrubsteppe significantly influenced the presence of shrub-obligate species. Because of restoration difficulties, the disturbance of semiarid shrubsteppe may cause irreversible loss of habitat and significant long-term consequences for the conservation of shrub-obligate birds.

40 CFR 280.63 - Initial site characterization.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 26 2010-07-01 2010-07-01 false Initial site characterization. 280.63... Hazardous Substances § 280.63 Initial site characterization. (a) Unless directed to do otherwise by the implementing agency, owners and operators must assemble information about the site and the nature of the...

Toward the identification of the cardiac cGMP inhibited-phosphodiesterase catalytic site

NASA Astrophysics Data System (ADS)

Fossa, Paola; Boggia, Raffaella; Mosti, Luisa

1998-07-01

Cyclic nucleotide phosphodiesterases (PDEs) comprise a complex group of enzymes; five major PDE families or classes with distinctive properties have been identified. Among these a great deal of interest has recently been focused on the so called cGMP-inhibited low Km cAMP phosphodiesterase (cGI PDE) or PDE III. A number of positive inotropic agents, including the well-known milrinone, display a specific inhibition of PDE III as primary mechanism of action. Recent studies have been carried out to develop a pharmacophore model of the PDE III active site. We therefore performed molecular modelling and 3D-SAR studies so as to better define structural requirements for potent and selective enzymatic inhibition. The DISCO (DIStance COmparison) strategy has been applied on a set of compounds taken from literature and a milrinone analogue previously synthesized by us, all of which are characterized by a marked inotropic effect but with varying degrees of enzyme selectivity. A common pharmacophoric model was derived, validated and considered as starting point to perform a 3D-SAR study using the GRID force field and PCA (Principal Component Analysis) with the aim of rationally designing more selective inhibitors. This paper presents the results of this theoretical approach.

[Content of selected metals in forest fruits depending on the harvest site].

PubMed

Rusinek, Elzbieta; Sembratowicz, Iwona; Ognik, Katarzyna

2008-01-01

Contents of selected metals (Pb, Cd, Cu, Zn, Fe, Mn) were determined in samples of forest fruits: blueberry, raspberry and wild strawberry harvested in Lublin region from areas considered as potentially not exposed to pollution (Skierbieszów Landscape Park) and potentially polluted areas (Cement Factory Rejowiec S.A.). Analyzed fruits originating from stands more exposed to pollution were characterized by higher lead (except from raspberry) as well as other metals contents than those from Krasiczyn commune. Among studied fruits, blueberry was distinguished by the lowest contents of Pb, Zn, Fe, Mn, wild strawberry contained the highest levels of Pb, Zn and Mn. Cadmium content in analyzed plant materials was high.

GO-Cu7S4 catalyzed ortho-aminomethylation of phenol derivatives with N,N-dimethylbenzylamines: site-selective oxidative CDC.

PubMed

Gupta, Sonu; Chandna, Nisha; Dubey, Pooja; Singh, Ajai K; Jain, Nidhi

2018-06-21

Copper chalcogenide nanoparticles (Cu7S4) supported on graphene oxide (GO) have been synthesized for the first time from Cu2S, and used as highly efficient heterogeneous catalysts for oxidative ortho-selective C-H aminomethylation of phenols with N,N-dimethylbenzylamines. The NPs (30-80 nm) have been characterized by HRTEM, SEM-EDX, PXRD, FTIR, Raman, ICP-AES and XPS analyses. The NP catalyzed sp2-sp3 cross dehydrogenative coupling (CDC) features a broad substrate scope, excellent functional group tolerance, high yields, use of an inexpensive and reusable copper catalyst, mild conditions, and no need for pre-functionalization of substrates.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, John R.

1986-01-01

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, J.R.

1984-10-10

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

On-line LC-MS approach combining collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced species for the trace-level characterization of proteins with post-translational modifications.

PubMed

Wu, Shiaw-Lin; Hühmer, Andreas F R; Hao, Zhiqi; Karger, Barry L

2007-11-01

We have expanded our recent on-line LC-MS platform for large peptide analysis to combine collision-induced dissociation (CID), electron-transfer dissociation (ETD), and CID of an isolated charge-reduced (CRCID) species derived from ETD to determine sites of phosphorylation and glycosylation modifications, as well as the sequence of large peptide fragments (i.e., 2000-10,000 Da) from complex proteins, such as beta-casein, epidermal growth factor receptor (EGFR), and tissue plasminogen activator (t-PA) at the low femtomol level. The incorporation of an additional CID activation step for a charge-reduced species, isolated from ETD fragment ions, improved ETD fragmentation when precursor ions with high m/z (approximately >1000) were automatically selected for fragmentation. Specifically, the identification of the exact phosphorylation sites was strengthened by the extensive coverage of the peptide sequence with a near-continuous product ion series. The identification of N-linked glycosylation sites in EGFR and an O-linked glycosylation site in t-PA were also improved through the enhanced identification of the peptide backbone sequence of the glycosylated precursors. The new strategy is a good starting survey scan to characterize enzymatic peptide mixtures over a broad range of masses using LC-MS with data-dependent acquisition, as the three activation steps can provide complementary information to each other. In general, large peptides can be extensively characterized by the ETD and CRCID steps, including sites of modification from the generated, near-continuous product ion series, supplemented by the CID-MS2 step. At the same time, small peptides (e.g.,

Archaeological Investigations in the Upper Tombigbee Valley, Mississippi: Phase I. Volume 1.

DTIC Science & Technology

1983-01-01

6.10 Site 221T563: Selected c,ramics; Alexander Incised .............................. 6.90 6.91 6.11 Site 221T563: Selected ceramics: Alexander... Incised .............................. 6.92 6.93 6.12 Site 221T563: Selected ceramics: Alexander Incised .............................. 6.94 6.95 6.13 Site...221T563: Selected ceramics: Alexander Incised .............................. 6.96 6.9i 6.14 Site 221T563: Selected ceramics: Alexander Incised

Environmental cleanup: The challenge at the Hanford Site, Washington, USA

NASA Astrophysics Data System (ADS)

Gray, Robert H.; Becker, C. Dale

1993-07-01

Numerous challenges face those involved with developing a coordinated and consistent approach to cleaning up the US Department of Energy’s (DOE) Hanford Site in southeastern Washington. These challenges are much greater than those encountered when the site was selected and the world’s first nuclear complex was developed almost 50 years ago. This article reviews Hanford’s history, operations, waste storage/disposal activities, environmental monitoring, and today’s approach to characterize and clean up Hanford under a Federal Facility Agreement and Consent Order, signed by DOE, the Environmental Protection Agency, and the Washington Sate Department of Ecology. Although cleanup of defense-related waste at Hanford holds many positive benefits, negative features include high costs to the US taxpayer, numerous uncertainties concerning the technologies to be employed and the risks involved, and the high probability that special interest groups and activists at large will never be completely satisfied. Issues concerning future use of the site, whether to protect and preserve its natural features or open it to public exploitation, remain to be resolved.

Precipitation, atmospheric deposition, streamflow, and water-quality data from selected sites in the city of Charlotte and Mecklenburg County, North Carolina, 1997–98

USGS Publications Warehouse

Sarver, Kathleen M.; Hazell, W.F.; Robinson, J.B.

1999-01-01

Precipitation data were collected at 46 precipitation sites and 3 atmospheric deposition sites, and hydrologic data were collected at 6 stream sites in the vicinity of Charlotte and Mecklenburg County, North Carolina, from July 1997 through September 1998. Data were collected to identify the type, concentration, and amount of nonpoint-source stormwater runoff in the study area. The data collected include measurements of precipitation; streamflow; physical characteristics, such as water temperature, pH, specific conductance, biochemical oxygen demand, oil and grease, and suspended-sediment concentrations; and concentrations of nutrients, metals and minor constituents, and organic compounds. These data will provide information needed for (1) planned watershed simulation models, (2) estimates of nonpoint-source constituent loadings to the Catawba River, and (3) characterization of water quality in relation to basin conditions. Streamflow and rainfall data have been used to provide early warnings of possible flooding.

Water-Quality, Bed-Sediment, and Biological Data (October 2007 through September 2008) and Statistical Summaries of Long-Term Data for Streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2009-01-01

Water, bed sediment, and biota were sampled in streams from Butte to near Missoula as part of a long-term monitoring program in the upper Clark Fork basin; additional water samples were collected in the Clark Fork basin from sites near Missoula downstream to near the confluence of the Clark Fork and Flathead River as part of a supplemental sampling program. The sampling programs were conducted in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 23 sites from October 2007 through September 2008. Bed-sediment and biota samples were collected once at 13 sites during August 2008. This report presents the analytical results and quality assurance data for water-quality, bed-sediment, and biota samples collected at all long-term and supplemental monitoring sites from October 2007 through September 2008. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at sites where seasonal daily values of turbidity were being determined and at Clark Fork above Missoula. Nutrients also were analyzed at all the supplemental water-quality sites, except for Clark Fork Bypass, near Bonner. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites, and seasonal daily values of turbidity were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of long-term water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

Signatures of sex-antagonistic selection on recombining sex chromosomes.

PubMed

Kirkpatrick, Mark; Guerrero, Rafael F

2014-06-01

Sex-antagonistic (SA) selection has major evolutionary consequences: it can drive genomic change, constrain adaptation, and maintain genetic variation for fitness. The recombining (or pseudoautosomal) regions of sex chromosomes are a promising setting in which to study SA selection because they tend to accumulate SA polymorphisms and because recombination allows us to deploy the tools of molecular evolution to locate targets of SA selection and quantify evolutionary forces. Here we use coalescent models to characterize the patterns of polymorphism expected within and divergence between recombining X and Y (or Z and W) sex chromosomes. SA selection generates peaks of divergence between X and Y that can extend substantial distances away from the targets of selection. Linkage disequilibrium between neutral sites is also inflated. We show how the pattern of divergence is altered when the SA polymorphism or the sex-determining region was recently established. We use data from the flowering plant Silene latifolia to illustrate how the strength of SA selection might be quantified using molecular data from recombining sex chromosomes. Copyright © 2014 by the Genetics Society of America.

Synthesis and characterization of aluminosilicate catalyst impregnated by nickel oxide

NASA Astrophysics Data System (ADS)

Maulida, Iffana Dani; Sriatun, Taslimah

2015-09-01

Aluminosilicate as a catalyst has been synthesized by pore-engineering using CetylTrimethylAmmonium-Bromide (CTAB) as templating agent. It can produce bigger aluminosilicate pore therefore it will be more suitable for bulky molecule. The aims of this research are to synthesize aluminosilicate supported by Nickel, using CTAB surfactant as templating agent for larger pore radius than natural zeolite and characterize the synthesis product, consist of total acid sites and surface area characteristic. This research has been done with following steps. First, making sodium silicate and sodium aluminate. Second, aluminosilicate was synthesized by direct methods, calcined at 550, 650 and 750°C variation temperature, characterized product by X-RD and FTIR spectrometer. Third, NiCl2 was impregnated to the aluminosilicate that has the best cristallinity and main TO4 functional groups product (550 sample). Variation of NiCl2:aluminosilicate (w/w) ratio were 25%:75%, 50%:50% and 75%:25%. Last but not least characterization of catalytic properties was performed. It comprised total acidity test (gravimetric method) and Surface Area Analyzer. The result shows that the product synthesized by direct method at 550oC calcination temperature has the best cristallinity and main functional groups of TO4. The highest total acid sites was 31.6 mmole/g (Imp-A sample). Surface Area Analyzer shows that Imp-B sample has the best pore distribution and highest total pore volume and specific surface area with value 32.424 cc/g and 46.8287 m2/g respectively. We can draw the conclusion that the most potential catalyst is Imp-A sample compared to Imp-B and Imp-C because it has the highest total acid sites. However the most effective catalyst used for product selectivity was Imp-B sample among all samples.

Selective modification of halloysite lumen with octadecylphosphonic acid: new inorganic tubular micelle.

PubMed

Yah, Weng On; Takahara, Atsushi; Lvov, Yuri M

2012-01-25

Selective fatty acid hydrophobization of the inner surface of tubule halloysite clay is demonstrated. Aqueous phosphonic acid was found to bind to alumina sites at the tube lumen and did not bind the tube's outer siloxane surface. The bonding was characterized with solid-state nuclear magnetic resonance ((29)Si, (13)C, (31)P NMR), Fourier transform infrared (FTIR), and X-ray photoelectron spectroscopy. NMR and FTIR spectroscopy of selectively modified tubes proved binding of octadecylphosphonic acid within the halloysite lumen through bidentate and tridentate P-O-Al linkage. Selective modification of the halloysite clay lumen creates an inorganic micelle-like architecture with a hydrophobic aliphatic chain core and a hydrophilic silicate shell. An enhanced capacity for adsorption of the modified halloysite toward hydrophobic derivatives of ferrocene was shown. This demonstrates that the different inner and outer surface chemistry of clay nanotubes can be used for selective modification, enabling different applications from water purification to drug immobilization and controlled release. © 2011 American Chemical Society

A Benthic Community Index for streams in the Northern Lakes and Forests Ecoregion

USGS Publications Warehouse

Butcher, Jason T.; Stewart, Paul M.; Simon, Thomas P.

2003-01-01

Encompassing the northern glaciated section of the Midwest United States, the Northern Lakes and Forests Ecoregion is characterized by mixed conifer and deciduous forests and wetlands. Sites were randomly selected in the ecoregion using the Environmental Protection Agency's Environmental Monitoring and Assessment Program designed to develop an index of biotic integrity for wadeable streams. Macroinvertebrates were sampled during the fall of 1998 and 1999 using a multi-habitat, composite-sample method. Two hundred forty-six invertebrate taxa in 97 families were collected from 94 sites. Ten of 42 candidate metrics satisfied metric selection criteria, including six structural metrics (number of Ephemeroptera taxa, number of Diptera taxa, richness, Shannon-Wiener diversity, percent Trichoptera abundance, and percent Crustacea and Mollusca abundance), two functional metrics (number of Filterer taxa and number of Scraper taxa), and two conditional metrics (number of Ephemeroptera, Trichoptera, and Plecoptera taxa and Hilsenhoff Biotic Index). These metrics were used to develop a Benthic Community Index to assess the biological integrity of wadeable streams in the ecoregion. Index values ranged from 10 to 50, and scores from impaired sites were significantly different than non-impaired sites (P<0.001). Index values were divided into three narrative interpretations of biological integrity (poor, fair, and good). After further testing, the index may provide a useful biological assessment tool for resource managers in the ecoregion.

Two cation exchange models for direct and inverse modelling of solution major cation composition in equilibrium with illite surfaces

NASA Astrophysics Data System (ADS)

Tournassat, Christophe; Gailhanou, Hélène; Crouzet, Catherine; Braibant, Gilles; Gautier, Anne; Lassin, Arnault; Blanc, Philippe; Gaucher, Eric C.

2007-03-01

Na/K, Na/Ca and Na/Mg exchange isotherms were performed on the fine fraction (<2 μm) of Imt-2 illite samples at a total normality of about 0.005 mol/L in anionic chloride medium. The derived selectivity coefficients for Na/K, Na/Ca and Na/Mg were found to vary as a function of the exchanger composition and compared well with the data collected in the literature for similar experimental conditions. Two models were built to reproduce the data: the first was a multi(2)-site model with constant Gaines and Thomas selectivity coefficients; the second was a one-site model taking into account surface species activity coefficients. The results of the models were in rather good agreement with both our data and literature data. The multi-site model proved to be efficient in predicting the exchanger composition as a function of the Na/Ca/Mg/K concentrations in solution, whereas the one-site model proved to be a better approach to derive the Na/Ca/Mg/K concentrations in solution based on the knowledge of the exchanger composition and the total normality of the solution. The interest of this approach is illustrated by the need for major cation solute concentration predictions in compacted clay for the characterization of nuclear deep disposal host rock repositories.

SEMINAR PUBLICATION: SITE CHARACTERIZATION FOR SUBSURFACE REMEDIATION

EPA Science Inventory

This seminar publication provides a comprehensive approach to site characterization for subsurface remediation. Chapter 1 describes a methodology for integrating site characterization with subsurface remediation. The rest of the handbook is divided into three parts. Part I covers...

Deployment Effects of Marin Renewable Energy Technologies

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

Brian Polagye; Mirko Previsic

2010-06-17

Given proper care in siting, design, deployment, operation and maintenance, marine and hydrokinetic technologies could become one of the more environmentally benign sources of electricity generation. In order to accelerate the adoption of these emerging hydrokinetic and marine energy technologies, navigational and environmental concerns must be identified and addressed. All developing hydrokinetic projects involve a wide variety of stakeholders. One of the key issues that site developers face as they engage with this range of stakeholders is that many of the possible conflicts (e.g., shipping and fishing) and environmental issues are not well-understood, due to a lack of technical certainty.more » In September 2008, re vision consulting, LLC was selected by the Department of Energy (DoE) to apply a scenario-based approach to the emerging wave and tidal technology sectors in order to evaluate the impact of these technologies on the marine environment and potentially conflicting uses. The project’s scope of work includes the establishment of baseline scenarios for wave and tidal power conversion at potential future deployment sites. The scenarios will capture variations in technical approaches and deployment scales to properly identify and characterize environmental impacts and navigational effects. The goal of the project is to provide all stakeholders with an improved understanding of the potential effects of these emerging technologies and focus all stakeholders onto the critical issues that need to be addressed. This groundwork will also help in streamlining siting and associated permitting processes, which are considered key hurdles for the industry’s development in the U.S. today. Re vision is coordinating its efforts with two other project teams funded by DoE which are focused on regulatory and navigational issues. The results of this study are structured into three reports: 1. Wave power scenario description 2. Tidal power scenario description 3. Framework for Identifying Key Environmental Concerns This is the second report in the sequence and describes the results of conceptual feasibility studies of tidal power plants deployed in Tacoma Narrows, Washington. The Narrows contain many of the same competing stakeholder interactions identified at other tidal power sites and serves as a representative case study. Tidal power remains at an early stage of development. As such, a wide range of different technologies are being pursued by different manufacturers. In order to properly characterize impacts, it is useful to characterize the range of technologies that could be deployed at the site of interest. An industry survey informs the process of selecting representative tidal power devices. The selection criteria is that such devices are at an advanced stage of development to reduce technical uncertainties and that enough data are available from the manufacturers to inform the conceptual design process of this study. Further, an attempt is made to cover the range of different technologies under development to capture variations in potential environmental effects. A number of other developers are also at an advanced stage of development including Verdant Power, which has demonstrated an array of turbines in the East River of New York, Clean Current, which has demonstrated a device off Race Rocks, BC, and OpenHydro, which has demonstrated a device at the European Marine Energy Test Center and is on the verge of deploying a larger device in the Bay of Fundy. MCT demonstrated their device both at Devon (UK) and Strangford Narrows (Northern Ireland). Furthermore OpenHydro, CleanCurrent, and MCT are the three devices being installed at the Minas Passage (Canada). Environmental effects will largely scale with the size of tidal power development. In many cases, the effects of a single device may not be measurable, while larger scale device arrays may have cumulative impacts that differ significantly from smaller scale deployments. In order to characterize these effects, scenarios are established at three deployment scales which nominally represent (1) a small pilot deployment, (2) an early, small commercial deployment, and (3) a large commercial scale plant. For the three technologies and scales at the selected site, this results in a total of nine deployment scenarios outlined in the report.« less

Annual agricultural pesticide use for Midwest Stream-Quality Assessment, 2012-13

USGS Publications Warehouse

Baker, Nancy T.; Stone, Wesley W.

