Insights from native mass spectrometry approaches for top- and middle- level characterization of site-specific antibody-drug conjugates

PubMed Central

Botzanowski, Thomas; Erb, Stéphane; Hernandez-Alba, Oscar; Ehkirch, Anthony; Colas, Olivier; Wagner-Rousset, Elsa; Rabuka, David; Beck, Alain; Drake, Penelope M.; Cianférani, Sarah

2017-01-01

ABSTRACT Antibody-drug conjugates (ADCs) have emerged as a family of compounds with promise as efficient immunotherapies. First-generation ADCs were generated mostly via reactions on either lysine side-chain amines or cysteine thiol groups after reduction of the interchain disulfide bonds, resulting in heterogeneous populations with a variable number of drug loads per antibody. To control the position and the number of drug loads, new conjugation strategies aiming at the generation of more homogeneous site-specific conjugates have been developed. We report here the first multi-level characterization of a site-specific ADC by state-of-the-art mass spectrometry (MS) methods, including native MS and its hyphenation to ion mobility (IM-MS). We demonstrate the versatility of native MS methodologies for site-specific ADC analysis, with the unique ability to provide several critical quality attributes within one single run, along with a direct snapshot of ADC homogeneity/heterogeneity without extensive data interpretation. The capabilities of native IM-MS to directly access site-specific ADC conformational information are also highlighted. Finally, the potential of these techniques for assessing an ADC's heterogeneity/homogeneity is illustrated by comparing the analytical characterization of a site-specific DAR4 ADC to that of first-generation ADCs. Altogether, our results highlight the compatibility, versatility, and benefits of native MS approaches for the analytical characterization of all types of ADCs, including site-specific conjugates. Thus, we envision integrating native MS and IM-MS approaches, even in their latest state-of-the-art forms, into workflows that benchmark bioconjugation strategies. PMID:28406343

Description of the Fork Mountain long-term soil productivity study: site characterization

Treesearch

Mary Beth Adams; James Burger; Lucian Zelazny; John Baumgras

2004-01-01

The effects of air pollution and timber harvesting on soil resources continue to be an important issue in eastern hardwood forests. This publication describes the Fork Mountain Long-term Soil Productivity Study (LTSP), located on the Fernow Experimental Forest, WV, and the pretreatment stand, soil and climatic conditions. Extensive vegetation surveys, biomass...

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

PubMed Central

Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

2015-01-01

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site

DOE PAGES

Sunden, Fanny; Peck, Ariana; Salzman, Julia; ...

2015-04-22

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modesmore » of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.« less

Parallel Comparison of N-Linked Glycopeptide Enrichment Techniques Reveals Extensive Glycoproteomic Analysis of Plasma Enabled by SAX-ERLIC.

PubMed

Totten, Sarah M; Feasley, Christa L; Bermudez, Abel; Pitteri, Sharon J

2017-03-03

Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments. SAX-ERLIC enrichment yielded 191 unique glycoforms across 72 glycosylation sites from 48 glycoproteins, which is more than double that detected using other enrichment techniques. The greatest glycoform diversity was observed in SAX-ERLIC enrichment, with no apparent bias toward specific glycan types. SAX-ERLIC enrichments were additionally analyzed by an Orbitrap Fusion Lumos mass spectrometer to maximize glycopeptide identifications for a more comprehensive assessment of protein glycosylation. In these experiments, 829 unique glycoforms were identified across 208 glycosylation sites from 95 plasma glycoproteins, a significant improvement from the initial method comparison and one of the most extensive site-specific glycosylation analysis in immunodepleted human plasma to date. Data are available via ProteomeXchange with identifier PXD005655.

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

Study of DNA binding sites using the Rényi parametric entropy measure.

PubMed

Krishnamachari, A; moy Mandal, Vijnan; Karmeshu

2004-04-07

Shannon's definition of uncertainty or surprisal has been applied extensively to measure the information content of aligned DNA sequences and characterizing DNA binding sites. In contrast to Shannon's uncertainty, this study investigates the applicability and suitability of a parametric uncertainty measure due to Rényi. It is observed that this measure also provides results in agreement with Shannon's measure, pointing to its utility in analysing DNA binding site region. For facilitating the comparison between these uncertainty measures, a dimensionless quantity called "redundancy" has been employed. It is found that Rényi's measure at low parameter values possess a better delineating feature of binding sites (of binding regions) than Shannon's measure. The critical value of the parameter is chosen with an outlier criterion.

Comparison of sap flux data from two instrumented tree species in a forested catchment with different levels of water stress

NASA Astrophysics Data System (ADS)

Hartsough, P. C.; Roudneva, E.; Malazian, A. I.; Meadows, M. W.; Kelly, A. E.; Bales, R. C.; Goulden, M.; Hopmans, J. W.