2014-01-01

This report provides estimates of annual agricultural use of 190 pesticide compounds for counties and selected watersheds of Midwestern States for 2012 and 2013 compiled for subsequent analysis by the National Water-Quality Assessment Program, Midwest Stream-Quality Assessment (MSQA). One of the goals of MSQA is to characterize contaminants at perennial-stream sites throughout the Corn Belt. Evaluating pesticide inputs from agricultural sources will aid in that characterization. Crop acres for selected Midwestern crops were obtained from the Cropland Data Layer of the U.S. Department of Agriculture’s National Agricultural Statistics Service and used in conjunction with GfK Kynetec, Inc. proprietary Crop Reporting District-level pesticide-use data to estimate pesticide use for counties and watersheds. Estimated pesticide use (EPest) values were calculated by using both the “EPest-high” and “EPest-low” methods, the distinction being that there are more counties with estimated pesticide use for EPest-high compared to EPest-low, owing to differing assumptions about missing survey data. County-level and watershed-level estimates of annual agricultural pesticide use are provided as downloadable, tab-delimited files for both EPest-high and Epest-low. Summary graphs of MSQA watershed-level pesticide use for selected crops are also provided.

Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling*

PubMed Central

Humphrey, Emily S.; Su, Shih-Ping; Nagrial, Adnan M.; Hochgräfe, Falko; Pajic, Marina; Lehrbach, Gillian M.; Parton, Robert G.; Yap, Alpha S.; Horvath, Lisa G.; Chang, David K.; Biankin, Andrew V.; Wu, Jianmin; Daly, Roger J.

2016-01-01

Comprehensive characterization of signaling in pancreatic ductal adenocarcinoma (PDAC) promises to enhance our understanding of the molecular aberrations driving this devastating disease, and may identify novel therapeutic targets as well as biomarkers that enable stratification of patients for optimal therapy. Here, we use immunoaffinity-coupled high-resolution mass spectrometry to characterize global tyrosine phosphorylation patterns across two large panels of human PDAC cell lines: the ATCC series (19 cell lines) and TKCC series (17 cell lines). This resulted in the identification and quantification of over 1800 class 1 tyrosine phosphorylation sites and the consistent segregation of both PDAC cell line series into three subtypes with distinct tyrosine phosphorylation profiles. Subtype-selective signaling networks were characterized by identification of subtype-enriched phosphosites together with pathway and network analyses. This revealed that the three subtypes characteristic of the ATCC series were associated with perturbations in signaling networks associated with cell-cell adhesion and epithelial-mesenchyme transition, mRNA metabolism, and receptor tyrosine kinase (RTK) signaling, respectively. Specifically, the third subtype exhibited enhanced tyrosine phosphorylation of multiple RTKs including the EGFR, ERBB3 and MET. Interestingly, a similar RTK-enriched subtype was identified in the TKCC series, and 'classifier' sites for each series identified using Random Forest models were able to predict the subtypes of the alternate series with high accuracy, highlighting the conservation of the three subtypes across the two series. Finally, RTK-enriched cell lines from both series exhibited enhanced sensitivity to the small molecule EGFR inhibitor erlotinib, indicating that their phosphosignature may provide a predictive biomarker for response to this targeted therapy. These studies highlight how resolution of subtype-selective signaling networks can provide a novel taxonomy for particular cancers, and provide insights into PDAC biology that can be exploited for improved patient management. PMID:27259358

Acid–base catalysis over perovskites: a review

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

Polo-Garzon, Felipe; Wu, Zili

We present that perovskite catalysts have been extensively studied for reduction–oxidation (redox) reactions; however, their acid–base catalytic properties are still under-explored. This review collects work aiming to study the acid–base catalytic properties of perovskites. Reports regarding combined acid–base/redox catalysis over perovskites lie beyond the scope of the present review. For the characterization of acid–base properties, researchers have studied the interaction of probe molecules with perovskite surfaces by means of multiple techniques that provide information about the density, strength and type of adsorption sites. The top-surface composition of perovskites, which relates to the abundance of the acid–base sites, has been studiedmore » by means of low energy ion scattering (LEIS), and, the less surface sensitive, conventional X-ray photoelectron spectroscopy (XPS). Probe reactions, with the conversion of 2-propanol as the common choice, have also been employed for characterizing the acid–base catalytic properties of perovskites. The complex nature of perovskite surfaces, which explains the still absent fundamental relations between the structure of the catalyst and reaction rates/selectivity, encounters a great challenge due to the surface reconstruction of these materials. In this review, we devote a special section to highlight recent publications that report the impact of surface reconstruction and particle shape on acid–base catalysis over perovskites. In addition, we review promising catalytic performances of perovskite catalysts for other reactions of interest. Challenges in acid–base catalysis over perovskites focus on the development of time-resolved monolayer-sensitive characterization of surfaces under operando conditions and the discernment of combined acid–base/redox reaction mechanisms. Finally, opportunities lay on tuning the acid–base characteristics of perovskites with computation-based catalytic descriptors to achieve desired selectivities and enhanced rates.« less

Acid–base catalysis over perovskites: a review

DOE PAGES

Polo-Garzon, Felipe; Wu, Zili

2018-01-15

We present that perovskite catalysts have been extensively studied for reduction–oxidation (redox) reactions; however, their acid–base catalytic properties are still under-explored. This review collects work aiming to study the acid–base catalytic properties of perovskites. Reports regarding combined acid–base/redox catalysis over perovskites lie beyond the scope of the present review. For the characterization of acid–base properties, researchers have studied the interaction of probe molecules with perovskite surfaces by means of multiple techniques that provide information about the density, strength and type of adsorption sites. The top-surface composition of perovskites, which relates to the abundance of the acid–base sites, has been studiedmore » by means of low energy ion scattering (LEIS), and, the less surface sensitive, conventional X-ray photoelectron spectroscopy (XPS). Probe reactions, with the conversion of 2-propanol as the common choice, have also been employed for characterizing the acid–base catalytic properties of perovskites. The complex nature of perovskite surfaces, which explains the still absent fundamental relations between the structure of the catalyst and reaction rates/selectivity, encounters a great challenge due to the surface reconstruction of these materials. In this review, we devote a special section to highlight recent publications that report the impact of surface reconstruction and particle shape on acid–base catalysis over perovskites. In addition, we review promising catalytic performances of perovskite catalysts for other reactions of interest. Challenges in acid–base catalysis over perovskites focus on the development of time-resolved monolayer-sensitive characterization of surfaces under operando conditions and the discernment of combined acid–base/redox reaction mechanisms. Finally, opportunities lay on tuning the acid–base characteristics of perovskites with computation-based catalytic descriptors to achieve desired selectivities and enhanced rates.« less

Demonstration of innovative monitoring technologies at the Savannah River Integrated Demonstration Site

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

Rossabi, J.; Jenkins, R.A.; Wise, M.B.

1993-12-31

The Department of Energy`s Office of Technology Development initiated an Integrated Demonstration Program at the Savannah River Site in 1989. The objective of this program is to develop, demonstrate, and evaluate innovative technologies that can improve present-day environmental restoration methods. The Integrated Demonstration Program at SRS is entitled ``Cleanup of Organics in Soils and Groundwater at Non-Arid Sites.`` New technologies in the areas of drilling, characterization, monitoring, and remediation are being demonstrated and evaluated for their technical performance and cost effectiveness in comparison with baseline technologies. Present site characterization and monitoring methods are costly, time-consuming, overly invasive, and often imprecise.more » Better technologies are required to accurately describe the subsurface geophysical and geochemical features of a site and the nature and extent of contamination. More efficient, nonintrusive characterization and monitoring techniques are necessary for understanding and predicting subsurface transport. More reliable procedures are also needed for interpreting monitoring and characterization data. Site characterization and monitoring are key elements in preventing, identifying, and restoring contaminated sites. The remediation of a site cannot be determined without characterization data, and monitoring may be required for 30 years after site closure.« less

Quantification of Functional Marker Genes for Denitrifying Microbial Populations in the Chandeleur Islands Impacted by the 2010 Gulf of Mexico Oil Spill

NASA Astrophysics Data System (ADS)

Crawford, P.; Flournoy, N.; Taylor, C.; Tatariw, C.; Mortazavi, B.; Sobecky, P.

2017-12-01

Barrier island ecosystems provide protection by reducing storm surges, dissipating wave energy, and economically through services such as fisheries, water catchment, and water quality. As these ecosystems are deteriorating and threatened in this century, services provided to humans are being valued monetarily to communicate their importance. Events such as the 2010 Gulf of Mexico oil spill, act as catalysts to accelerate deterioration and further loss of these vital ecosystem services. The oil spill impacted the Chandeleur Islands, barrier islands in Louisiana waters located forty miles south of Gulfport, MS. Island chain vegetation; i.e., Avicennia germinans and native Spartina alterniflora was heavily damaged as a result of the oil spill. As oil was deposited differentially, it was important to investigate the microbiology of oil-impacted areas as marsh vegetation is directly linked to microbe-driven ecosystem services such as denitrification, a nitrogen (N) cycle pathway. The objectives of this study were: i) characterize the biodiversity of microorganisms; ii) quantify denitrifying microbial populations using functional marker genes; and iii) measure rates of denitrification during a one-year period. Eco-functional marker genes narG, nirS, norB, nosZ, and nrfA were selected to represent denitrification. Three different marsh sites were selected for study based upon estimated amounts of prior oiling. Highest rates of denitrification were in September while the lowest rates were observed in February. The highest nirS abundance was detected for two of the three sites (Site 1 and 2) in September while Site 3 exhibited the highest abundance in November. Similarly, the highest abundances observed for norB and nosZ varied by site and by month. Weathered oil was also detected in some of the marsh sediment cores and chemically typed to Macondo oil. Studies such as this one are designed to characterize the barrier island microbial biodiversity and N cycle processes to better understand long-term effects disturbances such as the 2010 oil spill pose to an ecosystem service that contributes to maintaining marine water quality. This is especially important in light of the fact that weathered oil continues to be observed seven years post spill.

Screening and Characterization of RAPD Markers in Viscerotropic Leishmania Parasites

PubMed Central

Mkada–Driss, Imen; Talbi, Chiraz; Guerbouj, Souheila; Driss, Mehdi; Elamine, Elwaleed M.; Cupolillo, Elisa; Mukhtar, Moawia M.; Guizani, Ikram

2014-01-01

Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5′ end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents. PMID:25313833

sc-PDB: a 3D-database of ligandable binding sites—10 years on

PubMed Central

Desaphy, Jérémy; Bret, Guillaume; Rognan, Didier; Kellenberger, Esther

2015-01-01

The sc-PDB database (available at http://bioinfo-pharma.u-strasbg.fr/scPDB/) is a comprehensive and up-to-date selection of ligandable binding sites of the Protein Data Bank. Sites are defined from complexes between a protein and a pharmacological ligand. The database provides the all-atom description of the protein, its ligand, their binding site and their binding mode. Currently, the sc-PDB archive registers 9283 binding sites from 3678 unique proteins and 5608 unique ligands. The sc-PDB database was publicly launched in 2004 with the aim of providing structure files suitable for computational approaches to drug design, such as docking. During the last 10 years we have improved and standardized the processes for (i) identifying binding sites, (ii) correcting structures, (iii) annotating protein function and ligand properties and (iv) characterizing their binding mode. This paper presents the latest enhancements in the database, specifically pertaining to the representation of molecular interaction and to the similarity between ligand/protein binding patterns. The new website puts emphasis in pictorial analysis of data. PMID:25300483

Characterization of water quality in selected tributaries of the Alamosa River, southwestern Colorado, including comparisons to instream water-quality standards and toxicological reference values, 1995-97

USGS Publications Warehouse

Ortiz, Roderick F.; Ferguson, Sheryl A.

2001-01-01

A comprehensive water-quality sampling network was implemented by the U.S. Geological Survey from 1995 through 1997 at 12 tributary sites to the Alamosa River. The network was designed to address data gaps identified in the initial ecological risk assessment of the Summitville Superfund site. Tributaries draining hydrothermally altered areas had higher median values for nearly all measured properties and constituents than tributaries draining unaltered areas. Colorado instream standards for pH, copper, iron, and zinc were in attainment at most tributary sites. Instream standards for pH and chronic aquatic-life standards for iron were not attained in Jasper Creek. Toxicological reference values were most often exceeded at Iron Creek, Alum Creek, Bitter Creek, Wightman Fork, and Burnt Creek. These tributaries all drain hydrothermally altered areas.

Vegetative resistance to flow in south Florida; summary of vegetation sampling at sites NESRS3 and P33, Shark River slough, November, 1996

USGS Publications Warehouse

Carter, Virginia; Reel, J.T.; Rybicki, N.B.; Ruhl, H.; Gammon, P.T.; Lee, J.K.

1999-01-01

The U.S. Geological Survey is one of many agencies participating in the effort to restore the South Florida Everglades. We are sampling and characterizing the vegetation at selected sites in the Everglades as part of a study to quantify vegetative flow resistance. The objectives of the vegetation sampling are (1) to provide detailed information on species composition, vegetation characteristics, vegetation structure, and biomass for quantification of vegetative resistance to flow, and (2) to use this information to classify the vegetation and to improve existing vegetation maps for use with numerical models of surface-water flow. Vegetation was sampled at two sites in the Shark River Slough in November, 1996. The data collected and presented here include those for live and dead standing sawgrass, other dead material, periphyton biomass, vegetation characteristics and structure, and leaf area index.

Hydroisomerization of n-dodecane over Pt/Al-MCM-48 catalysts.

PubMed

Yun, Soyoung; Park, Young-Kwon; Jeong, Soon-Yong; Han, Jeongsik; Jeon, Jong-Ki

2014-04-01

The objective of this study is to evaluate the catalytic potential of Pt/Al-MCM-48 catalysts in hydroisomerization of n-dodecane. The effects of the Si/Al ratio and platinum loading on the acid characteristics of Al-MCM-48 and the catalytic performance in n-dodecane hydroisomerization were analyzed. The catalysts were characterized by X-ray diffraction, nitrogen adsorption, infrared spectroscopy of pyridine adsorption, and temperature programmed desorption of ammonia. The number of weak strength acid sites on Al-MCM-48 increased with 0.5 wt% platinum loading. The weak strength acid sites of Pt/Al-MCM-48 catalysts were ascribed to Lewis acid sites, which can be confirmed by NH3-TPD and FTIR spectra of pyridine adsorption. Iso-dodecane can be produced with high selectivity in n-dodecane hydrosisomerization over Pt/Al-MCM-48 catalysts. This is attributed to the mild acidic properties of Pt/Al-MCM-48 catalysts.

40 CFR 761.250 - Sample site selection for pipeline section abandonment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Sample site selection for pipeline... Disposal of Natural Gas Pipeline: Selecting Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.250 Sample site selection for pipeline section abandonment. This procedure...

40 CFR 761.250 - Sample site selection for pipeline section abandonment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Sample site selection for pipeline... Disposal of Natural Gas Pipeline: Selecting Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.250 Sample site selection for pipeline section abandonment. This procedure...

Design of Highly Selective Platinum Nanoparticle Catalysts for the Aerobic Oxidation of KA-Oil using Continuous-Flow Chemistry.

PubMed

Gill, Arran M; Hinde, Christopher S; Leary, Rowan K; Potter, Matthew E; Jouve, Andrea; Wells, Peter P; Midgley, Paul A; Thomas, John M; Raja, Robert

2016-03-08

Highly active and selective aerobic oxidation of KA-oil to cyclohexanone (precursor for adipic acid and ɛ-caprolactam) has been achieved in high yields using continuous-flow chemistry by utilizing uncapped noble-metal (Au, Pt & Pd) nanoparticle catalysts. These are prepared using a one-step in situ methodology, within three-dimensional porous molecular architectures, to afford robust heterogeneous catalysts. Detailed spectroscopic characterization of the nature of the active sites at the molecular level, coupled with aberration-corrected scanning transmission electron microscopy, reveals that the synthetic methodology and associated activation procedures play a vital role in regulating the morphology, shape and size of the metal nanoparticles. These active centers have a profound influence on the activation of molecular oxygen for selective catalytic oxidations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of stormwater runoff from the Naval Air Station and Naval Wepons Industrial Reserve Plant, Dallas, Texas, 1994-96

USGS Publications Warehouse

Raines, T.H.; Baldys, Stanley; Lizarraga, J.S.

1997-01-01

Median event-mean concentrations computed for 12 selected constituents in samples from NAS and NWIRP fixed sites were compared to median event-mean concentrations for residential, commercial, industrial, and highway land uses within the Dallas-Fort Worth area computed from data collected for the National Pollutant Discharge Elimination System program. NAS and NWIRP median event-mean concentrations also were compared to those for residential and commercial land uses from the Nationwide Urban Runoff Program.

Geochemical and radiological characterization of soils from former radium processing sites.

PubMed

Landa, E R

1984-02-01

Soil samples were collected from former radium processing sites in Denver, CO, and East Orange, NJ. Particle-size separations and radiochemical analyses of selected samples showed that while the greatest contents of both 226Ra and U were generally found in the finest (less than 45 micron) fraction, the pattern was not always of progressive increase in radionuclide content with decreasing particle size. Leaching tests on these samples showed a large portion of the 226Ra and U to be soluble in dilute hydrochloric acid. Radon-emanation coefficients measured for bulk samples of contaminated soil were about 20%. Recovery of residual uranium and vanadium, as an adjunct to any remedial action program, appears unlikely due to economic considerations.

Biogeochemical cycling in terrestrial ecosystems - Modeling, measurement, and remote sensing

NASA Technical Reports Server (NTRS)

Peterson, D. L.; Matson, P. A.; Lawless, J. G.; Aber, J. D.; Vitousek, P. M.

1985-01-01

The use of modeling, remote sensing, and measurements to characterize the pathways and to measure the rate of biogeochemical cycling in forest ecosystems is described. The application of the process-level model to predict processes in intact forests and ecosystems response to disturbance is examined. The selection of research areas from contrasting climate regimes and sites having a fertility gradient in that regime is discussed, and the sites studied are listed. The use of remote sensing in determining leaf area index and canopy biochemistry is analyzed. Nitrous oxide emission is investigated by using a gas measurement instrument. Future research projects, which include studying the influence of changes on nutrient cycling in ecosystems and the effect of pollutants on the ecosystems, are discussed.

Properties and Degradation of Polarization Reversal of Soft BaTiO3 Ceramics for Ferroelectric Thin-Film Devices

NASA Astrophysics Data System (ADS)

Thongrueng, Jirawat; Tsuchiya, Toshio; Masuda, Yoichiro; Fujita, Shigetaka; Nagata, Kunihiro

1999-09-01

Soft BaTiO3 ceramics having a very low coercive field of 65 V/mm were prepared by substituting 9 mol% Hf Zr for the Ti-site of BaTiO3, for applications to ferroelectric thin-film devices. Electrical properties of the soft BaTiO3 ceramics were measured and compared with those of normal BaTiO3 ceramics. By substituting Hf Zr for Ti-site, the phase transition temperatures were controlled, and we could select the preferred crystal structure from the tetragonal, orthorhombic and rhombohedral phases at room temperature. In addition, the preparation and characterization of the soft BaTiO3 thin-films using a sol-gel process were carried out.

Structural and functional characterization of Rpn12 identifies residues required for Rpn10 proteasome incorporation

PubMed Central

Boehringer, Jonas; Riedinger, Christiane; Paraskevopoulos, Konstantinos; Johnson, Eachan O. D.; Lowe, Edward D.; Khoudian, Christina; Smith, Dominique; Noble, Martin E. M.; Gordon, Colin; Endicott, Jane A.

2012-01-01

The ubiquitin–proteasome system targets selected proteins for degradation by the 26S proteasome. Rpn12 is an essential component of the 19S regulatory particle and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. In the present paper we report the crystal structure of Rpn12, a proteasomal PCI-domain-containing protein. The structure helps to define a core structural motif for the PCI domain and identifies potential sites through which Rpn12 might form protein–protein interactions. We demonstrate that mutating residues at one of these sites impairs Rpn12 binding to Rpn10 in vitro and reduces Rpn10 incorporation into proteasomes in vivo. PMID:22906049

Sorption selectivity of birnessite particle edges: a d-PDF analysis of Cd( ii ) and Pb( ii ) sorption by δ-MnO 2 and ferrihydrite

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

van Genuchten, Case M.; Peña, Jasquelin

2016-01-01

Birnessite minerals (layer-type MnO2), which bear both internal (cation vacancies) and external (particle edges) metal sorption sites, are important sinks of contaminants in soils and sediments. Although the particle edges of birnessite minerals often dominate the total reactive surface area, especially in the case of nanoscale crystallites, the metal sorption reactivity of birnessite particle edges remains elusive. In this study, we investigated the sorption selectivity of birnessite particle edges by combining Cd(II) and Pb(II) adsorption isotherms at pH 5.5 with surface structural characterization by differential pair distribution function (d-PDF) analysis. We compared the sorption reactivity of δ-MnO2 to that ofmore » the nanomineral, 2-line ferrihydrite, which exhibits only external surface sites. Our results show that, whereas Cd(II) and Pb(II) both bind to birnessite layer vacancies, only Pb(II) binds extensively to birnessite particle edges. For ferrihydrite, significant Pb(II) adsorption to external sites was observed (roughly 20 mol%), whereas Cd(II) sorption was negligible. These results are supported by bond valence calculations that show comparable degrees of saturation of oxygen atoms on birnessite and ferrihydrite particle edges. Therefore, we propose that the sorption selectivity of birnessite edges follows the same order of that reported previously for ferrihydrite: Ca(II) < Cd(II) < Ni(II) < Zn(II) < Cu(II) < Pb(II).« less

Site-selective growth of surface-anchored metal-organic frameworks on self-assembled monolayer patterns prepared by AFM nanografting

PubMed Central

Ladnorg, Tatjana; Welle, Alexander; Heißler, Stefan; Wöll, Christof

2013-01-01

Summary Surface anchored metal-organic frameworks, SURMOFs, are highly porous materials, which can be grown on modified substrates as highly oriented, crystalline coatings by a quasi-epitaxial layer-by-layer method (liquid-phase epitaxy, or LPE). The chemical termination of the supporting substrate is crucial, because the most convenient method for substrate modification is the formation of a suitable self-assembled monolayer. The choice of a particular SAM also allows for control over the orientation of the SURMOF. Here, we demonstrate for the first time the site-selective growth of the SURMOF HKUST-1 on thiol-based self-assembled monolayers patterned by the nanografting technique, with an atomic force microscope as a structuring tool. Two different approaches were applied: The first one is based on 3-mercaptopropionic acid molecules which are grafted in a 1-decanethiolate SAM, which serves as a matrix for this nanolithography. The second approach uses 16-mercaptohexadecanoic acid, which is grafted in a matrix of an 1-octadecanethiolate SAM. In both cases a site-selective growth of the SURMOF is observed. In the latter case the roughness of the HKUST-1 is found to be significantly higher than for the 1-mercaptopropionic acid. The successful grafting process was verified by time-of-flight secondary ion mass spectrometry and atomic force microscopy. The SURMOF structures grown via LPE were investigated and characterized by atomic force microscopy and Fourier-transform infrared microscopy. PMID:24205458

Using FEP's List and a PA Methodology for Evaluating Suitable Areas for the LLW Repository in Italy

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

Risoluti, P.; Ciabatti, P.; Mingrone, G.

2002-02-26

In Italy following a referendum held in 1987, nuclear energy has been phased out. Since 1998, a general site selection process covering the whole Italian territory has been under way. A GIS (Geographic Information System) methodology was implemented in three steps using the ESRI Arc/Info and Arc/View platforms. The screening identified approximately 0.8% of the Italian territory as suitable for locating the LLW Repository. 200 areas have been identified as suitable for the location of the LLW Repository, using a multiple exclusion criteria procedure (1:500,000), regional scale (1:100.000) and local scale (1:25,000-1:10,000). A methodology for evaluating these areas has beenmore » developed allowing, along with the evaluation of the long term efficiency of the engineered barrier system (EBS), the characterization of the selected areas in terms of physical and safety factors and planning factors. The first step was to identify, on a referenced FEPs list, a group of geomorphological, geological, hydrogeological, climatic and human behavior caused process and/or events, which were considered of importance for the site evaluation, taking into account the Italian situation. A site evaluation system was established ascribing weighted scores to each of these processes and events, which were identified as parameters of the new evaluation system. The score of each parameter is ranging from 1 (low suitability) to 3 (high suitability). The corresponding weight is calculated considering the effect of the parameter in terms of total dose to the critical group, using an upgraded AMBER model for PA calculation. At the end of the process an index obtained by a score weighted sum gives the degree of suitability of the selected areas for the LLW Repository location. The application of the methodology to two selected sites is given in the paper.« less

SITE CHARACTERIZATION LIBRARY: VOLUMN 1 (RELEASE 2.5)

EPA Science Inventory

This CD-ROM, Volume 1, Release 2.5, of EPA's National Exposure Research Laboratory (NERL - Las Vegas) Site Characterization Library, contains additional electronic documents and computer programs related to the characterization of hazardous waste sites. EPA has produced this libr...

Improving surface-subsurface water budgeting for Brownfield study sites using high resolution satellite imagery

NASA Astrophysics Data System (ADS)

Dujardin, J.; Boel, S.; Anibas, C.; Batelaan, O.; Canters, F.

2009-04-01

Countries around the world have problems with contaminated brownfield sites as resulting from a relatively anarchic economical and industrial development during the 19th and 20th centuries. Since a few decades policy makers and stakeholders have become more aware of the risk posed by these sites because some of these sites present direct public hazards. Water is often the main vector of the mobility of contaminants. In order to propose remediation measures for the contaminated sites, it is required to describe and to quantify as accurately as possible the surface and subsurface water fluxes in the polluted site. In this research a modelling approach with integrated remote sensing analysis has been developed for accurately calculating water and contaminant fluxes on the polluted sites. Groundwater pollution in urban environments is linked to patterns of land use, so to identify the sources of contamination with great accuracy in urban environments it is essential to characterize the land cover in a detailed way. The use of high resolution spatial information is required because of the complexity of the urban land use. An object-oriented classification approach applied on high resolution satellite data has been adopted. Cluster separability analysis and visual interpretation of the image objects belonging to each cluster resulted in the selection of 8 land-cover categories (water, bare soil, meadow, mixed forest, grey urban surfaces, red roofs, bright roofs and shadow).To assign the image objects to one of the 8 selected classes a multiple layer perceptron (MLP) approach was adopted, using the NeuralWorks Predict software. After a post-classification shadow removal and a rule-based classification enhancement a kappa-value of 0.86 was obtained. Once the land cover was characterized, the groundwater recharge has been simulated using the spatially distributed WetSpass model and the subsurface water flow was simulated with GMS 6.0 in order to identify and budget the water fluxes on the brownfield. The obtained land use map shows to have a strong impact on the groundwater recharge, resulting in a high spatial variability. Simulated groundwater fluxes from brownfield to a receiving river where independently verified by measurements and simulation of groundwater-surface water interaction based on thermal gradients in the river bed. It is concluded that in order to better quantify total fluxes of contaminants from brownfields in the groundwater, remote sensing imagery can be operationally integrated in a modelling procedure. The developed methodology is applied to a case site in Vilvoorde, Brussels (Belgium).

Evaluation of methods for identifying spawning sites and habitat selection for alosines

USGS Publications Warehouse

Harris, Julianne E.; Hightower, Joseph E.

2010-01-01

Characterization of riverine spawning habitat is important for the management and restoration of anadromous alosines. We examined the relative effectiveness of oblique plankton tows and spawning pads for collecting the eggs of American shad Alosa sapidissima, hickory shad A. mediocris, and “river herring” (a collective term for alewife A. pseudoharengus and blueback herring A. aestivalis) in the Roanoke River, North Carolina. Relatively nonadhesive American shad eggs were only collected by plankton tows, whereas semiadhesive hickory shad and river herring eggs were collected by both methods. Compared with spawning pads, oblique plankton tows had higher probabilities of collecting eggs and led to the identification of longer spawning periods. In assumed spawning areas, twice-weekly plankton sampling for 15 min throughout the spawning season had a 95% or greater probability of collecting at least one egg for all alosines; however, the probabilities were lower in areas with more limited spawning. Comparisons of plankton tows, spawning pads, and two other methods of identifying spawning habitat (direct observation of spawning and examination of female histology) suggested differences in effectiveness and efficiency. Riverwide information on spawning sites and timing for all alosines is most efficiently obtained by plankton sampling. Spawning pads and direct observations of spawning are the best ways to determine microhabitat selectivity for appropriate species, especially when spawning sites have previously been identified. Histological examination can help determine primary spawning sites but is most useful when information on reproductive biology and spawning periodicity is also desired. The target species, riverine habitat conditions, and research goals should be considered when selecting methods with which to evaluate alosine spawning habitat.

Strong Selective Adsorption of Polymers.

PubMed

Ge, Ting; Rubinstein, Michael

2015-06-09

A scaling theory is developed for selective adsorption of polymers induced by the strong binding between specific monomers and complementary surface adsorption sites. By "selective" we mean specific attraction between a subset of all monomers, called "sticky", and a subset of surface sites, called "adsorption sites". We demonstrate that, in addition to the expected dependence on the polymer volume fraction ϕ bulk in the bulk solution, selective adsorption strongly depends on the ratio between two characteristic length scales, the root-mean-square distance l between neighboring sticky monomers along the polymer, and the average distance d between neighboring surface adsorption sites. The role of the ratio l / d arises from the fact that a polymer needs to deform to enable the spatial commensurability between its sticky monomers and the surface adsorption sites for selective adsorption. We study strong selective adsorption of both telechelic polymers with two end monomers being sticky and multisticker polymers with many sticky monomers between sticky ends. For telechelic polymers, we identify four adsorption regimes at l / d < 1 that are characterized by the fraction of occupied adsorption sites and whether the dominant conformation of adsorbed chains is a single-end-adsorbed "mushroom" or double-end-adsorbed loop. For l / d > 1, we expect that the adsorption layer at exponentially low ϕ bulk consists of separated unstretched loops, while as ϕ bulk increases the layer crosses over to a brush of extended loops with a second layer of weakly overlapping tails. For multisticker chains, in the limit of exponentially low ϕ bulk , adsorbed polymers are well separated from each other. As l / d increases, the conformation of an individual polymer changes from a single-end-adsorbed "mushroom" to a random walk of loops. For high ϕ bulk , adsorbed polymers at small l / d are mushrooms that cover all the adsorption sites. At sufficiently large l / d , adsorbed multisticker polymers strongly overlap. We anticipate the formation of a self-similar carpet and with increasing l / d a two-layer structure with a brush of loops covered by a self-similar carpet. As l / d exceeds the threshold determined by the adsorption energy, the brush of loops under the carpet reaches a saturated state, resulting in a l / d -independent brush-under-carpet structure, which can also be applied to describe adsorbed multisticker polymers in nonselective adsorption where a sticker can strongly bind to any place on the adsorption surface. We examine the adsorbed amount Γ of multisticker polymers in different regimes for selective adsorption. If the adsorbed multisticker polymers are nonoverlapping mushrooms, the adsorbed amount Γ increases linearly with the surface density of adsorption sites Σ ≈ 1/ d 2 . In the self-similar carpet regime, Γ increases sublinearly as Σ 0.15 in a good solvent, while only logarithmically in a theta solvent. Formation of a brush layer under the carpet contributes an additional adsorbed amount. This additional amount increases linearly with Σ and eventually dominates the overall adsorbed amount Γ before saturating at a plateau value controlled by the adsorption energy.

Water-quality observations of the San Antonio segment of the Edwards aquifer, Texas, with an emphasis on processes influencing nutrient and pesticide geochemistry and factors affecting aquifer vulnerability, 2010–16

USGS Publications Warehouse

Opsahl, Stephen P.; Musgrove, MaryLynn; Mahler, Barbara J.; Lambert, Rebecca B.

2018-06-07

As questions regarding the influence of increasing urbanization on water quality in the Edwards aquifer are raised, a better understanding of the sources, fate, and transport of compounds of concern in the aquifer—in particular, nutrients and pesticides—is needed to improve water management decision-making capabilities. The U.S. Geological Survey, in cooperation with the San Antonio Water System, performed a study from 2010 to 2016 to better understand how water quality changes under a range of hydrologic conditions and in contrasting land-cover settings (rural and urban) in the Edwards aquifer. The study design included continuous hydrologic monitoring, continuous water-quality monitoring, and discrete sample collection for a detailed characterization of water quality at a network of sites throughout the aquifer system. The sites were selected to encompass a “source-to-sink” (that is, from aquifer recharge to aquifer discharge) approach. Network sites were selected to characterize rainfall, recharging surface water, and groundwater; groundwater sites included wells in the unconfined part of the aquifer (unconfined wells) and in the confined part of the aquifer (confined wells) and a major discharging spring. Storm-related samples—including rainfall samples, stormwater-runoff (surface-water) samples, and groundwater samples—were collected to characterize the aquifer response to recharge.Elevated nitrate concentrations relative to national background values and the widespread detection of pesticides indicate that the Edwards aquifer is vulnerable to contamination and that vulnerability is affected by factors such as land cover, aquifer hydrogeology, and changes in hydrologic conditions. Greater vulnerability of groundwater in urban areas relative to rural areas was evident from results for urban groundwater sites, which generally had higher nitrate concentrations, elevated δ15N-nitrate values, a greater diversity of pesticides, and higher pesticide concentrations. The continuum of water quality from unconfined rural groundwater sites (least affected by anthropogenic contamination) to unconfined urban groundwater sites (most affected by anthropogenic contamination) demonstrates enhanced vulnerability of urban versus rural land cover. Differences in contaminant occurrences and concentration among unconfined urban wells indicate that the urban parts of the aquifer are not uniformly vulnerable, but rather are affected by spatial differences in the sources of nutrients and pesticides. In urban areas, the shallow, unconfined groundwater sites showed greater temporal variability in both nutrient and pesticide concentrations, as well as a greater degree of contamination, than did deeper, confined groundwater sites. In comparison to that of the shallow, unconfined groundwater sites, the water quality of the deeper, confined groundwater sites was relatively invariant during this multiyear study. Although aquifer hydrogeology is an important factor related to aquifer vulnerability, land cover likely has a greater influence on pesticide contamination of groundwater. Temporal variability in hydrologic conditions for the Edwards aquifer is apparent in data for surface water as a source of groundwater recharge, water-level altitude in wells, spring discharge, and groundwater quality. This temporal variability affects recharge sources, recharge amounts, groundwater traveltimes, flow routing, water-rock interaction processes, dilution, mixing, and, in turn, water quality. Relations of land cover, aquifer hydrogeology, and changing hydrologic conditions to water quality are complex but provide insight into the vulnerability of Edwards aquifer groundwater—a vital drinking-water resource.

Regulatory requirements for nuclear power plant site selection in Malaysia-a review.

PubMed

Basri, N A; Hashim, S; Ramli, A T; Bradley, D A; Hamzah, K

2016-12-01

Malaysia has initiated a range of pre-project activities in preparation for its planned nuclear power programme. Clearly one of the first steps is the selection of sites that are deemed suitable for the construction and operation of a nuclear power plant. Here we outline the Malaysian regulatory requirements for nuclear power plant site selection, emphasizing details of the selection procedures and site characteristics needed, with a clear focus on radiation safety and radiation protection in respect of the site surroundings. The Malaysia Atomic Energy Licensing Board (AELB) site selection guidelines are in accord with those provided in International Atomic Energy Agency (IAEA) and United Stated Nuclear Regulatory Commission (USNRC) documents. To enhance the suitability criteria during selection, as well as to assist in the final decision making process, possible assessments using the site selection characteristics and information are proposed.

Using maximum entropy modeling for optimal selection of sampling sites for monitoring networks

USGS Publications Warehouse

Stohlgren, Thomas J.; Kumar, Sunil; Barnett, David T.; Evangelista, Paul H.

2011-01-01

Environmental monitoring programs must efficiently describe state shifts. We propose using maximum entropy modeling to select dissimilar sampling sites to capture environmental variability at low cost, and demonstrate a specific application: sample site selection for the Central Plains domain (453,490 km2) of the National Ecological Observatory Network (NEON). We relied on four environmental factors: mean annual temperature and precipitation, elevation, and vegetation type. A “sample site” was defined as a 20 km × 20 km area (equal to NEON’s airborne observation platform [AOP] footprint), within which each 1 km2 cell was evaluated for each environmental factor. After each model run, the most environmentally dissimilar site was selected from all potential sample sites. The iterative selection of eight sites captured approximately 80% of the environmental envelope of the domain, an improvement over stratified random sampling and simple random designs for sample site selection. This approach can be widely used for cost-efficient selection of survey and monitoring sites.

Hydrologic and geologic characteristics of the Yucca Mountain site relevant to the performance of a potential repository

USGS Publications Warehouse

Levich, R.A.; Linden, R.M.; Patterson, R.L.; Stuckless, J.S.

2000-01-01

Yucca Mountain, located ~100 mi northwest of Las Vegas, Nevada, has been designated by Congress as a site to be characterized for a potential mined geologic repository for high-level radioactive waste. This field trip will examine the regional geologic and hydrologic setting for Yucca Mountain, as well as specific results of the site characterization program. The first day focuses on the regional setting with emphasis on current and paleo hydrology, which are both of critical concern for predicting future performance of a potential repository. Morning stops will be southern Nevada and afternoon stops will be in Death Valley. The second day will be spent at Yucca Mountain. The field trip will visit the underground testing sites in the "Exploratory Studies Facility" and the "Busted Butte Unsaturated Zone Transport Field Test" plus several surface-based testing sites. Much of the work at the site has concentrated on studies of the unsaturated zone, an element of the hydrologic system that historically has received little attention. Discussions during the second day will compromise selected topics of Yucca Mountain geology, hydrology and geochemistry and will include the probabilistic volcanic hazard analysis and the seismicity and seismic hazard in the Yucca Mountain area. Evening discussions will address modeling of regional groundwater flow, the results of recent hydrologic studies by the Nye County Nuclear Waste Program Office, and the relationship of the geology and hydrology of Yucca Mountain to the performance of a potential repository. Day 3 will examine the geologic framework and hydrology of the Pahute Mesa-Oasis Valley Groundwater Basin and then will continue to Reno via Hawthorne, Nevada and the Walker Lake area.

Nitrate reduction mechanisms and rates in an unconfined eogenetic karst aquifer in two sites with different redox potential

NASA Astrophysics Data System (ADS)

Henson, W. R.; Huang, L.; Graham, W. D.; Ogram, A.