2011-12-01

Two trees were instrumented with heat pulse sapflux sensors in the Southern Sierra Critical Zone Observatory (SSCZO) within the Kings River Experimental Watershed (KREW) to better understand transpiration as it relates to water availability from deeper sources. At the first instrumented site, CZT-1, a White Fir (Abies concolor) was instrumented on a flat ridge with access to deep soil moisture. Extensive monitoring of shallow and deep soil regions confirm that there is significant soil water available from 100-400cm as the tree exhausts water from shallower depths. A root excavation of an adjacent tree shows the roots distributed from 30-150cm with limited roots available to access deeper soil water and water stored in the saprolite. At the second instrumented site, CZT-2, a Ponderosa Pine (Pinus Ponderosa) was instrumented with a similar suite of sap flow and soil sensors. The CZT-2 site is on a slight slope and is characterized by shallow soils (<90cm) with extensive cobbles and bedrock outcrops with limited access to deeper soil or saprolite water. The second site also sits in the open while the first site is more protected in a closed forest. The two sites show different responses to changes in rain and snow loading from above as well as soil drainage and water depletion from below. They also have different thresholds for transpiration shut down both due to late season water deficit and also during winter periods where air temperatures are high enough to permit photosynthesis. Sap flux data are supplemented by extensive soil water content and potential measurements around both trees as well as evapotranspiration measurements from a 50m flux tower located between the two instrumented trees.

Characterizing the proposed geologic repository for high-level radioactive waste at Yucca Mountain, Nevada--hydrology and geochemistry

USGS Publications Warehouse

Stuckless, John S.; Levich, Robert A.

2012-01-01

This hydrology and geochemistry volume is a companion volume to the 2007 Geological Society of America Memoir 199, The Geology and Climatology of Yucca Mountain and Vicinity, Southern Nevada and California, edited by Stuckless and Levich. The work in both volumes was originally reported in the U.S. Department of Energy regulatory document Yucca Mountain Site Description, for the site characterization study of Yucca Mountain, Nevada, as the proposed U.S. geologic repository for high-level radioactive waste. The selection of Yucca Mountain resulted from a nationwide search and numerous committee studies during a period of more than 40 yr. The waste, largely from commercial nuclear power reactors and the government's nuclear weapons programs, is characterized by intense penetrating radiation and high heat production, and, therefore, it must be isolated from the biosphere for tens of thousands of years. The extensive, unique, and often innovative geoscience investigations conducted at Yucca Mountain for more than 20 yr make it one of the most thoroughly studied geologic features on Earth. The results of these investigations contribute extensive knowledge to the hydrologic and geochemical aspects of radioactive waste disposal in the unsaturated zone. The science, analyses, and interpretations are important not only to Yucca Mountain, but also to the assessment of other sites or alternative processes that may be considered for waste disposal in the future. Groundwater conditions, processes, and geochemistry, especially in combination with the heat from radionuclide decay, are integral to the ability of a repository to isolate waste. Hydrology and geochemistry are discussed here in chapters on unsaturated zone hydrology, saturated zone hydrology, paleohydrology, hydrochemistry, radionuclide transport, and thermally driven coupled processes affecting long-term waste isolation. This introductory chapter reviews some of the reasons for choosing to study Yucca Mountain as a repository site.

Characterizing the proposed geologic repository for high-level radioactive waste at Yucca Mountain, Nevada: hydrology and geochemistry

USGS Publications Warehouse

Stuckless, John S.; Levich, Robert A.

2012-01-01

This hydrology and geochemistry volume is a companion volume to the 2007 Geological Society of America Memoir 199, The Geology and Climatology of Yucca Mountain and Vicinity, Southern Nevada and California, edited by Stuckless and Levich. The work in both volumes was originally reported in the U.S. Department of Energy regulatory document Yucca Mountain Site Description, for the site characterization study of Yucca Mountain, Nevada, as the proposed U.S. geologic repository for high-level radioactive waste. The selection of Yucca Mountain resulted from a nationwide search and numerous committee studies during a period of more than 40 yr. The waste, largely from commercial nuclear power reactors and the government's nuclear weapons programs, is characterized by intense penetrating radiation and high heat production, and, therefore, it must be isolated from the biosphere for tens of thousands of years. The extensive, unique, and often innovative geoscience investigations conducted at Yucca Mountain for more than 20 yr make it one of the most thoroughly studied geologic features on Earth. The results of these investigations contribute extensive knowledge to the hydrologic and geochemical aspects of radioactive waste disposal in the unsaturated zone. The science, analyses, and interpretations are important not only to Yucca Mountain, but also to the assessment of other sites or alternative processes that may be considered for waste disposal in the future. Groundwater conditions, processes, and geochemistry, especially in combination with the heat from radionuclide decay, are integral to the ability of a repository to isolate waste. Hydrology and geochemistry are discussed here in chapters on unsaturated zone hydrology, saturated zone hydrology, paleohydrology, hydrochemistry, radionuclide transport, and thermally driven coupled processes affecting long-term waste isolation. This introductory chapter reviews some of the reasons for choosing to study Yucca Mountain as a repository site.

Wireless Channel Characterization: Modeling the 5 GHz Microwave Landing System Extension Band for Future Airport Surface Communications

NASA Technical Reports Server (NTRS)

Matolak, D. W.; Apaza, Rafael; Foore, Lawrence R.

2006-01-01

We describe a recently completed wideband wireless channel characterization project for the 5 GHz Microwave Landing System (MLS) extension band, for airport surface areas. This work included mobile measurements at large and small airports, and fixed point-to-point measurements. Mobile measurements were made via transmission from the air traffic control tower (ATCT), or from an airport field site (AFS), to a receiving ground vehicle on the airport surface. The point-to-point measurements were between ATCT and AFSs. Detailed statistical channel models were developed from all these measurements. Measured quantities include propagation path loss and power delay profiles, from which we obtain delay spreads, frequency domain correlation (coherence bandwidths), fading amplitude statistics, and channel parameter correlations. In this paper we review the project motivation, measurement coordination, and illustrate measurement results. Example channel modeling results for several propagation conditions are also provided, highlighting new findings.

Statistical Tools for Designing Initial and Post-Removal UXO Characterization Surveys

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

Pulsipher, Brent A.; Gilbert, Richard O.; Wilson, John E.

2002-09-06

The Department of Defense (DoD) is in the process of assessing and remediating closed, transferred, and transferring ranges. It is estimated that over 20 million acres of land in the United States potentially contain UXO. The release of DoD sites for public use will require high confidence that UXO is not present. This high confidence may be achieved solely from an extensive knowledge of historical site operations as documented in the conceptual site model or in combination with geophysical sensor surveys designed to have a sufficiently high probability of finding UXO contaminated zones. Many of these sites involve very largemore » geographical areas such that it is often impractical and/or cost prohibitive to perform 100% surveys of the entire site of interest. In that case, it is necessary to be explicit about the performance required of a survey that covers less than 100% of the site.« less

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

Integrated characterization of the geologic framework of a contaminated site in West Trenton, New Jersey

USGS Publications Warehouse

Ellefsen, Karl J.; Burton, William C.; Lacombe, Pierre J.

2012-01-01

Fractured sedimentary bedrock and groundwater at the former Naval Air Warfare Center in West Trenton, New Jersey (United States of America) are contaminated with chlorinated solvents. Predicting contaminant migration or removing the contaminants requires an understanding of the geology. Consequently, the geologic framework near the site was characterized with four different methods having different spatial scales: geologic field mapping, analyses of bedrock drill core, analyses of soil and regolith, and S-wave refraction surveys. A fault zone is in the southeast corner of the site and separates two distinct sedimentary formations; the fault zone dips (steeply) southeasterly, strikes northeasterly, and extends at least 550 m along its strike direction. Drill core from the fault zone is extensively brecciated and includes evidence of tectonic contraction. Approximately 300 m east of this fault zone is another fault zone, which offsets the contact between the two sedimentary formations. The S-wave refraction surveys identified both fault zones beneath soil and regolith and thereby provided constraints on their lateral extent and location.

Gypsy Field project in reservoir characterization

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

Castagna, John P.; Jr., O'Meara, Daniel J.

The overall objective of this project was to use extensive Gypsy Field Laboratory and data as a focus for developing and testing reservoir characterization methods that are targeted at improved recovery of conventional oil. This report describes progress since project report DOE/BC/14970-7 and covers the period June 1997-September 1998 and represents one year of funding originally allocated for the year 1996. During the course of the work previously performed, high resolution geophysical and outcrop data revealed the importance of fractures at the Gypsy site. In addition, personnel changes and alternative funding (OCAST and oil company support of various kinds) allowedmore » the authors to leverage DOE contributions and focus more on geophysical characterization.« less

Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site

PubMed Central

Strauss, Mike; Schotte, Lise; Thys, Bert; Filman, David J.

2016-01-01

ABSTRACT Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. IMPORTANCE We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed. PMID:26764003

Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site.

PubMed

Strauss, Mike; Schotte, Lise; Thys, Bert; Filman, David J; Hogle, James M

2016-01-13

Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Using pre-screening methods for an effective and reliable site characterization at megasites.

PubMed

Algreen, Mette; Kalisz, Mariusz; Stalder, Marcel; Martac, Eugeniu; Krupanek, Janusz; Trapp, Stefan; Bartke, Stephan

2015-10-01

This paper illustrates the usefulness of pre-screening methods for an effective characterization of polluted sites. We applied a sequence of site characterization methods to a former Soviet military airbase with likely fuel and benzene, toluene, ethylbenzene, and xylene (BTEX) contamination in shallow groundwater and subsoil. The methods were (i) phytoscreening with tree cores; (ii) soil gas measurements for CH4, O2, and photoionization detector (PID); (iii) direct-push with membrane interface probe (MIP) and laser-induced fluorescence (LIF) sensors; (iv) direct-push sampling; and (v) sampling from soil and from groundwater monitoring wells. Phytoscreening and soil gas measurements are rapid and inexpensive pre-screening methods. Both indicated subsurface pollution and hot spots successfully. The direct-push sensors yielded 3D information about the extension and the volume of the subsurface plume. This study also expanded the applicability of tree coring to BTEX compounds and tested the use of high-resolution direct-push sensors for light hydrocarbons. Comparison of screening results to results from conventional soil and groundwater sampling yielded in most cases high rank correlation and confirmed the findings. The large-scale application of non- or low-invasive pre-screening can be of help in directing and focusing the subsequent, more expensive investigation methods. The rapid pre-screening methods also yielded useful information about potential remediation methods. Overall, we see several benefits of a stepwise screening and site characterization scheme, which we propose in conclusion.