2017-05-01

This study integrates push-pull tracer tests (PPTT) with microbial characterization of extracted water via quantitative polymerase chain reaction (qPCR) and reverse transcriptase qPCR (RT-qPCR) of selected functional N transformation genes to quantify nitrate reduction mechanisms and rates in sites with different redox potential in a karst aquifer. PPTT treatments with nitrate (AN) and nitrate-fumarate (ANC) were executed in two wells representing anoxic and oxic geochemical end-members. Oxic aquifer zero-order nitrate loss rates (mmol L-1 h-1) were similar for AN and ANC treatment, ranging from 0.03 ± 0.01 to 0.05 ± 0.01. Anoxic aquifer zero-order nitrate loss rates ranged from 0.03 ± 0.02 (AN) to 0.13 ± 0.02 (ANC). Microbial characterization indicates mechanisms influencing these rates were dissimilatory nitrate reduction to ammonium (DNRA) at the anoxic site with AN treatment, assimilatory reduction of nitrate to ammonium (ANRA) with ANC treatment in the water column at both sites, and additional documented nitrate reduction that occurred in unsampled biofilms. With carbon treatment, total numbers of microbes (16S rRNA genes) significantly increased (fourteenfold to thirtyfold), supporting stimulated growth with resulting ANRA. Decreased DNRA gene concentrations (nrfA DNA) and increased DNRA activity ratio (nrfA-cDNA/DNA) supported the assertion that DNRA occurred in the anoxic zone with AN and ANC treatment. Furthermore, decreased DNRA gene copy numbers at the anoxic site with ANC treatment suggests that DNRA microbes in the anoxic site are chemolithoautotrophic. Increased RT-qPCR denitrification gene expression (nirK and nirS) was not observed in water samples, supporting that any observed NO3-N loss due to denitrification may be occurring in unsampled microbial biofilms.

40 CFR 228.6 - Specific criteria for site selection.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Specific criteria for site selection... selection. (a) In the selection of disposal sites, in addition to other necessary or appropriate factors...) Existence at or in close proximity to the site of any significant natural or cultural features of historical...

Water-Quality, Bed-Sediment, and Biological Data (October 2006 through September 2007) and Statistical Summaries of Long-Term Data for Streams in the Clark Fork Basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2008-01-01

Water, bed sediment, and biota were sampled in streams from Butte to below Milltown Reservoir as part of a long-term monitoring program in the upper Clark Fork basin; additional water-quality samples were collected in the Clark Fork basin from sites near Milltown Reservoir downstream to near the confluence of the Clark Fork and Flathead River as part of a supplemental sampling program. The sampling programs were conducted in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water-quality samples were collected periodically at 22 sites from October 2006 through September 2007. Bed-sediment and biological samples were collected once at 12 sites during August 2007. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at all long-term and supplemental monitoring sites from October 2006 through September 2007. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for samples collected at sites where seasonal daily values of turbidity were being determined. Nutrients also were analyzed in the supplemental water-quality samples. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites, and seasonal daily values of turbidity were determined for five sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of long-term water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

Water-quality, bed-sediment, and biological data (October 2008 through September 2009) and statistical summaries of long-term data for streams in the Clark Fork basin, Montana

USGS Publications Warehouse

Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

2010-01-01

Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a long-term monitoring program in the upper Clark Fork basin; additional water samples were collected in the Clark Fork basin from sites near Missoula downstream to near the confluence of the Clark Fork and Flathead River as part of a supplemental sampling program. The sampling programs were conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 24 sites from October 2008 through September 2009. Bed-sediment and biota samples were collected once at 13 sites during August 2009. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at all long-term and supplemental monitoring sites from October 2008 through September 2009. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined as well as at Clark Fork above Missoula. Nutrients also were analyzed at all the supplemental water-quality sites, except for Clark Fork Bypass, near Bonner. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of long-term water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

A magnetotelluric study of the sensitivity of an area to seismoelectric signals

USGS Publications Warehouse

Balasis, G.; Bedrosian, P.A.; Eftaxias, K.

2005-01-01

During recent years, efforts at better understanding the physical properties of precursory ultra-low frequency pre-seismic electric signals (SES) have been intensified. Experiments show that SES cannot be observed at all points of the Earth's surface but only at certain so-called sensitive sites. Moreover, a sensitive site is capable of collecting SES from only a restricted number of seismic areas (selectivity effect). Tberefore the installation of a permanent station appropriate for SES collection should necessarily be preceded by a pilot study over a broad area and for a long duration. In short, a number of temporary stations are installed and, after the occurrence of several significant earthquakes (EQs) from a given seismic area, the most appropriate (if any) of these temporary stations, in the sense that they happen to collect SES, can be selected as permanent. Such a long experiment constitutes a serious disadvantage in identifying a site as SES sensitive. However, the SES sensitivity of a site should be related to the geoelectric structure of the area that hosts the site as well as the regional geoelectric structure between the station and the seismic focal area. Thus, knowledge of the local and regional geoelectric structure can dramatically reduce the time involved in identifying SES sites. hi this paper the magnetotelluric method is used to investigate the conductivity structure of an area where a permanent SES station is in operation. Although general conclusions cannot be drawn, the area surrounding an SES site near Ioannina, Greece is characterized by: (1) major faults in the vicinity; (2) highly resistive structure flanked by abrupt conductivity contrasts associated with large-scale geologic contacts, and (3) local inhomogeneities in conductivity structure. The above results are consistent with the fact that electric field amplitudes from remotely-generated signals should be appreciably stronger at such sites when compared to neighboring sites. European Geosciences Union ?? 2005 Author(s). This work is licensed under a Creative Commons License.

Orange-red emitting Gd2Zr2O7:Sm3+: Structure-property correlation, optical properties and defect spectroscopy

NASA Astrophysics Data System (ADS)

Gupta, Santosh K.; Reghukumar, C.; Sudarshan, K.; Ghosh, P. S.; Pathak, Nimai; Kadam, R. M.

2018-05-01

Local structure analysis of dopant ion, understanding host to dopant energy transfer dynamics and defects characterization in a doped material which plays an important role in the designing a highly efficient opto-electronic material. In this connection a new Sm3+ doped Gd2Zr2O7 pyrochlore material was synthesized using gel-combustion technique and was characterized systematically using X-ray diffraction (XRD), time resolved photoluminescence spectroscopy (TRPLS), positron annihilation lifetime spectroscopy (PALS) and density functional theory (DFT) based ab-initio calculation. Based on DFT site selective energetics calculation and luminescence decay measurement, it was observed that the Sm3+ was distributed at both Gd3+ and Zr4+ site with higher Sm3+ fraction at the Gd3+ site. PALS was used to probe the presence of defects in the phosphor. In this work intense orange-red emission is realized through manipulating the energy transfer from host defect emission (oxygen vacancies) to Sm3+ which allows color emission from green in undoped to orange-red in doped samples. Effect of dopant concentration and annealing temperature was probed using TRPLS and PALS. These all information is highly important for researcher looking to achieve pyrochlore based phosphor materials with high quantum yield.

Utilization of an Airborne Plant Chlorophyll Imaging System for Detection of Septic System Malfunction

NASA Technical Reports Server (NTRS)

Spiering, Bruce A.; Carter, Gregory A.

2001-01-01

Malfunctioning, or leaking, sewer systems increase the supply of water and nutrients to surface vegetation. Excess nutrients and harmful bacteria in the effluent pollute ground water and local water bodies and are dangerous to humans and the aquatic ecosystems. An airborne multispectral plant chlorophyll imaging system (PCIS) was used to identify growth patterns in the vegetation covering onsite and public sewer systems. The objective was to evaluate overall performance of the PCIS as well as to determine the best operational configuration for this application. The imaging system was flown in a light aircraft over selected locations Mobile County, Alabama. Calibration panels were used to help characterize instrument performance. Results demonstrated that the PCIS performed well and was capable of detecting septic leakage patterns from altitudes as high as 915 m. From 915 m, 6 of 18 sites were suspected to have sewage leakage. Subsequent ground inspections confirmed leakage on 3 of the 6 sites. From 610 m, 3 of 8 known leakage sites were detected. Tree cover and shadows near residential structures prevented detection of several known malfunctioning systems. Also some leakages known to occur in clear areas were not detected. False detections occurred in areas characterized by surface water drainage problems or recent excavation.

Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.

PubMed

Marques, Catarina A; Dickens, Nicholas J; Paape, Daniel; Campbell, Samantha J; McCulloch, Richard

2015-10-19

DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.

DESIGNING AN OPPORTUNITY FUEL WITH BIOMASS AND TIRE-DERIVED FUEL FOR COFIRING AT WILLOW ISLAND GENERATING STATION

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

K. Payette; D. Tillman

During the period January 1, 2001-March 31, 2001, Allegheny Energy Supply Co., LLC (Allegheny) finalized the engineering of the Willow Island cofiring project, completed the fuel characterizations for both the Willow Island and Albright Generating Station projects, and initiated construction of both projects. Allegheny and its contractor, Foster Wheeler, selected appropriate fuel blends and issued purchase orders for all processing and mechanical equipment to be installed at both sites. This report summarizes the activities associated with the Designer Opportunity Fuel program, and demonstrations at Willow Island and Albright Generating Stations. The third quarter of the project involved completing the detailedmore » designs for the Willow Island Designer Fuel project. It also included complete characterization of the coal and biomass fuels being burned, focusing upon the following characteristics: proximate and ultimate analysis; higher heating value; carbon 13 nuclear magnetic resonance testing for aromaticity, number of aromatic carbons per cluster, and the structural characteristics of oxygen in the fuel; drop tube reactor testing for high temperature devolatilization kinetics and generation of fuel chars; thermogravimetric analyses (TGA) for char oxidation kinetics; and related testing. The construction at both sites commenced during this quarter, and was largely completed at the Albright Generating Station site.« less

A wave model test bed study for wave energy resource characterization

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

Yang, Zhaoqing; Neary, Vincent S.; Wang, Taiping

This paper presents a test bed study conducted to evaluate best practices in wave modeling to characterize energy resources. The model test bed off the central Oregon Coast was selected because of the high wave energy and available measured data at the site. Two third-generation spectral wave models, SWAN and WWIII, were evaluated. A four-level nested-grid approach—from global to test bed scale—was employed. Model skills were assessed using a set of model performance metrics based on comparing six simulated wave resource parameters to observations from a wave buoy inside the test bed. Both WWIII and SWAN performed well at themore » test bed site and exhibited similar modeling skills. The ST4 package with WWIII, which represents better physics for wave growth and dissipation, out-performed ST2 physics and improved wave power density and significant wave height predictions. However, ST4 physics tended to overpredict the wave energy period. The newly developed ST6 physics did not improve the overall model skill for predicting the six wave resource parameters. Sensitivity analysis using different wave frequencies and direction resolutions indicated the model results were not sensitive to spectral resolutions at the test bed site, likely due to the absence of complex bathymetric and geometric features.« less

Measurement Sets and Sites Commonly Used for Characterization

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Holekamp, Kara; Ryan, Robert; Sellers, Richard; Davis, Bruce; Zanoni, Vicki

2002-01-01

Scientists at NASA's Earth Science Applications Directorate are creating a well-characterized Verification & Validation (V&V) site at the Stennis Space Center. This site enables the in-flight characterization of remote sensing systems and the data they acquire. The data are predominantly acquired by commercial, high spatial resolution satellite systems, such as IKONOS and QuickBird 2, and airborne systems. The smaller scale of these newer high resolution remote sensing systems allows scientists to characterize the geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the techniques used to characterize data from the earlier, coarser spatial resolution systems. Scientists are also using the SSC V&V site to characterize thermal infrared systems and active LIDAR systems. SSC employs geodetic targets, edge targets, radiometric tarps, and thermal calibration ponds to characterize remote sensing data products. This paper presents a proposed set of required measurements for visible through long-wave infrared remote sensing systems and a description of the Stennis characterization. Other topics discussed include: 1) The use of ancillary atmospheric and solar measurements taken at SSC that support various characterizations; 2) Additional sites used for radiometric, geometric, and spatial characterization in the continental United States; 3) The need for a standardized technique to be adopted by CEOS and other organizations.

Nest-site selection and nest success of an Arctic-breeding passerine, Smith's Longspur, in a changing climate

USGS Publications Warehouse

McFarland, Heather R.; Kendall, Steve J.; Powell, Abby

2017-01-01

Despite changes in shrub cover and weather patterns associated with climate change in the Arctic, little is known about the breeding requirements of most passerines tied to northern regions. We investigated the nesting biology and nest habitat characteristics of Smith's Longspurs (Calcarius pictus) in 2 study areas in the Brooks Range of Alaska, USA. First, we examined variation in nesting phenology in relation to local temperatures. We then characterized nesting habitat and analyzed nest-site selection for a subset of nests (n = 86) in comparison with paired random points. Finally, we estimated the daily survival rate of 257 nests found in 2007–2013 with respect to both habitat characteristics and weather variables. Nest initiation was delayed in years with snow events, heavy rain, and freezing temperatures early in the breeding season. Nests were typically found in open, low-shrub tundra, and never among tall shrubs (mean shrub height at nests = 26.8 ± 6.7 cm). We observed weak nest-site selection patterns. Considering the similarity between nest sites and paired random points, coupled with the unique social mating system of Smith's Longspurs, we suggest that habitat selection may occur at the neighborhood scale and not at the nest-site scale. The best approximating model explaining nest survival suggested a positive relationship with the numbers of days above 21°C that an individual nest experienced; there was little support for models containing habitat variables. The daily nest survival rate was high (0.972–0.982) compared with that of most passerines in forested or grassland habitats, but similar to that of passerines nesting on tundra. Considering their high nesting success and ability to delay nest initiation during inclement weather, Smith's Longspurs may be resilient to predicted changes in weather regimes on the breeding grounds. Thus, the greatest threat to breeding Smith's Longspurs associated with climate change may be the loss of low-shrub habitat types, which could significantly change the characteristics of breeding areas.

Using site-selection model to identify suitable sites for seagrass transplantation in the west coast of South Sulawesi

NASA Astrophysics Data System (ADS)

Lanuru, Mahatma; Mashoreng, S.; Amri, K.

2018-03-01

The success of seagrass transplantation is very much depending on the site selection and suitable transplantation methods. The main objective of this study is to develop and use a site-selection model to identify the suitability of sites for seagrass (Enhalus acoroides) transplantation. Model development was based on the physical and biological characteristics of the transplantation site. The site-selection process is divided into 3 phases: Phase I identifies potential seagrass habitat using available knowledge, removes unnecessary sites before the transplantation test is performed. Phase II involves field assessment and transplantation test of the best scoring areas identified in Phase I. Phase III is the final calculation of the TSI (Transplant Suitability Index), based on results from Phases I and II. The model was used to identify the suitability of sites for seagrass transplantation in the West coast of South Sulawesi (3 sites at Labakkang Coast, 3 sites at Awerange Bay, and 3 sites at Lale-Lae Island). Of the 9 sites, two sites were predicted by the site-selection model to be the most suitable sites for seagrass transplantation: Site II at Labakkang Coast and Site III at Lale-Lae Island.

Cholinesterases in Gambusia yucatana: Biochemical Characterization and its Relationship with Sex and Total Length.

PubMed

Rodríguez-Fuentes, Gabriela; Marín-López, Valeria; Hernández-Márquez, Esperanza

2016-12-01

Since several reports have indicated that cholinesterases (ChE) type and distribution is species specific and that in some species there is a relationship among gender, size and ChE activities, characterization has been suggested. The aim of the present study was to characterize the ChE present in head and muscle of Gambusia yucatana (using selective substrates and inhibitors) and to find its relationship with total length or gender. Results indicated that the ChE present in G. yucatana is an acetylcholinesterase (AChE) with high sensitivity to BW284C51 and an atypical smaller Km with butyrylthiocholine. Scatterplots indicated that there is no linearity between total length and AChE in male or female wild mosquitofish. There were no sex differences in AChE activities. Results indicated significant differences between a single collection site in the Yucatan peninsula and depurated organisms. This study emphasized the importance of characterizing ChE before usage in biomonitoring.

sc-PDB: a 3D-database of ligandable binding sites--10 years on.

PubMed

Desaphy, Jérémy; Bret, Guillaume; Rognan, Didier; Kellenberger, Esther

2015-01-01

The sc-PDB database (available at http://bioinfo-pharma.u-strasbg.fr/scPDB/) is a comprehensive and up-to-date selection of ligandable binding sites of the Protein Data Bank. Sites are defined from complexes between a protein and a pharmacological ligand. The database provides the all-atom description of the protein, its ligand, their binding site and their binding mode. Currently, the sc-PDB archive registers 9283 binding sites from 3678 unique proteins and 5608 unique ligands. The sc-PDB database was publicly launched in 2004 with the aim of providing structure files suitable for computational approaches to drug design, such as docking. During the last 10 years we have improved and standardized the processes for (i) identifying binding sites, (ii) correcting structures, (iii) annotating protein function and ligand properties and (iv) characterizing their binding mode. This paper presents the latest enhancements in the database, specifically pertaining to the representation of molecular interaction and to the similarity between ligand/protein binding patterns. The new website puts emphasis in pictorial analysis of data. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Bioprospecting for hyper-lipid producing microalgal strains for sustainable biofuel production.

PubMed

Mutanda, T; Ramesh, D; Karthikeyan, S; Kumari, S; Anandraj, A; Bux, F

2011-01-01

Global petroleum reserves are shrinking at a fast pace, increasing the demand for alternate fuels. Microalgae have the ability to grow rapidly, and synthesize and accumulate large amounts (approximately 20-50% of dry weight) of neutral lipid stored in cytosolic lipid bodies. A successful and economically viable algae based biofuel industry mainly depends on the selection of appropriate algal strains. The main focus of bioprospecting for microalgae is to identify unique high lipid producing microalgae from different habitats. Indigenous species of microalgae with high lipid yields are especially valuable in the biofuel industry. Isolation, purification and identification of natural microalgal assemblages using conventional techniques is generally time consuming. However, the recent use of micromanipulation as a rapid isolating tool allows for a higher screening throughput. The appropriate media and growth conditions are also important for successful microalgal proliferation. Environmental parameters recorded at the sampling site are necessary to optimize in vitro growth. Identification of species generally requires a combination of morphological and genetic characterization. The selected microalgal strains are grown in upscale systems such as raceway ponds or photobireactors for biomass and lipid production. This paper reviews the recent methodologies adopted for site selection, sampling, strain selection and identification, optimization of cultural conditions for superior lipid yield for biofuel production. Energy generation routes of microalgal lipids and biomass are discussed in detail. Copyright © 2010 Elsevier Ltd. All rights reserved.

Computational Design of Ligand Binding Proteins with High Affinity and Selectivity

PubMed Central

Dou, Jiayi; Doyle, Lindsey; Nelson, Jorgen W.; Schena, Alberto; Jankowski, Wojciech; Kalodimos, Charalampos G.; Johnsson, Kai; Stoddard, Barry L.; Baker, David

2014-01-01

The ability to design proteins with high affinity and selectivity for any given small molecule would have numerous applications in biosensing, diagnostics, and therapeutics, and is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition phenomena. Attempts to design ligand binding proteins have met with little success, however, and the computational design of precise molecular recognition between proteins and small molecules remains an “unsolved problem”1. We describe a general method for the computational design of small molecule binding sites with pre-organized hydrogen bonding and hydrophobic interfaces and high overall shape complementary to the ligand, and use it to design protein binding sites for the steroid digoxigenin (DIG). Of 17 designs that were experimentally characterized, two bind DIG; the highest affinity design has the lowest predicted interaction energy and the most pre-organized binding site in the set. A comprehensive binding-fitness landscape of this design generated by library selection and deep sequencing was used to guide optimization of binding affinity to a picomolar level, and two X-ray co-crystal structures of optimized complexes show atomic level agreement with the design models. The designed binder has a high selectivity for DIG over the related steroids digitoxigenin, progesterone, and β-estradiol, which can be reprogrammed through the designed hydrogen-bonding interactions. Taken together, the binding fitness landscape, co-crystal structures, and thermodynamic binding parameters illustrate how increases in binding affinity can result from distal sequence changes that limit the protein ensemble to conformers making the most energetically favorable interactions with the ligand. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics, and diagnostics. PMID:24005320

Biofouling of contaminated ground-water recovery wells: Characterization of microorganisms

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

Taylor, S.W.; Lange, C.R.; Lesold, E.A.