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia

PubMed Central

2010-01-01

Background Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. Results The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. Conclusions The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases. PMID:20691110

Molecular characterization of partial fusion gene and C-terminus extension length of haemagglutinin-neuraminidase gene of recently isolated Newcastle disease virus isolates in Malaysia.

PubMed

Berhanu, Ayalew; Ideris, Aini; Omar, Abdul R; Bejo, Mohd Hair

2010-08-08

Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a highly contagious disease of birds and has been one of the major causes of economic losses in the poultry industry. Despite routine vaccination programs, sporadic cases have occasionally occurred in the country and remain a constant threat to commercial poultry. Hence, the present study was aimed to characterize NDV isolates obtained from clinical cases in various locations of Malaysia between 2004 and 2007 based on sequence and phylogenetic analysis of partial F gene and C-terminus extension length of HN gene. The coding region of eleven NDV isolates fusion (F) gene and carboxyl terminal region of haemagglutinin-neuraminidase (HN) gene including extensions were amplified by reverse transcriptase PCR and directly sequenced. All the isolates have shown to have non-synonymous to synonymous base substitution rate ranging between 0.081 - 0.264 demonstrating presence of negative selection. Analysis based on F gene showed the characterized isolates possess three different types of protease cleavage site motifs; namely 112RRQKRF117, 112RRRKRF117 and 112GRQGRL117 and appear to show maximum identities with isolates in the region such as cockatoo/14698/90 (Indonesia), Ch/2000 (China), local isolate AF2240 indicating the high similarity of isolates circulating in the South East Asian countries. Meanwhile, one of the isolates resembles commonly used lentogenic vaccine strains. On further characterization of the HN gene, Malaysian isolates had C-terminus extensions of 0, 6 and 11 amino acids. Analysis of the phylogenetic tree revealed that the existence of three genetic groups; namely, genotype II, VII and VIII. The study concluded that the occurrence of three types of NDV genotypes and presence of varied carboxyl terminus extension lengths among Malaysian isolates incriminated for sporadic cases.

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.

Characterization of N-glycosylation sites on the extracellular domain of NOX1/NADPH oxidase.

PubMed

Matsumoto, Misaki; Katsuyama, Masato; Iwata, Kazumi; Ibi, Masakazu; Zhang, Jia; Zhu, Kai; Nauseef, William M; Yabe-Nishimura, Chihiro

2014-03-01

Extensive evidence demonstrates the pathophysiological importance of NOX1, the catalytic subunit of superoxide-generating enzyme NADPH oxidase, as a source of reactive oxygen species in nonphagocytic cells. However, the biochemical properties of NOX1 have not been extensively characterized due to a lack of specific immunological tools. We used a newly raised NOX1 polyclonal antibody to investigate posttranslational modifications of NOX1 overexpressed in cultured cells and in the colon, where endogenous NOX1 is highly expressed. Immunoblots of lysates from cells expressing NOX1 revealed a doublet of 56 and 60kDa accompanied by a broad band of 60-90kDa. Based on differential sensitivity to glycosidases, the doublet was identified as two high-mannose-type glycoforms of NOX1, whereas the broad band represented NOX1 with complex-type N-linked oligosaccharides. Deglycosylated NOX1 migrated at ~53kDa and N-glycosylation was demonstrated in NOX1 derived from both rat and human. Site-directed mutagenesis identified N-glycosylation sites at Asn(161) and Asn(241) on the extracellular loop of mouse NOX1. Elimination of N-glycosylation on NOX1 did not affect its electron transferase activity, protein stability, targeting to the cell surface, or localization in F-actin-positive membrane protrusions. Taken together, these data identify the two specific sites of N-linked glycosylation of murine NOX1 and demonstrate that they are not required for normal enzyme activity, protein stability, and membrane trafficking. As is true for NOX2, the contribution of glycosylation in NOX1 to its biologic function(s) merits further study. Copyright © 2013 Elsevier Inc. All rights reserved.

Seabed characterization for the development of marine renewable energy on the Pacific margin of Canada

NASA Astrophysics Data System (ADS)

Barrie, J. Vaughn; Conway, Kim W.

2014-07-01

An inventory of Canada's marine renewable energy resources based on numerical modeling of the potential tidal, wave and wind energy has been published that identifies areas with maximum resource potential. However, the inventory does not consider the seabed geological conditions that will control the safe development of seabed installations and cable corridors. The Geological Survey of Canada (Natural Resources Canada) has therefore undertaken an assessment of seafloor geological characteristics and physical environmental parameters that will be encountered during any extensive deployment of marine renewable energy systems for the Pacific offshore of Canada. Here we present an overview of seabed characterization for key sites for each of the three energy types. Narrow passages exiting the Salish Sea near the Canadian boundary with the United States and northwards out of the Strait of Georgia provide very promising sites for tidal generation. Here, elliptical fields of very large subaqueous dunes, from 12 to 28 m in height, present a significant challenge to site development. Along the exposed continental shelf of Vancouver Island focused wave-energy close to shore (40-60 m water depth) offers significant energy potential, but any engineering systems would have to be founded on a seafloor made up of a mobile gravel lag and an extensive boulder pavement. A large wind farm proposed for the Pacific North Coast would be built on an extensive shallow bank that has active sediment transport and a large field of sand ridges that have developed within a macrotidal environment. A significant challenge is providing for a safe seafloor cable corridor of over 100 km that crosses a large subaqueous dune field to connect to the electrical grid on the mainland. These examples show how geoscience has and will provide critical information to project proponents and regulators for the safe development of marine renewable energy.

Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori.

PubMed

Hu, Heidi Q; Johnson, Ryan C; Merrell, D Scott; Maroney, Michael J

2017-02-28

The human pathogen Helicobacter pylori requires nickel for colonization of the acidic environment of the stomach. HypA, a Ni metallochaperone that is typically associated with hydrogenase maturation, is also required for urease maturation and acid survival of H. pylori. There are two proposed Ni site structures for HypA; one is a paramagnetic six-coordinate site characterized by X-ray absorption spectroscopy (XAS) in unmodified HypA, while another is a diamagnetic four-coordinate planar site characterized by solution nuclear magnetic resonance in an N-terminally modified HypA construct. To determine the role of the N-terminal amine in Ni binding of HypA, an N-terminal extension variant, L2*-HypA, in which a leucine residue was inserted into the second position of the amino acid sequence in the proposed Ni-binding motif, was characterized in vitro and in vivo. Structural characterization of the Ni site using XAS showed a coordination change from six-coordinate in wild-type HypA (WT-HypA) to five-coordinate pyramidal in L2*-HypA, which was accompanied by the loss of two N/O donor protein ligands and the addition of an exogenous bromide ligand from the buffer. The magnetic properties of the Ni sites in WT-HypA compared to those of the Ni sites in L2*-HypA confirmed that a spin-state change from high to low spin accompanied this change in structure. The L2*-HypA H. pylori strain was shown to be acid sensitive and deficient in urease activity in vivo. In vitro characterization showed that L2*-HypA did not disrupt the HypA-UreE interaction that is essential for urease maturation but was at least 20-fold weaker in Ni binding than WT-HypA. Characterization of the L2*-HypA variant clearly demonstrates that the N-terminal amine of HypA is involved in proper Ni coordination and is necessary for urease activity and acid survival.

Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori

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

Hu, Heidi Q.; Johnson, Ryan C.; Merrell, D. Scott

The human pathogen Helicobacter pylori requires nickel for colonization of the acidic environment of the stomach. HypA, a Ni metallochaperone that is typically associated with hydrogenase maturation, is also required for urease maturation and acid survival of H. pylori. There are two proposed Ni site structures for HypA; one is a paramagnetic six-coordinate site characterized by X-ray absorption spectroscopy (XAS) in unmodified HypA, while another is a diamagnetic four-coordinate planar site characterized by solution nuclear magnetic resonance in an N-terminally modified HypA construct. To determine the role of the N-terminal amine in Ni binding of HypA, an N-terminal extension variant,more » L2*-HypA, in which a leucine residue was inserted into the second position of the amino acid sequence in the proposed Ni-binding motif, was characterized in vitro and in vivo. Structural characterization of the Ni site using XAS showed a coordination change from six-coordinate in wild-type HypA (WT-HypA) to five-coordinate pyramidal in L2*-HypA, which was accompanied by the loss of two N/O donor protein ligands and the addition of an exogenous bromide ligand from the buffer. The magnetic properties of the Ni sites in WT-HypA compared to those of the Ni sites in L2*-HypA confirmed that a spin-state change from high to low spin accompanied this change in structure. The L2*-HypA H. pylori strain was shown to be acid sensitive and deficient in urease activity in vivo. In vitro characterization showed that L2*-HypA did not disrupt the HypA–UreE interaction that is essential for urease maturation but was at least 20-fold weaker in Ni binding than WT-HypA. Characterization of the L2*-HypA variant clearly demonstrates that the N-terminal amine of HypA is involved in proper Ni coordination and is necessary for urease activity and acid survival.« less

Rehabilitation of El Yahoudia dumping site, Tunisia.

PubMed

Zaïri, M; Ferchichi, M; Ismaïl, A; Jenayeh, M; Hammami, H

2004-01-01

As in all developing countries, cities in Tunisia face serious problems of environmental pollution caused mainly by the inadequate and inefficient final disposal of their generated solid wastes. The Tunisian government launched a development program including the construction of landfills in the main cities and the closure of the contaminated sites issued from solid wastes landrising practice. The project of the Henchir El Yahoudia landfill restoration is the first experience in this programme. It has been suggested to convert the site to a green park and to implement an ornamental plant nursery. The whole surface of the landfill is approximately 100 ha from which 30 ha have been already transformed to an urban recreational area and the remaining 70 ha have to be characterized for the project extension. A field investigation by boring was conducted in order to define the geological and the hydrogeological conditions, the vertical and horizontal wastes layer extension, content and degree of decomposition and the composition and quantities of leachate and landfill gas. Representative samples of waste, soil, groundwater and leachate were collected for laboratory analyses. Several of these borings were converted to piezometers to define the flow regime in the site. The results showed that the biogas (CH4, H2S, and CO2), leachate and waste, distribution in the site is mainly affected by the temporal variation of the site operating method. The underlying fissured clay layer facilitated leachate infiltration into the groundwater where high BOD, COD and nitrogen concentrations were registered.

Localized amyloidosis masquerading as nasopharyngeal tumor: a review.

PubMed

Panda, Naresh K; Saravanan, Karuppiah; Purushotaman, Gilbert Pragache; Gurunathan, Ramesh Kumar; Mahesha, Vankalakunti

2007-01-01

Amyloidosis comprises a diverse collection of disease characterized by the presence of amorphous extracellular eosinophilic deposits of unique protein fibrils that gives apple green birefringence under polarized light after staining with Congo red. Head and neck region is the commonest site for localized form of amyloidosis. We report a case of a 43-year-old man with localized amyloidosis of nasopharynx with oropharyngeal extension and its management, along with a review of relevant literatures.

Baccalaureate nursing education at extension sites: a survey.

PubMed

Tiffany, J C; Burson, J Z

1986-03-01

The use of extension sites in baccalaureate nursing education has increased significantly since 1978. This survey found that the majority of extension sites were developed for RNs although large numbers of generic students are also served. The use of extension sites ranges from delivering selected courses away from the lead campus to delivering an entire program. Extension sites may be located on other university campuses or may be found in a store front setting or other community agency. Administrative control of extension sites emanates from the lead campus. Faculty participation in faculty activities, such as school of nursing or university committees, is expected. The degree to which this is accomplished, however, may vary. In order to maintain program integrity, the curriculum must remain the same regardless of where it is implemented. One of the primary ways of doing this is to use the same syllabi, texts and, in many cases, the same exams. Faculty may be stationary at established extended sites or may travel from the lead campus to teach, carrying with them educational materials. Extension sites are a phenomenon of the here and now. They provide a way of delivering baccalaureate nursing education to students who might otherwise be denied this level of education. Extension sites may be operationally cumbersome, challenging, and costly, but they are meeting a need. With the advent of more sophisticated telecommunications and the continued demand for baccalaureate level education, the possibility exists for even greater variation and potential for this type of program.

Hanford Site Groundwater Monitoring for Fiscal Year 2000

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

Hartman, Mary J.; Morasch, Launa F.; Webber, William D.

2001-03-01

This report presents the results of groundwater and vadose zone monitoring and remediation for fiscal year 2000 on the U.S. Department of Energy's Hanford Site, Washington. The most extensive contaminant plumes are tritium, iodine-129, and nitrate, which all had multiple sources and are very mobile in groundwater. Carbon tetrachloride and associated organic constituents form a relatively large plume beneath the central part of the Site. Hexavalent chromium is present in smaller plumes beneath the reactor areas along the river and beneath the central part of the site. Strontium-90 exceeds standards beneath each of the reactor areas, and technetium-99 and uraniummore » are present in the 200 Areas. RCRA groundwater monitoring continued during fiscal year 2000. Vadose zone monitoring, characterization, remediation, and several technical demonstrations were conducted in fiscal year 2000. Soil gas monitoring at the 618-11 burial ground provided a preliminary indication of the location of tritium in the vadose zone and in groundwater. Groundwater modeling efforts focused on 1) identifying and characterizing major uncertainties in the current conceptual model and 2) performing a transient inverse calibration of the existing site-wide model. Specific model applications were conducted in support of the Hanford Site carbon tetrachloride Innovative Treatment Remediation Technology; to support the performance assessment of the Immobilized Low-Activity Waste Disposal Facility; and in development of the System Assessment Capability, which is intended to predict cumulative site-wide effects from all significant Hanford Site contaminants.« less

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

PubMed Central

Alquezar-Planas, David E.; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N.; Lenz, Dorina; Helgen, Kristofer M.; Roca, Alfred L.; Hartman, Stefanie

2016-01-01

Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

Involvement of two classes of binding sites in the interactions of cyclophilin B with peripheral blood T-lymphocytes.

PubMed

Denys, A; Allain, F; Carpentier, M; Spik, G

1998-12-15

Cyclophilin B (CyPB) is a cyclosporin A (CsA)-binding protein, mainly associated with the secretory pathway, and is released in biological fluids. We recently reported that CyPB specifically binds to T-lymphocytes and promotes enhanced incorporation of CsA. The interactions with cellular binding sites involved, at least in part, the specific N-terminal extension of the protein. In this study, we intended to specify further the nature of the CyPB-binding sites on peripheral blood T-lymphocytes. We first provide evidence that the CyPB binding to heparin-Sepharose is prevented by soluble sulphated glycosaminoglycans (GAG), raising the interesting possibility that such interactions may occur on the T-cell surface. We then characterized CyPB binding to T-cell surface GAG and found that these interactions involved the N-terminal extension of CyPB, but not its conserved CsA-binding domain. In addition, we determined the presence of a second CyPB binding site, which we termed a type I site, in contrast with type II for GAG interactions. The two binding sites exhibit a similar affinity but the expression of the type I site was 3-fold lower. The conclusion that CyPB binding to the type I site is distinct from the interactions with GAG was based on the findings that it was (1) resistant to NaCl wash and GAG-degrading enzyme treatments, (2) reduced in the presence of CsA or cyclophilin C, and (3) unmodified in the presence of either the N-terminal peptide of CyPB or protamine. Finally, we showed that the type I binding sites were involved in an endocytosis process, supporting the hypothesis that they may correspond to a functional receptor for CyPB.