1997-11-01

The taxonomy and physiology of microorganisms isolated from contaminated ground-water recovery wells prone to biofouling are characterized for an industrial site in Rochester, New York. Principal aquifer contaminants include acetone, cyclohexane, dichloroethane, dichloromethane, 1,4-dioxane, isopropanol, methanol, and toluene. These contaminants represent a significant fraction (up to 95%) of the total organic carbon in the ground water. Ground-water samples from 12 recovery wells were used to isolate, quantify, and identify aerobic and anaerobic bacterial populations. Samples from selected wells were also characterized geochemically to assess redox conditions and availability of essential and trace nutrients. Dominant bacteria, listed in order of descendingmore » numbers, including sulfate-reducers (Desulfovibrio desulfuricans), anaerobic heterotrophs (Actinomyces, Bacteriodes, Bacillus, Agrobacterium), aerobic heterotrophs (Pseudomonas, Flavobacterium, Nocardia, Citrobacter), iron-oxidizers (Gallionella ferruginea, Crenothrix polyspora), iron-reducers (Shewanella), and sulfur-oxidizers (Thiobacillus ferrooxidans). Fungi were also recovered in low numbers. Both aerobic and anaerobic heterotrophs were able to utilize all principal contaminants as sole carbon and energy sources except 1,4-dioxane. The prevalence of heterotrophic bacteria and their ability to use the available anthropogenic carbon suggests that aerobic and anaerobic heterotrophs contribute to the biofouling of wells at this site, in addition to the often cited fouling due to iron-oxidizing bacteria and sulfate-reducing bacteria.« less

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

Leenheer, J.A.; Brown, G.K.; Cabaniss, S.E.

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca{sup 2+}, Cd{sup 2+}, Cu{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca{sup 2+} ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The metal binding fraction was characterized by quantitative {sup 13}C NMR, {sup 1}H NMR, and FT-IR spectrometry andmore » elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca{sup 2+} binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.« less

FIELD EVALUATION OF IN-SITU BIODEGRADATION OF CHLORINATED ETHENES: PART I, METHODOLOGY AND FIELD SITE CHARACTERIZATION

EPA Science Inventory

Careful site characterization and implementation of quantitative monitoring methods are prerequisites for a convincing evaluation of enhanced biostimulation for aquifer restoration. his paper describes the characterization of a site at Moffett Naval Air Station, Mountain View, Ca...

SITE CHARACTERIZATION AND ANALYSIS PENETROMETER SYSTEM(SCAPS) LAZER-INDUCED FLUORESCENCE (LIF) SENSOR AND SUPPORT SYSTEM

EPA Science Inventory

The Consortium for Site Characterization Technology (CSCT) has established a formal program to accelerate acceptance and application of innovative monitoring and site characterization technologies that improve the way the nation manages its environmental problems. In 1995 the CS...

Copper-catalyst-controlled site-selective allenylation of ketones and aldehydes with propargyl boronates.

PubMed

Fandrick, Keith R; Ogikubo, Junichi; Fandrick, Daniel R; Patel, Nitinchandra D; Saha, Jaideep; Lee, Heewon; Ma, Shengli; Grinberg, Nelu; Busacca, Carl A; Senanayake, Chris H

2013-03-15

A practical and highly site-selective copper-PhBPE-catalyst-controlled allenylation with propargyl boronates has been developed. The methodology has shown to be tolerant of diverse ketones and aldehydes providing the allenyl adducts in high selectivity. The BPE ligand and boronate substituents were shown to direct the site selectivity for which either propargyl or allenyl adducts can be acquired in high selectivity. A model is proposed that explains the origin of the site selectivity.

COMPARISON OF RANDOM AND SYSTEMATIC SITE SELECTION FOR ASSESSING ATTAINMENT OF AQUATIC LIFE USES IN SEGMENTS OF THE OHIO RIVER

EPA Science Inventory

This report is a description of field work and data analysis results comparing a design comparable to systematic site selection with one based on random selection of sites. The report is expected to validate the use of random site selection in the bioassessment program for the O...

Importance of geologic characterization of potential low-level radioactive waste disposal sites

USGS Publications Warehouse

Weibel, C.P.; Berg, R.C.

1991-01-01

Using the example of the Geff Alternative Site in Wayne County, Illinois, for the disposal of low-level radioactive waste, this paper demonstrates, from a policy and public opinion perspective, the importance of accurately determining site stratigraphy. Complete and accurate characterization of geologic materials and determination of site stratigraphy at potential low-level waste disposal sites provides the frame-work for subsequent hydrologic and geochemical investigations. Proper geologic characterization is critical to determine the long-term site stability and the extent of interactions of groundwater between the site and its surroundings. Failure to adequately characterize site stratigraphy can lead to the incorrect evaluation of the geology of a site, which in turn may result in a lack of public confidence. A potential problem of lack of public confidence was alleviated as a result of the resolution and proper definition of the Geff Alternative Site stratigraphy. The integrity of the investigation was not questioned and public perception was not compromised. ?? 1991 Springer-Verlag New York Inc.

ExoMars 2018: the four final candidate Landing Sites

NASA Astrophysics Data System (ADS)

Loizeau, Damien; Flahaut, Jessica; Vago, Jorge L.; Hauber, Ernst; Bridges, John C.

2015-04-01

The ExoMars 2018 mission will land a rover on Mars, its scientific objectives are to search for signs of past and present life on Mars and to investigate the water/geochemical environment as a function of depth in the shallow subsurface. The rover will be able to travel several kilometres, analyzing surface and subsurface samples, down to a 2 meter depth. The very powerful combination of mobility with the ability to access in-depth locations, where organic molecules can be well preserved, is unique to this mission [1]. An invitation has been sent to the community to propose scientifically compelling sites for the mission [2], which comply to the main engineering constraints for landing and operation safety. Scientifically interesting sites include locations with evidence for long duration or frequently recurring aqueous activity, low energy transport and deposition, fined-grained, recently exposed sediments, and/or hydrated minerals such as clays or evaporites. The outcrops of interest must be distributed over the landing ellipse to ensure that the rover can access some of them over a short distance [2]. The received proposals have been reviewed by the Landing Site Selection Working Group (LSSWG) and at first eight sites were found to be compliant with the science, engineering, and planetary protection requirements [3]. These sites were presented by their proposers and discussed at the first landing site workshop that took place in ESAC, Spain, 26-28 March 2014. Following that workshop, four sites were selected for further investigation, on the base of their higher potential for long lived water activity, the presence of fine grained sediments, and also importantly on the high concentration of potential targets of interest over the whole landing ellipse [3]. The analysis of these sites, both in term of scientific relevance and engineering safety, is still on-going. Latest findings were presented during a second workshop that took place in ALTEC, Torino, Italy, 11 December 2014. The Aram Dorsum site comprises Noachian layered sedimentary rocks with a prominent inverted channel system (>80 km long). Potential targets include the inverted channel, the channel margins, a channel transition unit, and pits present within the floodplain. The Hypanis Vallis site lies near two fluvial fan/deltaic systems at the termination of Hypanis and Sabrina Valles. Potential targets include mainly outcrops of expected fine-grained sediments on the smooth transition unit that surrounds the delta/fan, and units around the rim of Magong crater. The Mawrth Vallis site contains one of the largest exposures of phyllosilicates detected on the Martian surface, in Noachian terrain [8]. Potential targets include the mineralogically diverse clay-rich outcrops and ancient channels. The Oxia Planum site lies on Fe/Mg phyllosilicates-rich exposures associated to layered rocks that may be related to the Mawrth Vallis sequence. Potential targets include the clay-rich outcrops as well as channels and inverted channels and delta-fan deposits. New data are being actively acquired by the HiRISE, CRISM and HRSC teams to support the ExoMars 2018 landing site selection process. The ellipses are large and new data are important for characterizing the potential targets and evaluating the safety of the sites. The proposing teams, the ExoMars project team and the LSSWG will continue their analysis and comparison of the sites, aiming to complete the certification of at least one site by September 2016 -- in time for the start of the mission's Critical Design Review (CDR). The final selection of the landing site is expected within 2017. References: [1] http://exploration.esa.int/mars/48088-mission-overview/ [2] http://exploration.esa.int/mars/53462-call-for-exo mars-2018-landing-site-selection/ [3] ExoMars 2018 LSSWG recommendation: http://exploration.esa.int/mars/54707-recommendation-for-the-narrowing-of-exomars-2018-landing-sites/

Molecular Characterization of Monoclonal Antibodies that Inhibit Acetylcholinesterase by Targeting the Peripheral Site and Backdoor Region

PubMed Central

Essono, Sosthène; Mondielli, Grégoire; Lamourette, Patricia; Boquet, Didier; Grassi, Jacques; Marchot, Pascale

2013-01-01

The inhibition properties and target sites of monoclonal antibodies (mAbs) Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE), have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab) retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis. PMID:24146971

Site selection for MSFC operational tests of solar heating and cooling systems

NASA Technical Reports Server (NTRS)

1978-01-01

The criteria, methodology, and sequence aspects of the site selection process are presented. This report organized the logical thought process that should be applied to the site selection process, but final decisions are highly selective.

UTSA-74: A MOF-74 Isomer with Two Accessible Binding Sites per Metal Center for Highly Selective Gas Separation.

PubMed

Luo, Feng; Yan, Changsheng; Dang, Lilong; Krishna, Rajamani; Zhou, Wei; Wu, Hui; Dong, Xinglong; Han, Yu; Hu, Tong-Liang; O'Keeffe, Michael; Wang, Lingling; Luo, Mingbiao; Lin, Rui-Biao; Chen, Banglin

2016-05-04

A new metal-organic framework Zn2(H2O)(dobdc)·0.5(H2O) (UTSA-74, H4dobdc = 2,5-dioxido-1,4-benzenedicarboxylic acid), Zn-MOF-74/CPO-27-Zn isomer, has been synthesized and structurally characterized. It has a novel four coordinated fgl topology with one-dimensional channels of about 8.0 Å. Unlike metal sites in the well-established MOF-74 with a rod-packing structure in which each of them is in a five coordinate square pyramidal coordination geometry, there are two different Zn(2+) sites within the binuclear secondary building units in UTSA-74 in which one of them (Zn1) is in a tetrahedral while another (Zn2) in an octahedral coordination geometry. After activation, the two axial water molecules on Zn2 sites can be removed, generating UTSA-74a with two accessible gas binding sites per Zn2 ion. Accordingly, UTSA-74a takes up a moderately high and comparable amount of acetylene (145 cm(3)/cm(3)) to Zn-MOF-74. Interestingly, the accessible Zn(2+) sites in UTSA-74a are bridged by carbon dioxide molecules instead of being terminally bound in Zn-MOF-74, so UTSA-74a adsorbs a much smaller amount of carbon dioxide (90 cm(3)/cm(3)) than Zn-MOF-74 (146 cm(3)/cm(3)) at room temperature and 1 bar, leading to a superior MOF material for highly selective C2H2/CO2 separation. X-ray crystal structures, gas sorption isotherms, molecular modeling, and simulated and experimental breakthroughs comprehensively support this result.

Rationally designed fluorescently labeled sulfate-binding protein mutants: evaluation in the development of a sensing system for sulfate

NASA Technical Reports Server (NTRS)

Shrestha, Suresh; Salins, Lyndon L E.; Mark Ensor, C.; Daunert, Sylvia

2002-01-01

Periplasmic binding proteins from E. coli undergo large conformational changes upon binding their respective ligands. By attaching a fluorescent probe at rationally selected unique sites on the protein, these conformational changes in the protein can be monitored by measuring the changes in fluorescence intensity of the probe which allow the development of reagentless sensing systems for their corresponding ligands. In this work, we evaluated several sites on bacterial periplasmic sulfate-binding protein (SBP) for attachment of a fluorescent probe and rationally designed a reagentless sensing system for sulfate. Eight different mutants of SBP were prepared by employing the polymerase chain reaction (PCR) to introduce a unique cysteine residue at a specific location on the protein. The sites Gly55, Ser90, Ser129, Ala140, Leu145, Ser171, Val181, and Gly186 were chosen for mutagenesis by studying the three-dimensional X-ray crystal structure of SBP. An environment-sensitive fluorescent probe (MDCC) was then attached site-specifically to the protein through the sulfhydryl group of the unique cysteine residue introduced. Each fluorescent probe-conjugated SBP mutant was characterized in terms of its fluorescence properties and Ser171 was determined to be the best site for the attachment of the fluorescent probe that would allow for the development of a reagentless sensing system for sulfate. Three different environment-sensitive fluorescent probes (1,5-IAEDANS, MDCC, and acylodan) were studied with the SBP171 mutant protein. A calibration curve for sulfate was constructed using the labeled protein and relating the change in the fluorescence intensity with the amount of sulfate present in the sample. The detection limit for sulfate was found to be in the submicromolar range using this system. The selectivity of the sensing system was demonstrated by evaluating its response to other anions. A fast and selective sensing system with detection limits for sulfate in the submicromolar range was developed. Copyright 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 517-526, 2002.

Coalescence and genetic diversity in sexual populations under selection.

PubMed

Neher, Richard A; Kessinger, Taylor A; Shraiman, Boris I

2013-09-24

In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting interference between linked alleles reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we present a simple but powerful scaling analysis identifying the unit of selection as the genomic "linkage block" with a characteristic length, , determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with the strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra compared with computer simulations. This linkage block approximation is accurate for the entire spectrum of strength of selection and is particularly powerful in scenarios with many weakly selected loci. The latter limit allows us to characterize coalescence, genetic diversity, and the speed of adaptation in the infinitesimal model of quantitative genetics.

Active Site Metal Identity Alters Histone Deacetylase 8 Substrate Selectivity: A Potential Novel Regulatory Mechanism.

PubMed

Castaneda, Carol Ann; Lopez, Jeffrey E; Joseph, Caleb G; Scholle, Michael D; Mrksich, Milan; Fierke, Carol A

2017-10-24

Histone deacetylase 8 (HDAC8) is a well-characterized member of the class I acetyl-lysine deacetylase (HDAC) family. Previous work has shown that the efficiency of HDAC8-catalyzed deacetylation of a methylcoumarin peptide varies depending on the identity of the divalent metal ion in the HDAC8 active site. Here we demonstrate that both HDAC8 activity and substrate selectivity for a diverse range of peptide substrates depend on the identity of the active site metal ion. Varied deacetylase activities of Fe(II)- and Zn(II)-HDAC8 toward an array of peptide substrates were identified using self-assembled monolayers for matrix-assisted laser desorption ionization (SAMDI) mass spectrometry. Subsequently, the metal dependence of deacetylation of peptides of biological interest was measured using an in vitro peptide assay. While Fe(II)-HDAC8 is generally more active than Zn(II)-HDAC8, the Fe(II)/Zn(II) HDAC8 activity ratio varies widely (from 2 to 150) among the peptides tested. These data provide support for the hypothesis that HDAC8 may undergo metal switching in vivo that, in turn, may regulate its activity. However, future studies are needed to explore the identity of the metal ion bound to HDAC8 in cells under varied conditions.

Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3

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

Artavanis-Tsakonas, Katerina; Weihofen, Wilhelm A.; Antos, John M.

Like their human hosts, Plasmodium falciparum parasites rely on the ubiquitin-proteasome system for survival. We previously identified PfUCHL3, a deubiquitinating enzyme, and here we characterize its activity and changes in active site architecture upon binding to ubiquitin. We find strong evidence that PfUCHL3 is essential to parasite survival. The crystal structures of both PfUCHL3 alone and in complex with the ubiquitin-based suicide substrate UbVME suggest a rather rigid active site crossover loop that likely plays a role in restricting the size of ubiquitin adduct substrates. Molecular dynamics simulations of the structures and a model of the PfUCHL3-PfNedd8 complex allowed themore » identification of shared key interactions of ubiquitin and PfNedd8 with PfUCHL3, explaining the dual specificity of this enzyme. Distinct differences observed in ubiquitin binding between PfUCHL3 and its human counterpart make it likely that the parasitic DUB can be selectively targeted while leaving the human enzyme unaffected.« less

Robustness of non-interdependent and interdependent networks against dependent and adaptive attacks

NASA Astrophysics Data System (ADS)

Tyra, Adam; Li, Jingtao; Shang, Yilun; Jiang, Shuo; Zhao, Yanjun; Xu, Shouhuai

2017-09-01

Robustness of complex networks has been extensively studied via the notion of site percolation, which typically models independent and non-adaptive attacks (or disruptions). However, real-life attacks are often dependent and/or adaptive. This motivates us to characterize the robustness of complex networks, including non-interdependent and interdependent ones, against dependent and adaptive attacks. For this purpose, dependent attacks are accommodated by L-hop percolation where the nodes within some L-hop (L ≥ 0) distance of a chosen node are all deleted during one attack (with L = 0 degenerating to site percolation). Whereas, adaptive attacks are launched by attackers who can make node-selection decisions based on the network state in the beginning of each attack. The resulting characterization enriches the body of knowledge with new insights, such as: (i) the Achilles' Heel phenomenon is only valid for independent attacks, but not for dependent attacks; (ii) powerful attack strategies (e.g., targeted attacks and dependent attacks, dependent attacks and adaptive attacks) are not compatible and cannot help the attacker when used collectively. Our results shed some light on the design of robust complex networks.

Computerized stratified random site-selection approaches for design of a ground-water-quality sampling network

USGS Publications Warehouse

Scott, J.C.

1990-01-01

Computer software was written to randomly select sites for a ground-water-quality sampling network. The software uses digital cartographic techniques and subroutines from a proprietary geographic information system. The report presents the approaches, computer software, and sample applications. It is often desirable to collect ground-water-quality samples from various areas in a study region that have different values of a spatial characteristic, such as land-use or hydrogeologic setting. A stratified network can be used for testing hypotheses about relations between spatial characteristics and water quality, or for calculating statistical descriptions of water-quality data that account for variations that correspond to the spatial characteristic. In the software described, a study region is subdivided into areal subsets that have a common spatial characteristic to stratify the population into several categories from which sampling sites are selected. Different numbers of sites may be selected from each category of areal subsets. A population of potential sampling sites may be defined by either specifying a fixed population of existing sites, or by preparing an equally spaced population of potential sites. In either case, each site is identified with a single category, depending on the value of the spatial characteristic of the areal subset in which the site is located. Sites are selected from one category at a time. One of two approaches may be used to select sites. Sites may be selected randomly, or the areal subsets in the category can be grouped into cells and sites selected randomly from each cell.

A FIELD EVALUATION OF IN-SITU BIODEGRADATION OF CHLORINATED ETHENES: PART I, METHODOLOGY AND FIELD SITE CHARACTERIZATION

EPA Science Inventory

Careful site characterization and implementation of quantitative monitoring methods are prerequisites for a convincing evaluation of enhanced biostimulation for aquifer restoration. This paper describes the characterization of a site at Moffett Naval Air Station, Mountain View, C...

10 CFR 60.16 - Site characterization plan required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Site characterization plan required. 60.16 Section 60.16 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.16 Site characterization plan required. Before proceeding to...