Foraging habitat quality constrains effectiveness of artificial nest-site provisioning in reversing population declines in a colonial cavity nester.

PubMed

Catry, Inês; Franco, Aldina M A; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

2013-01-01

Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ± 1.7 vs. 1.8 km ± 0.4 and 1.9 km ± 0.6) and had significant larger foraging-ranges (144 km(2) vs. 18.8 and 14.8 km(2)) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas through safe nest-site provisioning.

Foraging Habitat Quality Constrains Effectiveness of Artificial Nest-Site Provisioning in Reversing Population Declines in a Colonial Cavity Nester

PubMed Central

Catry, Inês; Franco, Aldina M. A.; Rocha, Pedro; Alcazar, Rita; Reis, Susana; Cordeiro, Ana; Ventim, Rita; Teodósio, Joaquim; Moreira, Francisco

2013-01-01

Among birds, breeding numbers are mainly limited by two resources of major importance: food supply and nest-site availability. Here, we investigated how differences in land-use and nest-site availability affected the foraging behaviour, breeding success and population trends of the colonial cavity-dependent lesser kestrel Falco naumanni inhabiting two protected areas. Both areas were provided with artificial nests to increase nest-site availability. The first area is a pseudo-steppe characterized by traditional extensive cereal cultivation, whereas the second area is a previous agricultural zone now abandoned or replaced by forested areas. In both areas, lesser kestrels selected extensive agricultural habitats, such as fallows and cereal fields, and avoided scrubland and forests. In the second area, tracked birds from one colony travelled significantly farther distances (6.2 km ±1.7 vs. 1.8 km ±0.4 and 1.9 km ±0.6) and had significant larger foraging-ranges (144 km2 vs. 18.8 and 14.8 km2) when compared to the birds of two colonies in the extensive agricultural area. Longer foraging trips were reflected in lower chick feeding rates, lower fledging success and reduced chick fitness. Availability and occupation of artificial nests was high in both areas but population followed opposite trends, with a positive increment recorded exclusively in the first area with a large proportion of agricultural areas. Progressive habitat loss around the studied colony in the second area (suitable habitat decreased from 32% in 1990 to only 7% in 2002) is likely the main driver of the recorded population decline and suggests that the effectiveness of bird species conservation based on nest-site provisioning is highly constrained by habitat quality in the surrounding areas. Therefore, the conservation of cavity-dependent species may be enhanced firstly by finding the best areas of remaining habitat and secondly by increasing the carrying capacity of high-quality habitat areas through safe nest-site provisioning. PMID:23484016

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

Banfield, Jillian; Comolli, Luis R.; Singer, Steve

Of central interest in this study were microbial communities attached to sediment particles and in associated groundwater. Are the communities similar? What do the organisms look like and how do they associated with each other? Research was conducted on samples collected from the Department of Energy's (DOE) Rifle Integrated Field Research Challenge (IFRC) site in Rifle, Colorado, USA. This site served first as a test case for in situ bioremediation via biostimulation, and more recently as a location for studying the role of microbial communities in the carbon and other linked biogeochemical cycles. We addressed the question of the naturemore » of planktonic to sediment-attached microbial communities using field and laboratory experimental studies with a range of methods that provide 2- and 3-dimensional topological information coupled to information about chemical speciation, organism type, and activity levels. The research leveraged data from metagenomics and proteomics analyses that obtained through parallel work at the Rifle site in the context of the IFRC. In this project we integrated characterization methods with extensive genomic sequence information and associated environmental data to better understand the processes that occur within groundwater and sediment-attached communities. Notable is the range of characterization methods, including scanning transmission x-ray microscopy (STXM), micro-EXAFS/XANES and microdiffraction and 2D and 3D cryo-electron tomographic analysis, and high-resolutino transmission electron microscope (HRTEM) analysis to characterize these natural microbial communities. A cryo-TEM work was unique because samples for electron microscopic characterization were cryo-plunged directly on site immediately after sampling. This step minimizes post-collection alterations, including cell damages and change of redox state. Among many achievements documented in publications listed at the end of this report, we highlight the following: 1) The development of a platform for routine correlative cryogenic microscopy and spectroscopy with samples prepared on-site. 2) The determination of which organisms dominate planktonic and biofilm communities in the subsurface. 3) Identification of microorganism-mineral associations and discovery of a novel mechanism that sustains activity of iron-reducing bacteria. 4) The detection of bacteria from the OP11-OD1-WWE3 (etc.) radiation and elucidation of their remarkable structural organization by cryog-TEM cryo-electron tomograhpy (cryo-ET). 5) Extensive analysis of biofilms and documentation of the association of cells and Se minerals. 6) The comparison of expressed c-type cytochromes between pure cultures of G. bemidjiensis and related field populations, provided insight into possible molecular mechanisms for U(VI) reduction in the aquifer. At least sixteen publications will result from this project (partial support), which provide both graduate student and post doctoral training.« less

Amino-Acid Network Clique Analysis of Protein Mutation Non-Additive Effects: A Case Study of Lysozme.