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

PubMed

Weininger, Ulrich; Respondek, Michal; Akke, Mikael

2012-09-01

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

Measurement Sets and Sites Commonly used for Characterizations

NASA Technical Reports Server (NTRS)

Pagnutti, Mary; Holekamp, Kara; Ryan, Robert; Blonski, Slawomir; Sellers, Richard; Davis, Bruce; Zanoni, Vicki

2002-01-01

Scientists with NASA's Earth Science Applications Directorate are creating a well-characterized Verification & Validation (V&V) site at the Stennis Space Center (SSC). This site enables the in-flight characterization of remote sensing systems and the data that they require. The data are predominantly acquired by commercial, high-spatial resolution satellite systems, such as IKONOS and QuickBird 2, and airborne systems. The smaller scale of these newer high-resolution remote sensing systems allows scientists to characterize the geometric, spatial, and radiometric data properties using a single V&V site. The targets and techniques used to characterize data from these newer systems can differ significantly from the earlier, coarser spatial resolution systems. Scientists are also using the SSC V&V site to characterize thermal infrared systems and active Light Detection and Ranging (LIDAR) systems. SSC employs geodetic targets, edge targets, radiometric tarps, and thermal calibration ponds to characterize remote sensing data products. This paper presents a proposed set of required measurements for visible-through-longwave infrared remote sensing systems, and a description of the Stennis characterization. Other topics discussed inslude: 1) use of ancillary atmospheric and solar measurements taken at SSC that support various characterizations, 2) other sites used for radiometric, geometric, and spatial characterization in the continental United States,a nd 3) the need for a standardized technique to be adopted by the Committee on Earth Observation Satellites (CEOS) and other organizations.

Static and dynamic characterization of alluvial deposits in the Tiber River Valley: New data for assessing potential ground motion in the City of Rome

NASA Astrophysics Data System (ADS)

Bozzano, F.; Caserta, A.; Govoni, A.; Marra, F.; Martino, S.

2008-01-01

The paper presents the results of a case study conducted on the Holocene alluvial deposits of the Tiber River valley, in the city of Rome. The main test site selected for the study, Valco S. Paolo, is located about 2 km South of Rome's historical centre. The alluvial deposits were dynamically characterized in a comprehensive way via site investigations and geotechnical laboratory tests. Normalized shear modulus decay and damping curves (G/G0 and D/D0 vs γ) were obtained for the dominantly fine-grained levels. The curves demonstrate that these levels have a more marked shear stiffness decay if compared with the underlying Pliocene bedrock. Decay curves from laboratory tests for the Tiber alluvia correlated well with the trend of the function proposed by Hardin and Drnevich, making it possible to derive their specific interpolation function coefficients. Use was made of the extrapolation of the findings from the Valco S. Paolo test site to a large part of Rome's historical centre by means of two other test sites, supported by an engineering-geology model of the complex spatial distribution of the Tiber alluvia. The experimental Valco S. Paolo Vs profile was extrapolated to the other test sites on the basis of a stratigraphic criterion; the analysis of seismic noise measurements, obtained for the three test sites, validated the engineering-geology based extrapolation and showed that the main rigidity contrast occurs inside the alluvial body (at the contact with the underlying basal gravel-level G) and not between the alluvia and the Plio-Pleistocene bedrock, composed of highly consistent clay (Marne Vaticane). The 1D modeling of local seismic response to the maximum expected earthquakes in the city of Rome confirms that the deposits have one principal mode of vibration at about 1 Hz. However, the simulation also evidenced that the silty-clay deposits (level C), making up the most part of the Tiber alluvial body, play a key role in characterizing the soil column deformation profile since it can be affected by non linear effects induced by the maximum expected earthquake when some stratigraphic conditions are satisfied.

Sandhill crane roost selection, human disturbance, and forage resources

USGS Publications Warehouse

Pearse, Aaron T.; Krapu, Gary; Brandt, David

2017-01-01

Sites used for roosting represent a key habitat requirement for many species of birds because availability and quality of roost sites can influence individual fitness. Birds select roost sites based on numerous factors, requirements, and motivations, and selection of roosts can be dynamic in time and space because of various ecological and environmental influences. For sandhill cranes (Antigone canadensis) at their main spring-staging area along the Platte River in south-central Nebraska, USA, past investigations of roosting cranes focused on physical channel characteristics related to perceived security as motivating roost distribution. We used 6,310 roost sites selected by 313 sandhill cranes over 5 spring migration seasons (2003–2007) to quantify resource selection functions of roost sites on the central Platte River using a discrete choice analysis. Sandhill cranes generally showed stronger selection for wider channels with shorter bank vegetation situated farther from potential human disturbance features such as roads, bridges, and dwellings. Furthermore, selection for roost sites with preferable physical characteristics (wide channels with short bank vegetation) was more resilient to nearby disturbance features than more narrow channels with taller bank vegetation. The amount of cornfields surrounding sandhill crane roost sites positively influenced relative probability of use but only for more narrow channels < 100 m and those with shorter bank vegetation. We confirmed key resource features that sandhill cranes selected at river channels along the Platte River, and after incorporating spatial variation due to human disturbance, our understanding of roost site selection was more robust, providing insights on how disturbance may interact with physical habitat features. Managers can use information on roost-site selection when developing plans to increase probability of crane use at existing roost sites and to identify new areas for potential use if existing sites become limited.

Characterization of site conditions for selected seismic stations in eastern part of Romania

NASA Astrophysics Data System (ADS)

Grecu, B.; Zaharia, B.; Diaconescu, M.; Bala, A.; Nastase, E.; Constantinescu, E.; Tataru, D.

2018-02-01

Strong motion data are essential for seismic hazard assessment. To correctly understand and use this kind of data is necessary to have a good knowledge of local site conditions. Romania has one of the largest strong motion networks in Europe with 134 real-time stations. In this work, we aim to do a comprehensive site characterization for eight of these stations located in the eastern part of Romania. We make use of a various seismological dataset and we perform ambient noise and earthquake-based investigations to estimate the background noise level, the resonance frequencies and amplification of each site. We also derive the Vs30 parameter from the surface shear-wave velocity profiles obtained through the inversion of the Rayleigh waves recorded in active seismic measurements. Our analyses indicate similar results for seven stations: high noise levels for frequencies larger than 1 Hz, well defined fundamental resonance at low frequencies (0.15-0.29 Hz), moderate amplification levels (up to 4 units) for frequencies between 0.15 and 5-7 Hz and same soil class (type C) according to the estimated Vs30 and Eurocode 8. In contrast, the eighth station for which the soil class is evaluated of type B exhibits a very good noise level for a wide range of frequencies (0.01-20 Hz), a broader fundamental resonance at high frequencies ( 8 Hz) and a flat amplification curve between 0.1 and 3-4 Hz.

The path to a successful one-million tonne demonstration of geological sequestration: Characterization, cooperation, and collaboration

USGS Publications Warehouse

Finley, R.J.; Greenberg, S.E.; Frailey, S.M.; Krapac, I.G.; Leetaru, H.E.; Marsteller, S.

2011-01-01

The development of the Illinois Basin-Decatur USA test site for a 1 million tonne injection of CO2 into the Mount Simon Sandstone saline reservoir beginning in 2011 has been a multiphase process requiring a wide array of personnel and resources that began in 2003. The process of regional characterization took two years as part of a Phase I effort focused on the entire Illinois Basin, located in Illinois, Indiana, and Kentucky, USA. Seeking the cooperation of an industrial source of CO2 and site selection within the Basin took place during Phase II while most of the concurrent research emphasis was on a set of small-scale tests of Enhanced Oil Recovery (EOR) and CO2 injection into a coal seam. Phase III began the commitment to the 1 million-tonne test site development through the collaboration of the Archer Daniels Midland Company (ADM) who is providing a site, the CO2, and developing a compression facility, of Schlumberger Carbon Services who is providing expertise for operations, drilling, geophysics, risk assessment, and reservoir modelling, and of the Illinois State Geological Survey (ISGS) whose geologists and engineers lead the Midwest Geological Sequestration Consortium (MGSC). Communications and outreach has been a collaborative effort of ADM, ISGS and Schlumberger Carbon Services. The Consortium is one of the seven Regional Carbon Sequestration Partnerships, a carbon sequestration research program supported by the National Energy Technology Laboratory of the U.S. Department of Energy. ?? 2011 Published by Elsevier Ltd.

An assessment of health risks associated with arsenic exposure via consumption of homegrown vegetables near contaminated glassworks sites.

PubMed

Uddh-Söderberg, Terese E; Gunnarsson, Sara J; Hogmalm, K Johan; Lindegård, M I Boel G; Augustsson, Anna L M

2015-12-01

The health risk posed by arsenic in vegetables grown in private gardens near 22 contaminated glassworks sites was investigated in this study. Firstly, vegetable (lettuce and potato) and soil samples were collected and arsenic concentrations measured to characterize the arsenic uptake in the selected crops. Secondly, a probabilistic exposure assessment was conducted to estimate the average daily intake (ADIveg), which was then evaluated against toxicological reference values by the calculation of hazard quotients (HQs) and cancer risks (CRs). The results show that elevated arsenic concentrations in residential garden soils are mirrored by elevated concentrations in vegetables, and that consumption of these vegetables alone may result in an unacceptable cancer risk; the calculated reasonable maximum exposure, for example, corresponded to a cancer incidence 20 times higher than the stated tolerance limit. However, the characterization of risk depends to a great extent on which toxicological reference value is used for comparison, as well as how the exposure is determined. Based on the assumptions made in the present study, the threshold levels for chronic non-carcinogenic or acute effects were not exceeded, but the cancer risks indicated highlight the need for further exposure studies, as dietary intake involves more than just homegrown vegetables and total exposure is a function of more than just one exposure pathway. In addition, glassworks sites--and contaminated sites in general--contain multiple contaminants, affecting the final and total risk. Copyright © 2015. Published by Elsevier B.V.

Human recombinant beta-secretase immobilized enzyme reactor for fast hits' selection and characterization from a virtual screening library.

PubMed

De Simone, Angela; Mancini, Francesca; Cosconati, Sandro; Marinelli, Luciana; La Pietra, Valeria; Novellino, Ettore; Andrisano, Vincenza

2013-01-25

In the present work, a human recombinant BACE1 immobilized enzyme reactor (hrBACE1-IMER) has been applied for the sensitive fast screening of 38 compounds selected through a virtual screening approach. HrBACE1-IMER was inserted into a liquid chromatograph coupled with a fluorescent detector. A fluorogenic peptide substrate (M-2420), containing the β-secretase site of the Swedish mutation of APP, was injected and cleaved in the on-line HPLC-hrBACE1-IMER system, giving rise to the fluorescent product. The compounds of the library were tested for their ability to inhibit BACE1 in the immobilized format and to reduce the area related to the chromatographic peak of the fluorescent enzymatic product. The results were validated in solution by using two different FRET methods. Due to the efficient virtual screening methodology, more than fifty percent of the selected compounds showed a measurable inhibitory activity. One of the most active compound (a bis-indanone derivative) was characterized in terms of IC(50) and K(i) determination on the hrBACE1-IMER. Thus, the hrBACE1-IMER has been confirmed as a valid tool for the throughput screening of different chemical entities with potency lower than 30μM for the fast hits' selection and for mode of action determination. Copyright © 2012 Elsevier B.V. All rights reserved.

A simple and highly selective 2,2-diferrocenylpropane-based multi-channel ion pair receptor for Pb(2+) and HSO4(-).

PubMed

Wan, Qian; Zhuo, Ji-Bin; Wang, Xiao-Xue; Lin, Cai-Xia; Yuan, Yao-Feng

2015-03-28

A structurally simple, 2,2-diferrocenylpropane-based ion pair receptor 1 was synthesized and characterized by (1)H NMR, (13)C NMR, HRMS, elemental analyses, and single-crystal X-ray diffraction. The ion pair receptor 1 showed excellent selectivity and sensitivity towards Pb(2+) with multi-channel responses: a fluorescence enhancement (more than 42-fold), a notable color change from yellow to red, redox anodic shift (ΔE1/2 = 151 mV), while HSO4(-) promoted fluorescence enhancement when Pb(2+) or Zn(2+) was bonded to the cation binding-site. (1)H NMR titration and density functional theory were performed to reveal the sensing mechanism based on photo-induced electron transfer (PET).

Zeolite-encapsulated Co(II), Mn(II), Cu(II) and Cr(III) salen complexes as catalysts for efficient selective oxidation of benzyl alcohol

NASA Astrophysics Data System (ADS)

Li, F. H.; Bi, H.; Huang, D. X.; Zhang, M.; Song, Y. B.

2018-01-01

Co(II), Mn(II), Cu(II) and Cr(III) salen type complexes were synthesized in situ in Y zeolite by the reaction of ion-exchanged metal ions with the flexible ligand molecules that had diffused into the cavities. Data of characterization indicates the formation of metal salen complexes in the pores without affecting the zeolite framework structure, the absence of any extraneous species and the geometry of encapsulated complexes. The catalytic activity results show that Cosalcyen Y exhibited higher catalytic activity in the water phase selective oxidation of benzyl alcohol, which could be attributed to their geometry and the steric environment of the metal actives sites.

Site-Specific Recombination at XerC/D Sites Mediates the Formation and Resolution of Plasmid Co-integrates Carrying a blaOXA-58- and TnaphA6-Resistance Module in Acinetobacter baumannii

PubMed Central

Cameranesi, María M.; Morán-Barrio, Jorgelina; Limansky, Adriana S.; Repizo, Guillermo D.; Viale, Alejandro M.

2018-01-01

Members of the genus Acinetobacter possess distinct plasmid types which provide effective platforms for the acquisition, evolution, and dissemination of antimicrobial resistance structures. Many plasmid-borne resistance structures are bordered by short DNA sequences providing potential recognition sites for the host XerC and XerD site-specific tyrosine recombinases (XerC/D-like sites). However, whether these sites are active in recombination and how they assist the mobilization of associated resistance structures is still poorly understood. Here we characterized the plasmids carried by Acinetobacter baumannii Ab242, a multidrug-resistant clinical strain belonging to the ST104 (Oxford scheme) which produces an OXA-58 carbapenem-hydrolyzing class-D β-lactamase (CHDL). Plasmid sequencing and characterization of replication, stability, and adaptive modules revealed the presence in Ab242 of three novel plasmids lacking self-transferability functions which were designated pAb242_9, pAb242_12, and pAb242_25, respectively. Among them, only pAb242_25 was found to carry an adaptive module encompassing an ISAba825-blaOXA-58 arrangement accompanied by a TnaphA6 transposon, the whole structure conferring simultaneous resistance to carbapenems and aminoglycosides. Ab242 plasmids harbor several XerC/D-like sites, with most sites found in pAb242_25 located in the vicinity or within the adaptive module described above. Electrotransformation of susceptible A. nosocomialis cells with Ab242 plasmids followed by imipenem selection indicated that the transforming plasmid form was a co-integrate resulting from the fusion of pAb242_25 and pAb242_12. Further characterization by cloning and sequencing studies indicated that a XerC/D site in pAb242_25 and another in pAb242_12 provided the active sister pair for the inter-molecular site-specific recombination reaction mediating the fusion of these two plasmids. Moreover, the resulting co-integrate was found also to undergo intra-molecular resolution at the new pair of XerC/D sites generated during fusion thus regenerating the original pAb242_25 and pAb242_12 plasmids. These observations provide the first evidence indicating that XerC/D-like sites in A. baumannii plasmids can provide active pairs for site-specific recombination mediating inter-molecular fusions and intra-molecular resolutions. The overall results shed light on the evolutionary dynamics of A. baumannii plasmids and the underlying mechanisms of dissemination of genetic structures responsible for carbapenem and other antibiotics resistance among the Acinetobacter clinical population. PMID:29434581

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

PubMed Central

McElroy, Kerensa; Gaudieri, Silvana; Pham, Son T.; Chopra, Abha; Cameron, Barbara; Maher, Lisa; Dore, Gregory J.; White, Peter A.; Lloyd, Andrew R.

2011-01-01

Hepatitis C is a pandemic human RNA virus, which commonly causes chronic infection and liver disease. The characterization of viral populations that successfully initiate infection, and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design. A comprehensive and longitudinal analysis of the viral population was conducted in four subjects followed from very early acute infection to resolution of disease outcome. By means of next generation sequencing (NGS) and standard cloning/Sanger sequencing, genetic diversity and viral variants were quantified over the course of the infection at frequencies as low as 0.1%. Phylogenetic analysis of reassembled viral variants revealed acute infection was dominated by two sequential bottleneck events, irrespective of subsequent chronicity or clearance. The first bottleneck was associated with transmission, with one to two viral variants successfully establishing infection. The second occurred approximately 100 days post-infection, and was characterized by a decline in viral diversity. In the two subjects who developed chronic infection, this second bottleneck was followed by the emergence of a new viral population, which evolved from the founder variants via a selective sweep with fixation in a small number of mutated sites. The diversity at sites with non-synonymous mutation was higher in predicted cytotoxic T cell epitopes, suggesting immune-driven evolution. These results provide the first detailed analysis of early within-host evolution of HCV, indicating strong selective forces limit viral evolution in the acute phase of infection. PMID:21912520

A remote-sensing, GIS-based approach to identify, characterize, and model spawning habitat for fall-run chum salmon in a sub-arctic, glacially fed river

USGS Publications Warehouse

Wirth, Lisa; Rosenberger, Amanda; Prakash, Anupma; Gens, Rudiger; Margraf, F. Joseph; Hamazaki, Toshihide

2012-01-01

At northern limits of a species’ distribution, fish habitat requirements are often linked to thermal preferences, and the presence of overwintering habitat. However, logistical challenges and hydrologic processes typical of glacial systems could compromize the identification of these habitats, particularly in large river environments. Our goal was to identify and characterize spawning habitat for fall-run chum salmon Oncorhynchus keta and model habitat selection from spatial distributions of tagged individuals in the Tanana River, Alaska using an approach that combined ground surveys with remote sensing. Models included braiding, sinuosity, ice-free water surface area (indicating groundwater influence), and persistent ice-free water (i.e., consistent presence of ice-free water for a 12-year period according to satellite imagery). Candidate models containing persistent ice-free water were selected as most likely, highlighting the utility of remote sensing for monitoring and identifying salmon habitat in remote areas. A combination of ground and remote surveys revealed spatial and temporal thermal characteristics of these habitats that could have strong biological implications. Persistent ice-free sites identified using synthetic aperture radar appear to serve as core areas for spawning fall chum salmon, and the importance of stability through time suggests a legacy of successful reproductive effort for this homing species. These features would not be captured with a one-visit traditional survey but rather required remote-sensing monitoring of the sites through time.

Development of a High-Throughput Ion-Exchange Resin Characterization Workflow.

PubMed

Liu, Chun; Dermody, Daniel; Harris, Keith; Boomgaard, Thomas; Sweeney, Jeff; Gisch, Daryl; Goltz, Bob

2017-06-12

A novel high-throughout (HTR) ion-exchange (IEX) resin workflow has been developed for characterizing ion exchange equilibrium of commercial and experimental IEX resins against a range of different applications where water environment differs from site to site. Because of its much higher throughput, design of experiment (DOE) methodology can be easily applied for studying the effects of multiple factors on resin performance. Two case studies will be presented to illustrate the efficacy of the combined HTR workflow and DOE method. In case study one, a series of anion exchange resins have been screened for selective removal of NO 3 - and NO 2 - in water environments consisting of multiple other anions, varied pH, and ionic strength. The response surface model (RSM) is developed to statistically correlate the resin performance with the water composition and predict the best resin candidate. In case study two, the same HTR workflow and DOE method have been applied for screening different cation exchange resins in terms of the selective removal of Mg 2+ , Ca 2+ , and Ba 2+ from high total dissolved salt (TDS) water. A master DOE model including all of the cation exchange resins is created to predict divalent cation removal by different IEX resins under specific conditions, from which the best resin candidates can be identified. The successful adoption of HTR workflow and DOE method for studying the ion exchange of IEX resins can significantly reduce the resources and time to address industry and application needs.

Bed site selection by neonate deer in grassland habitats on the northern Great Plains

USGS Publications Warehouse

Grovenburg, T.W.; Jacques, C.N.; Klaver, R.W.; Jenks, J.A.

2010-01-01

Bed site selection is an important behavioral trait influencing neonate survival. Vegetation characteristics of bed sites influence thermal protection of neonates and concealment from predators. Although previous studies describe bed site selection of neonatal white-tailed deer (Odocoileus virginianus) in regions of forested cover, none determined microhabitat effects on neonate bed site selection in the Northern Great Plains, an area of limited forest cover. During summers 2007–2009, we investigated bed site selection (n  =  152) by 81 radiocollared neonate white-tailed deer in north-central South Dakota, USA. We documented 80 (52.6%) bed sites in tallgrass–Conservation Reserve Program lands, 35 (23.0%) bed sites in forested cover, and 37 (24.3%) in other habitats (e.g., pasture, alfalfa, wheat). Bed site selection varied with age and sex of neonate. Tree canopy cover (P < 0.001) and tree basal area (P < 0.001) decreased with age of neonates, with no bed sites observed in forested cover after 18 days of age. Male neonates selected sites with less grass cover (P < 0.001), vertical height of understory vegetation (P < 0.001), and density of understory vegetation (P < 0.001) but greater bare ground (P  =  0.047), litter (P  =  0.028), and wheat (P  =  0.044) than did females. Odds of bed site selection increased 3.5% (odds ratio  =  1.035, 95% CI  =  1.008–1.062) for every 1-cm increase in vertical height of understory vegetation. Management for habitat throughout the grasslands of South Dakota that maximizes vertical height of understory vegetation would enhance cover characteristics selected by neonates.

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

SH-wave refraction/reflection and site characterization

USGS Publications Warehouse

Wang, Z.; Street, R.L.; Woolery, E.W.; Madin, I.P.

2000-01-01

Traditionally, nonintrusive techniques used to characterize soils have been based on P-wave refraction/reflection methods. However, near-surface unconsolidated soils are oftentimes water-saturated, and when groundwater is present at a site, the velocity of the P-waves is more related to the compressibility of the pore water than to the matrix of the unconsolidated soils. Conversely, SH-waves are directly relatable to the soil matrix. This makes SH-wave refraction/reflection methods effective in site characterizations where groundwater is present. SH-wave methods have been used extensively in site characterization and subsurface imaging for earthquake hazard assessments in the central United States and western Oregon. Comparison of SH-wave investigations with geotechnical investigations shows that SH-wave refraction/reflection techniques are viable and cost-effective for engineering site characterization.

Factors of soil diversity in the Batumi delta (Georgia)

NASA Astrophysics Data System (ADS)

Turgut, Bülent; Ateş, Merve

2017-01-01

The aim of this study was to determine certain basic properties of soils in the Batumi delta (southwestern Georgia) to determine the relationships of studied properties and to identify differences with regards to these properties between different sampling sites in the delta that were selected based on the delta morphology. In this context, a total of 125 soil samples were collected from five different sampling sites, and the clay, silt and sand content of the samples were determined along with their mean weight diameter (MWD) values, aggregate stability (AS) values, amount of water retained under -33 (FC) and -1500 kPa (WP) pressure and organic matter (OM) content. Correlation analysis indicated that clay content and OM were positively correlated with MWD, and OM was positively correlated with AS. However, the sand content was found to be negatively correlated with MWD. In addition, clay, silt and OM content were positive correlated with FC and WP. Variance analysis results determined statistically significant differences between the sampling sites with respect to all of the evaluated properties. The active delta section of the study area was characterized by high sand content, while the lower delta plain was characterized by high OM and AS values, and the upper delta plain was characterized by high MWD values, high FC and WP moisture content levels and high clay and silt content. In conclusion, it was demonstrated that the examined properties were significantly affected by the different morphological positions and usages of these different areas. These results may help with the management of agricultural lands in the Batumi delta, which has never been studied before.

Characterization of spontaneous mutants of Magnaporthe grisea expressing stable resistance to the Qo-inhibiting fungicide azoxystrobin.

PubMed

Avila-Adame, Cruz; Köller, Wolfram

2003-03-01

The class of Qo-inhibiting fungicides (QoIs) act as respiration inhibitors by binding to the Qo center of cytochrome b. The longevity of these fungicides has been challenged by the selection of fungal sub-populations resisting high doses of QoI fungicides, with a G143A amino acid exchange in the cytochrome b target site identified as the most common cause of resistance. In contrast, the mechanism of alternative respiration, as another mechanism of fungal QoI resistance, has thus far not been affiliated with practical resistance. In the present study, azoxystrobin-resistant mutants of Magnaporthe grisea were generated and characterized. Emergence of these spontaneous mutants was facilitated when resting melanized mycelia were allowed to escape full inhibition by azoxystrobin. This escape was related to the intactness of alternative respiration, indicating that residual expression of this rescue mechanism was involved in the spontaneous emergence of target-site mutants. The two mutants characterized resisted high doses of the QoI, azoxystrobin, with resistance factors exceeding 1,000. Two different mutations of the cytochrome b gene were identified as exchanges of guanine, leading to a G143A or a G143S amino acid exchange. Resistance of both target-site mutants remained stable during four consecutive disease cycles in the absence of azoxystrobin. Several parameters tested to measure fitness penalties inherent to the mutational changes revealed that the G143A mutant was not compromised. In contrast, the conidia production of the G143S mutant was significantly lower under both saprophytic and pathogenic conditions of reproduction.

Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites

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

Derebe, Mehabaw G.; Sauer, David B.; Zeng, Weizhong

2015-11-30

Selective ion conduction across ion channel pores is central to cellular physiology. To understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores based on the nonselective NaK channel and determined their structures to high resolution. These structures showcase an ensemble of selectivity filters with a various number of contiguous ion binding sites ranging from 2 to 4, with each individual site maintaining a geometry and ligand environment virtually identical to that of equivalent sites in K{sup +} channel selectivity filters. Combined with single channel electrophysiology, we show that only themore » channel with four ion binding sites is K{sup +} selective, whereas those with two or three are nonselective and permeate Na{sup +} and K{sup +} equally well. These observations strongly suggest that the number of contiguous ion binding sites in a single file is the key determinant of the channel's selectivity properties and the presence of four sites in K{sup +} channels is essential for highly selective and efficient permeation of K{sup +} ions.« less

π-Clamp-mediated cysteine conjugation

NASA Astrophysics Data System (ADS)

Zhang, Chi; Welborn, Matthew; Zhu, Tianyu; Yang, Nicole J.; Santos, Michael S.; van Voorhis, Troy; Pentelute, Bradley L.

2016-02-01

Site-selective functionalization of complex molecules is one of the most significant challenges in chemistry. Typically, protecting groups or catalysts must be used to enable the selective modification of one site among many that are similarly reactive, and general strategies that selectively tune the local chemical environment around a target site are rare. Here, we show a four-amino-acid sequence (Phe-Cys-Pro-Phe), which we call the ‘π-clamp’, that tunes the reactivity of its cysteine thiol for site-selective conjugation with perfluoroaromatic reagents. We use the π-clamp to selectively modify one cysteine site in proteins containing multiple endogenous cysteine residues. These examples include antibodies and cysteine-based enzymes that would be difficult to modify selectively using standard cysteine-based methods. Antibodies modified using the π-clamp retained binding affinity to their targets, enabling the synthesis of site-specific antibody-drug conjugates for selective killing of HER2-positive breast cancer cells. The π-clamp is an unexpected approach to mediate site-selective chemistry and provides new avenues to modify biomolecules for research and therapeutics.

Innovations in Site Characterization Case Study: The Role of a Conceptual Site Model for Expedited Site Characterization Using the Triad Approach at the Poudre River Site, Fort Collins, Colorado

EPA Pesticide Factsheets

This case study examines how systematic planning, an evolving conceptual site model (CSM), dynamic work strategies, and real time measurement technologies can be used to unravel complex contaminant distribution patterns...

Mechanism and Site of Inhibition of AMPA Receptors: Pairing a Thiadiazole with a 2,3-Benzodiazepine Scaffold

PubMed Central

2013-01-01

2,3-Benzodiazepine compounds are synthesized as drug candidates for treatment of various neurological disorders involving excessive activity of AMPA receptors. Here we report that pairing a thiadiazole moiety with a 2,3-benzodiazepine scaffold via the N-3 position yields an inhibitor type with >28-fold better potency and selectivity on AMPA receptors than the 2,3-benzodiazepine scaffold alone. Using whole-cell recording, we characterized two thiadiazolyl compounds, that is, one contains a 1,3,4-thiadiazole moiety and the other contains a 1,2,4-thiadiazole-3-one moiety. These compounds exhibit potent, equal inhibition of both the closed-channel and the open-channel conformations of all four homomeric AMPA receptor channels and two GluA2R-containing complex AMPA receptor channels. Furthermore, these compounds bind to the same receptor site as GYKI 52466 does, a site we previously termed as the “M” site. A thiadiazole moiety is thought to occupy more fully the side pocket of the receptor site or the “M” site, thereby generating a stronger, multivalent interaction between the inhibitor and the receptor binding site. We suggest that, as a heterocycle, a thiadiazole can be further modified chemically to produce a new class of even more potent, noncompetitive inhibitors of AMPA receptors. PMID:24313227

Reliable Refuge: Two Sky Island Scorpion Species Select Larger, Thermally Stable Retreat Sites.

PubMed

Becker, Jamie E; Brown, Christopher A

2016-01-01

Sky island scorpions shelter under rocks and other surface debris, but, as with other scorpions, it is unclear whether these species select retreat sites randomly. Furthermore, little is known about the thermal preferences of scorpions, and no research has been done to identify whether reproductive condition might influence retreat site selection. The objectives were to (1) identify physical or thermal characteristics for retreat sites occupied by two sky island scorpions (Vaejovis cashi Graham 2007 and V. electrum Hughes 2011) and those not occupied; (2) determine whether retreat site selection differs between the two study species; and (3) identify whether thermal selection differs between species and between gravid and non-gravid females of the same species. Within each scorpion's habitat, maximum dimensions of rocks along a transect line were measured and compared to occupied rocks to determine whether retreat site selection occurred randomly. Temperature loggers were placed under a subset of occupied and unoccupied rocks for 48 hours to compare the thermal characteristics of these rocks. Thermal gradient trials were conducted before parturition and after dispersal of young in order to identify whether gravidity influences thermal preference. Vaejovis cashi and V. electrum both selected larger retreat sites that had more stable thermal profiles. Neither species appeared to have thermal preferences influenced by reproductive condition. However, while thermal selection did not differ among non-gravid individuals, gravid V. electrum selected warmer temperatures than its gravid congener. Sky island scorpions appear to select large retreat sites to maintain thermal stability, although biotic factors (e.g., competition) could also be involved in this choice. Future studies should focus on identifying the various biotic or abiotic factors that could influence retreat site selection in scorpions, as well as determining whether reproductive condition affects thermal selection in other arachnids.

Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.

PubMed

Spielman, Stephanie J; Wilke, Claus O

2016-11-01

The mutation-selection model of coding sequence evolution has received renewed attention for its use in estimating site-specific amino acid propensities and selection coefficient distributions. Two computationally tractable mutation-selection inference frameworks have been introduced: One framework employs a fixed-effects, highly parameterized maximum likelihood approach, whereas the other employs a random-effects Bayesian Dirichlet Process approach. While both implementations follow the same model, they appear to make distinct predictions about the distribution of selection coefficients. The fixed-effects framework estimates a large proportion of highly deleterious substitutions, whereas the random-effects framework estimates that all substitutions are either nearly neutral or weakly deleterious. It remains unknown, however, how accurately each method infers evolutionary constraints at individual sites. Indeed, selection coefficient distributions pool all site-specific inferences, thereby obscuring a precise assessment of site-specific estimates. Therefore, in this study, we use a simulation-based strategy to determine how accurately each approach recapitulates the selective constraint at individual sites. We find that the fixed-effects approach, despite its extensive parameterization, consistently and accurately estimates site-specific evolutionary constraint. By contrast, the random-effects Bayesian approach systematically underestimates the strength of natural selection, particularly for slowly evolving sites. We also find that, despite the strong differences between their inferred selection coefficient distributions, the fixed- and random-effects approaches yield surprisingly similar inferences of site-specific selective constraint. We conclude that the fixed-effects mutation-selection framework provides the more reliable software platform for model application and future development. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Catalysis by clusters with precise numbers of atoms

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

Tyo, Eric C.; Vajda, Stefan

2015-07-03

Clusters that contain only a small number of atoms can exhibit unique and often unexpected properties. The clusters are of particular interest in catalysis because they can act as individual active sites, and minor changes in size and composition – such as the addition or removal of a single atom – can have a substantial influence on the activity and selectivity of a reaction. Here we review recent progress in the synthesis, characterization and catalysis of well-defined sub-nanometre clusters. We examine work on size-selected supported clusters in ultra-high vacuum environments and under realistic reaction conditions, and explore the use ofmore » computational methods to provide a mechanistic understanding of their catalytic properties. We also highlight the potential of size-selected clusters to provide insights into important catalytic processes and their use in the development of novel catalytic systems.« less

Band gap tuning in transition metal oxides by site-specific substitution

DOEpatents

Lee, Ho Nyung; Chisholm, Jr., Matthew F; Jellison, Jr., Gerald Earle; Singh, David J; Choi, Woo Seok

2013-12-24

A transition metal oxide insulator composition having a tuned band gap includes a transition metal oxide having a perovskite or a perovskite-like crystalline structure. The transition metal oxide includes at least one first element selected form the group of Bi, Ca, Ba, Sr, Li, Na, Mg, K, Pb, and Pr; and at least one second element selected from the group of Ti, Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zr, Nb, Mo, Ru, Rh, Hf, Ta, W, Re, Os, Ir, and Pt. At least one correlated insulator is integrated into the crystalline structure, including REMO.sub.3, wherein RE is at least one Rare Earth element, and wherein M is at least one element selected from the group of Co, V, Cr, Ni, Mn, and Fe. The composition is characterized by a band gap of less of 4.5 eV.

Quantification of the Impact of the HIV-1-Glycan Shield on Antibody Elicitation

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

Zhou, Tongqing; Doria-Rose, Nicole A.; Cheng, Cheng

While the HIV-1-glycan shield is known to shelter Env from the humoral immune response, its quantitative impact on antibody elicitation has been unclear. Here, we use targeted deglycosylation to measure the impact of the glycan shield on elicitation of antibodies against the CD4 supersite. We engineered diverse Env trimers with select glycans removed proximal to the CD4 supersite, characterized their structures and glycosylation, and immunized guinea pigs and rhesus macaques. Immunizations yielded little neutralization against wild-type viruses but potent CD4-supersite neutralization (titers 1: >1,000,000 against four-glycan-deleted autologous viruses with over 90% breadth against four-glycan-deleted heterologous strains exhibiting tier 2 neutralizationmore » character). To a first approximation, the immunogenicity of the glycan-shielded protein surface was negligible, with Env-elicited neutralization (ID50) proportional to the exponential of the protein-surface area accessible to antibody. Based on these high titers and exponential relationship, we propose site-selective deglycosylated trimers as priming immunogens to increase the frequency of site-targeting antibodies.« less

An allosteric Sec61 inhibitor traps nascent transmembrane helices at the lateral gate

PubMed Central

MacKinnon, Andrew L; Paavilainen, Ville O; Sharma, Ajay; Hegde, Ramanujan S; Taunton, Jack

2014-01-01

Membrane protein biogenesis requires the coordinated movement of hydrophobic transmembrane domains (TMD) from the cytosolic vestibule of the Sec61 channel into the lipid bilayer. Molecular insight into TMD integration has been hampered by the difficulty of characterizing intermediates during this intrinsically dynamic process. In this study, we show that cotransin, a substrate-selective Sec61 inhibitor, traps nascent TMDs in the cytosolic vestibule, permitting detailed interrogation of an early pre-integration intermediate. Site-specific crosslinking revealed the pre-integrated TMD docked to Sec61 near the cytosolic tip of the lateral gate. Escape from cotransin-arrest depends not only on cotransin concentration, but also on the biophysical properties of the TMD. Genetic selection of cotransin-resistant cancer cells uncovered multiple mutations clustered near the lumenal plug of Sec61α, thus revealing cotransin’s likely site of action. Our results suggest that TMD/lateral gate interactions facilitate TMD transfer into the membrane, a process that is allosterically modulated by cotransin binding to the plug. DOI: http://dx.doi.org/10.7554/eLife.01483.001 PMID:24497544

Thermal power systems, small power systems application project. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

Marriott, A. T.

1979-01-01

Current small power system technology as applied to power plants up to 10 MWe in size was assessed. Markets for small power systems were characterized and cost goals were established. Candidate power plant system design concepts were selected for evaluation and preliminary performance and cost assessments were made. Economic studies were conducted and breakeven capital costs were determined for leading contenders among the candidate systems. An application study was made of the potential use of small power systems in providing part of the demand for pumping power by the extensive aqueduct system of California, estimated to be 1000 MWe by 1985. Criteria and methodologies were developed for application to the ranking of candidate power plant system design concepts. Experimental power plants concepts of 1 MWe rating were studied leading toward the definition of a power plant configuration for subsequent detail design, construction, testing and evaluation as Engineering Experiment No. 1 (EE No. 1). Site selection criteria and ground rules for the solicitation of EE No. 1 site participation proposals by DOE were developed.

Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2

NASA Astrophysics Data System (ADS)

Kalinić, Marko; Zloh, Mire; Erić, Slavica

2014-11-01

Enhancer of Zeste Homolog 2 (EZH2) is a SET domain protein lysine methyltransferase (PKMT) which has recently emerged as a chemically tractable and therapeutically promising epigenetic target, evidenced by the discovery and characterization of potent and highly selective EZH2 inhibitors. However, no experimental structures of the inhibitors co-crystallized to EZH2 have been resolved, and the structural basis for their activity and selectivity remains unknown. Considering the need to minimize cross-reactivity between prospective PKMT inhibitors, much can be learned from understanding the molecular basis for selective inhibition of EZH2. Thus, to elucidate the binding of small-molecule inhibitors to EZH2, we have developed a model of its fully-formed cofactor binding site and used it to carry out molecular dynamics simulations of protein-ligand complexes, followed by molecular mechanics/generalized born surface area calculations. The obtained results are in good agreement with biochemical inhibition data and reflect the structure-activity relationships of known ligands. Our findings suggest that the variable and flexible post-SET domain plays an important role in inhibitor binding, allowing possibly distinct binding modes of inhibitors with only small variations in their structure. Insights from this study present a good basis for design of novel and optimization of existing compounds targeting the cofactor binding site of EZH2.

Model Validation and Site Characterization for Early Deployment MHK Sites and Establishment of Wave Classification Scheme

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

Kilcher, Levi F

Model Validation and Site Characterization for Early Deployment Marine and Hydrokinetic Energy Sites and Establishment of Wave Classification Scheme presentation from from Water Power Technologies Office Peer Review, FY14-FY16.

One- and two-objective approaches to an area-constrained habitat reserve site selection problem

Treesearch

Stephanie Snyder; Charles ReVelle; Robert Haight

2004-01-01

We compare several ways to model a habitat reserve site selection problem in which an upper bound on the total area of the selected sites is included. The models are cast as optimization coverage models drawn from the location science literature. Classic covering problems typically include a constraint on the number of sites that can be selected. If potential reserve...

Bifunctional Molybdenum Polyoxometalates for the Combined Hydrodeoxygenation and Alkylation of Lignin-Derived Model Phenolics.

PubMed

Anderson, Eric; Crisci, Anthony; Murugappan, Karthick; Román-Leshkov, Yuriy

2017-05-22

Reductive catalytic fractionation of biomass has recently emerged as a powerful lignin extraction and depolymerization method to produce monomeric aromatic oxygenates in high yields. Here, bifunctional molybdenum-based polyoxometalates supported on titania (POM/TiO 2 ) are shown to promote tandem hydrodeoxygenation (HDO) and alkylation reactions, converting lignin-derived oxygenated aromatics into alkylated benzenes and alkylated phenols in high yields. In particular, anisole and 4-propylguaiacol were used as model compounds for this gas-phase study using a packed-bed flow reactor. For anisole, 30 % selectivity for alkylated aromatic compounds (54 % C-alkylation of the methoxy groups by methyl balance) with an overall 72 % selectivity for HDO at 82 % anisole conversion was observed over H 3 PMo 12 O 40 /TiO 2 at 7 h on stream. Under similar conditions, 4-propylguaiacol was mainly converted into 4-propylphenol and alkylated 4-propylphenols with a selectivity to alkylated 4-propylphenols of 42 % (77 % C-alkylation) with a total HDO selectivity to 4-propylbenzene and alkylated 4-propylbenzenes of 4 % at 92 % conversion (7 h on stream). Higher catalyst loadings pushed the 4-propylguaiacol conversion to 100 % and resulted in a higher selectivity to propylbenzene of 41 %, alkylated aromatics of 21 % and alkylated phenols of 17 % (51 % C-alkylation). The reactivity studies coupled with catalyst characterization revealed that Lewis acid sites act synergistically with neighboring Brønsted acid sites to simultaneously promote alkylation and hydrodeoxygenation activity. A reaction mechanism is proposed involving activation of the ether bond on a Lewis acid site, followed by methyl transfer and C-alkylation. Mo-based POMs represent a versatile catalytic platform to simultaneously upgrade lignin-derived oxygenated aromatics into alkylated arenes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improved selective cholesterol adsorption by molecularly imprinted poly(methacrylic acid)/silica (PMAA-SiO₂) hybrid material synthesized with different molar ratios.

PubMed

Clausen, Débora Nobile; Pires, Igor Matheus Ruiz; Tarley, César Ricardo Teixeira

2014-11-01

The present paper describes the synthesis of molecularly imprinted polymer - poly(methacrylic acid)/silica and reports its performance feasibility with desired adsorption capacity and selectivity for cholesterol extraction. Two imprinted hybrid materials were synthesized at different methacrylic acid (MAA)/tetraethoxysilane (TEOS) molar ratios (6:1 and 1:5) and characterized by FT-IR, TGA, SEM and textural data. Cholesterol adsorption on hybrid materials took place preferably in apolar solvent medium, especially in chloroform. From the kinetic data, the equilibrium time was reached quickly, being 12 and 20 min for the polymers synthesized at MAA/TEOS molar ratio of 6:1 and 1:5, respectively. The pseudo-second-order model provided the best fit for cholesterol adsorption on polymers, confirming the chemical nature of the adsorption process, while the dual-site Langmuir-Freundlich equation presented the best fit to the experimental data, suggesting the existence of two kinds of adsorption sites on both polymers. The maximum adsorption capacities obtained for the polymers synthesized at MAA/TEOS molar ratios of 6:1 and 1:5 were found to be 214.8 and 166.4 mg g(-1), respectively. The results from isotherm data also indicated higher adsorption capacity for both imprinted polymers regarding to corresponding non-imprinted polymers. Nevertheless, taking into account the retention parameters and selectivity of cholesterol in the presence of structurally analogue compounds (5-α-cholestane and 7-dehydrocholesterol), it was observed that the polymer synthesized at the MAA/TEOS molar ratio of 6:1 was much more selective for cholesterol than the one prepared at the ratio of 1:5, thus suggesting that selective binding sites ascribed to the carboxyl group from MAA play a central role in the imprinting effect created on MIP. Copyright © 2014 Elsevier B.V. All rights reserved.

Recent Experience Using Active Love Wave Techniques to Characterize Seismographic Station Sites

NASA Astrophysics Data System (ADS)

Martin, A. J.; Yong, A.; Salomone, L.

2014-12-01

Active-source Love waves recorded by the multi-channel analysis of surface wave (MASLW) technique were recently analyzed in two site characterization projects. Between 2010 and 2011, the 2009 American Recovery and Reinvestment Act (ARRA) funded GEOVision to conduct geophysical investigations at 189 seismographic stations—185 in California and 4 in the Central Eastern U.S. (CEUS). The original project plan was to utilize active and passive Rayleigh wave-based techniques to obtain shear-wave velocity (VS) profiles to a minimum depth of 30 m and the time-averaged VS of the upper 30 meters (VS30). Early in the investigation it became evident that Rayleigh wave techniques, such as multi-channel analysis of surface waves (MASRW), were not effective at characterizing all sites. Shear-wave seismic refraction and MASLW techniques were therefore applied. The MASLW technique was deployed at a total of 38 sites, in addition to other methods, and used as the primary technique to characterize 22 sites, 5 of which were also characterized using Rayleigh wave techniques. In 2012, the Electric Power Research Institute funded characterization of 33 CEUS station sites. Based on experience from the ARRA investigation, both MASRW and MASLW data were acquired by GEOVision at 24 CEUS sites—the remaining 9 sites and 2 overlapping sites were characterized by University of Texas, Austin. Of the 24 sites characterized by GEOVision, 16 were characterized using MASLW data, 4 using both MASLW and MASRW data and 4 using MASRW data. Love wave techniques were often found to perform better, or at least yield phase velocity data that could be more readily modeled using the fundamental mode assumption, at shallow rock sites, sites with steep velocity gradients, and, sites with a thin, low velocity, surficial soil layer overlying stiffer sediments. These types of velocity structure often excite dominant higher modes in Rayleigh wave data, but not in Love wave data. At such sites, it may be possible to model Rayleigh wave data using multi- or effective-mode techniques; however, in many cases extraction of adequate Rayleigh wave dispersion data for modeling was difficult. These results imply that field procedures should include careful scrutiny of Rayleigh wave-based dispersion data in order to collect Love wave data when warranted.

On validating remote sensing simulations using coincident real data

NASA Astrophysics Data System (ADS)

Wang, Mingming; Yao, Wei; Brown, Scott; Goodenough, Adam; van Aardt, Jan

2016-05-01

The remote sensing community often requires data simulation, either via spectral/spatial downsampling or through virtual, physics-based models, to assess systems and algorithms. The Digital Imaging and Remote Sensing Image Generation (DIRSIG) model is one such first-principles, physics-based model for simulating imagery for a range of modalities. Complex simulation of vegetation environments subsequently has become possible, as scene rendering technology and software advanced. This in turn has created questions related to the validity of such complex models, with potential multiple scattering, bidirectional distribution function (BRDF), etc. phenomena that could impact results in the case of complex vegetation scenes. We selected three sites, located in the Pacific Southwest domain (Fresno, CA) of the National Ecological Observatory Network (NEON). These sites represent oak savanna, hardwood forests, and conifer-manzanita-mixed forests. We constructed corresponding virtual scenes, using airborne LiDAR and imaging spectroscopy data from NEON, ground-based LiDAR data, and field-collected spectra to characterize the scenes. Imaging spectroscopy data for these virtual sites then were generated using the DIRSIG simulation environment. This simulated imagery was compared to real AVIRIS imagery (15m spatial resolution; 12 pixels/scene) and NEON Airborne Observation Platform (AOP) data (1m spatial resolution; 180 pixels/scene). These tests were performed using a distribution-comparison approach for select spectral statistics, e.g., established the spectra's shape, for each simulated versus real distribution pair. The initial comparison results of the spectral distributions indicated that the shapes of spectra between the virtual and real sites were closely matched.

Rational selection of alternative, environmentally compatible surfactants for biotechnological production of pharmaceuticals--a step toward green biotechnology.

PubMed

Straub, Jürg Oliver; Shearer, Russel; Studer, Martin

2014-09-01

The biotechnological production of pharmaceutical active substances needs ancillary substances. Surfactants are used at the end of the cell culture as a protection against potential viral or bacterial contamination and to lyse the producing cells for isolation and purification of the products. To find a replacement for a surfactant that had raised environmental concern, environmentally relevant data for potential alternatives were searched for in the literature. Significant data gaps were filled with additional tests: biodegradability, algal growth inhibition, acute daphnid immobilization and chronic daphnid reproduction toxicity, acute fish toxicity, and activated sludge respiration inhibition. The results were used to model removal in the wastewater treatment plants (WWTPs) serving 3 biotechnological production sites in the Roche Group. Predicted environmental concentrations (PECs) were calculated using realistic amounts of surfactants and site-specific wastewater fluxes, modeled removals for the WWTPs and dilution factors by the respective receiving waters. Predicted no-effect concentrations (PNECs) were derived for WWTPs and for both fresh and marine receiving waters as the treated wastewater of 1 production site is discharged into a coastal water. This resulted in a spreadsheet showing PECs, PNECs, and PEC ÷ PNEC risk characterization ratios for the WWTPs and receiving waters for all investigated surfactants and all 3 sites. This spreadsheet now serves as a selection support for the biotechnological developers. This risk-based prioritization of surfactants is a step toward green biotechnological production. © 2014 SETAC.

Molecular Characterization of Voltage-Gated Sodium Channels and Their Relations with Paralytic Shellfish Toxin Bioaccumulation in the Pacific Oyster Crassostrea gigas

PubMed Central

Boullot, Floriane; Castrec, Justine; Bidault, Adeline; Dantas, Natanael; Payton, Laura; Perrigault, Mickael; Tran, Damien; Amzil, Zouher; Boudry, Pierre; Soudant, Philippe; Hégaret, Hélène; Fabioux, Caroline

2017-01-01

Paralytic shellfish toxins (PST) bind to voltage-gated sodium channels (Nav) and block conduction of action potential in excitable cells. This study aimed to (i) characterize Nav sequences in Crassostrea gigas and (ii) investigate a putative relation between Nav and PST-bioaccumulation in oysters. The phylogenetic analysis highlighted two types of Nav in C. gigas: a Nav1 (CgNav1) and a Nav2 (CgNav2) with sequence properties of sodium-selective and sodium/calcium-selective channels, respectively. Three alternative splice transcripts of CgNav1 named A, B and C, were characterized. The expression of CgNav1, analyzed by in situ hybridization, is specific to nervous cells and to structures corresponding to neuromuscular junctions. Real-time PCR analyses showed a strong expression of CgNav1A in the striated muscle while CgNav1B is mainly expressed in visceral ganglia. CgNav1C expression is ubiquitous. The PST binding site (domain II) of CgNav1 variants possess an amino acid Q that could potentially confer a partial saxitoxin (STX)-resistance to the channel. The CgNav1 genotype or alternative splicing would not be the key point determining PST bioaccumulation level in oysters. PMID:28106838

CO adsorption on ion bombarded Ni(111): characterization by photoemission from adsorbed xenon

NASA Astrophysics Data System (ADS)

Fu, Sabrina S.; Malafsky, Geoffrey P.; Hsu, David S. Y.

1993-11-01

The adsorption of CO on Ni(111), ion bombarded with various fluences of 1.0 keV Ar + ions, has been investigated using photoemission from adsorbed xenon (PAX). After ion bombardment of the Ni(111) surface, various amounts of CO were adsorbed, followed by adsorption of xenon at 85 K. Two pressures of xenon were used in examining the 3d {5}/{2} peak of xenon: 5 × 10 -6 and 7 × 10 -10 Torr. PAX data taken at both pressures show that CO selectively adsorbs onto the defect (step) sites created by ion bombardment. In addition, it was found that the amount of CO which could occupy a defect site previously occupied by one Xe atom varied from 10 to 2.5, depending on the ion fluence.

10 CFR 960.3-2-2 - Nomination of sites as suitable for characterization.

Code of Federal Regulations, 2010 CFR

2010-01-01

... OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-2 Nomination of... of each repository site. For the second repository, at least three of the sites shall not have been nominated previously. Any site nominated as suitable for characterization for the first repository, but not...

Ames expedited site characterization demonstration at the former manufactured gas plant site, Marshalltown, Iowa

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

Bevolo, A.J.; Kjartanson, B.H.; Wonder, J.D.

1996-03-01

The goal of the Ames Expedited Site Characterization (ESC) project is to evaluate and promote both innovative technologies (IT) and state-of-the-practice technologies (SOPT) for site characterization and monitoring. In April and May 1994, the ESC project conducted site characterization, technology comparison, and stakeholder demonstration activities at a former manufactured gas plant (FMGP) owned by Iowa Electric Services (IES) Utilities, Inc., in Marshalltown, Iowa. Three areas of technology were fielded at the Marshalltown FMGP site: geophysical, analytical and data integration. The geophysical technologies are designed to assess the subsurface geological conditions so that the location, fate and transport of the targetmore » contaminants may be assessed and forecasted. The analytical technologies/methods are designed to detect and quantify the target contaminants. The data integration technology area consists of hardware and software systems designed to integrate all the site information compiled and collected into a conceptual site model on a daily basis at the site; this conceptual model then becomes the decision-support tool. Simultaneous fielding of different methods within each of the three areas of technology provided data for direct comparison of the technologies fielded, both SOPT and IT. This document reports the results of the site characterization, technology comparison, and ESC demonstration activities associated with the Marshalltown FMGP site. 124 figs., 27 tabs.« less

Design and methods of the Pacific Northwest Stream Quality Assessment (PNSQA), 2015

USGS Publications Warehouse

Sheibley, Rich W.; Morace, Jennifer L.; Journey, Celeste A.; Van Metre, Peter C.; Bell, Amanda H.; Nakagaki, Naomi; Button, Daniel T.; Qi, Sharon L.

2017-08-25

In 2015, the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) project conducted the Pacific Northwest Stream Quality Assessment (PNSQA) to investigate stream quality across the western part of the Pacific Northwest. The goal of the PNSQA was to assess the health of streams in the region by characterizing multiple water-quality factors that are stressors to in-stream aquatic life and by evaluating the relation between these stressors and the condition of biological communities. The effects of urbanization and agriculture on stream quality for the Puget Lowland and Willamette Valley Level III Ecoregions were the focus of this regional study. Findings will help inform the public and policymakers about human and environmental factors that are the most critical in affecting stream quality and, thus, provide insights into possible strategies to protect or improve the health of streams in the region.Land-use data were used in the study to identify and select sites within the region that ranged in levels of urban and agricultural development. A total of 88 sites were selected across the region—69 were on streams that explicitly spanned a range of urban land use in their watersheds, 8 were on streams in agricultural watersheds, and 11 were reference sites with little or no development in their watersheds. Depending on the type of land use, sites were sampled for contaminants, nutrients, and sediment for either a 4- or 10-week period during April, May, and June 2015. This water-quality “index period” was immediately followed with an ecological survey of all sites that included stream habitat, benthic algae, benthic macroinvertebrates, and fish. Additionally, streambed sediment was collected during the ecological survey for analysis of sediment chemistry and toxicity testing.This report provides a detailed description of the specific study components and methods of the PNSQA, including (1) surveys of stream habitat and aquatic biota, (2) discrete water sampling, (3) deployment of passive polar organic chemical integrative samplers for pesticides and pharmaceuticals, and (4) sampling of streambed sediment. At selected study sites, toxicity testing of streambed sediment, continuous water-quality monitoring, and daily pesticide sampling also were conducted and are described.

The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.

PubMed Central

Nordborg, Magnus; Innan, Hideki

2003-01-01

A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present. PMID:12663556

The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.

PubMed

Nordborg, Magnus; Innan, Hideki

2003-03-01

A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.

Clinical trial allocation in multinational pharmaceutical companies - a qualitative study on influential factors.

PubMed

Dombernowsky, Tilde; Haedersdal, Merete; Lassen, Ulrik; Thomsen, Simon F

2017-06-01

Clinical trial allocation in multinational pharmaceutical companies includes country selection and site selection. With emphasis on site selection, the overall aim of this study was to examine which factors pharmaceutical companies value most when allocating clinical trials. The specific aims were (1) to identify key decision makers during country and site selection, respectively, (2) to evaluate by which parameters subsidiaries are primarily assessed by headquarters with regard to conducting clinical trials, and (3) to evaluate which site-related qualities companies value most when selecting trial sites. Eleven semistructured interviews were conducted among employees engaged in trial allocation at 11 pharmaceutical companies. The interviews were analyzed by deductive content analysis, which included coding of data to a categorization matrix containing categories of site-related qualities. The results suggest that headquarters and regional departments are key decision makers during country selection, whereas subsidiaries decide on site selection. Study participants argued that headquarters primarily value timely patient recruitment and quality of data when assessing subsidiaries. The site-related qualities most commonly emphasized during interviews were study population availability, timely patient recruitment, resources at the site, and site personnel's interest and commitment. Costs of running the trials were described as less important. Site personnel experience in conducting trials was described as valuable but not imperative. In conclusion, multinational pharmaceutical companies consider recruitment-related factors as crucial when allocating clinical trials. Quality of data and site personnel's interest and commitment are also essential, whereas costs seem less important. While valued, site personnel experience in conducting clinical trials is not imperative.

Site Characterization Technologies for DNAPL Investigations

EPA Pesticide Factsheets

This document is intended to help managers at sites with potential or confirmed DNAPL contamination identify suitable characterization technologies, screen the technologies for potential application, learn about applications at similar sites, and...

Preparation and characterization of a supported system of Ni2P/Ni12P5 nanoparticles and their use as the active phase in chemoselective hydrogenation of acetophenone

NASA Astrophysics Data System (ADS)

Costa, Dolly C.; Soldati, Analía L.; Pecchi, Gina; Bengoa, José Fernando; Marchetti, Sergio Gustavo; Vetere, Virginia

2018-05-01

Ni2P/Ni12P5 nanoparticles were obtained by thermal decomposition of nickel organometallic salt at low temperature. The use of different characterization techniques allowed us to determine that this process produced a mixture of two nickel phosphide phases: Ni2P and Ni12P5. These nickel phosphides nanoparticles, supported on mesoporous silica, showed activity and high selectivity for producing the hydrogenation of the acetophenone carbonyl group to obtain 1-phenylethanol. This is a first report that demonstrates the ability of supported Ni2P/Ni12P5 nanoparticles to produce the chemoselective hydrogenation of acetophenone. We attribute these special catalytic properties to the particular geometry of the Ni–P sites on the surface of the nanoparticles. This is an interesting result because the nickel phosphides have a wide composition range (from Ni3P to NiP3), with different crystallographic structures, therefore we think that different phases could be active and selective to hydrogenate many important molecules with more than one functional group.

32 CFR 644.22 - Site selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 4 2010-07-01 2010-07-01 true Site selection. 644.22 Section 644.22 National... HANDBOOK Project Planning Military (army and Air Force) and Other Federal Agencies § 644.22 Site selection... selection will be the primary responsibility of the using service. A representative of the appropriate...