PubMed

Ming, Dengming; Chen, Rui; Huang, He

2018-05-10

Optimizing amino-acid mutations in enzyme design has been a very challenging task in modern bio-industrial applications. It is well known that many successful designs often hinge on extensive correlations among mutations at different sites within the enzyme, however, the underpinning mechanism for these correlations is far from clear. Here, we present a topology-based model to quantitively characterize non-additive effects between mutations. The method is based on the molecular dynamic simulations and the amino-acid network clique analysis. It examines if the two mutation sites of a double-site mutation fall into to a 3-clique structure, and associates such topological property of mutational site spatial distribution with mutation additivity features. We analyzed 13 dual mutations of T4 phage lysozyme and found that the clique-based model successfully distinguishes highly correlated or non-additive double-site mutations from those additive ones whose component mutations have less correlation. We also applied the model to protein Eglin c whose structural topology is significantly different from that of T4 phage lysozyme, and found that the model can, to some extension, still identify non-additive mutations from additive ones. Our calculations showed that mutation non-additive effects may heavily depend on a structural topology relationship between mutation sites, which can be quantitatively determined using amino-acid network k -cliques. We also showed that double-site mutation correlations can be significantly altered by exerting a third mutation, indicating that more detailed physicochemical interactions should be considered along with the network clique-based model for better understanding of this elusive mutation-correlation principle.

Recombination between bacteriophage lambda and plasmid pBR322 in Escherichia coli.

PubMed Central

Pogue-Geile, K L; Dassarma, S; King, S R; Jaskunas, S R

1980-01-01

Recombinant lambda phages were isolated that resulted from recombination between the lambda genome and plasmid pBR322 in Escherichia coli, even though these deoxyribonucleic acids (DNAs) did not share extensive regions of homology. The characterization of these recombinant DNAs by heteroduplex analysis and restriction endonucleases is described. All but one of the recombinants appeared to have resulted from reciprocal recombination between a site on lambda DNA and a site on the plasmid. In general, there were two classes of recombinants. One class appeared to have resulted from recombination at the phage attachment site that probably resulted from lambda integration into secondary attachment sites on the plasmid. Seven different secondary attachment sites on pBR322 were found. The other class resulted from plasmid integration at other sites that were widely scattered on the lambda genome. For this second class of recombinants, more than one site on the plasmid could recombine with lambda DNA. Thus, the recombination did not appear to be site specific with respect to lambda or the plasmid. Possible mechanisms for generating these recombinants are discussed. Images PMID:6247334

Multiscale tomography of buried magnetic structures: its use in the localization and characterization of archaeological structures

NASA Astrophysics Data System (ADS)

Saracco, Ginette; Moreau, Frédérique; Mathé, Pierre-Etienne; Hermitte, Daniel; Michel, Jean-Marie

2007-10-01

We have previously developed a method for characterizing and localizing `homogeneous' buried sources, from the measure of potential anomalies at a fixed height above ground (magnetic, electric and gravity). This method is based on potential theory and uses the properties of the Poisson kernel (real by definition) and the continuous wavelet theory. Here, we relax the assumption on sources and introduce a method that we call the `multiscale tomography'. Our approach is based on the harmonic extension of the observed magnetic field to produce a complex source by use of a complex Poisson kernel solution of the Laplace equation for complex potential field. A phase and modulus are defined. We show that the phase provides additional information on the total magnetic inclination and the structure of sources, while the modulus allows us to characterize its spatial location, depth and `effective degree'. This method is compared to the `complex dipolar tomography', extension of the Patella method that we previously developed. We applied both methods and a classical electrical resistivity tomography to detect and localize buried archaeological structures like antique ovens from magnetic measurements on the Fox-Amphoux site (France). The estimates are then compared with the results of excavations.

What are hierarchical models and how do we analyze them?

USGS Publications Warehouse

Royle, Andy

2016-01-01

In this chapter we provide a basic definition of hierarchical models and introduce the two canonical hierarchical models in this book: site occupancy and N-mixture models. The former is a hierarchical extension of logistic regression and the latter is a hierarchical extension of Poisson regression. We introduce basic concepts of probability modeling and statistical inference including likelihood and Bayesian perspectives. We go through the mechanics of maximizing the likelihood and characterizing the posterior distribution by Markov chain Monte Carlo (MCMC) methods. We give a general perspective on topics such as model selection and assessment of model fit, although we demonstrate these topics in practice in later chapters (especially Chapters 5, 6, 7, and 10 Chapter 5 Chapter 6 Chapter 7 Chapter 10)

Production and characterization of immortal human neural stem cell line with multipotent differentiation property.

PubMed

Kim, Seung U; Nagai, Atsushi; Nakagawa, Eiji; Choi, Hyun B; Bang, Jung H; Lee, Hong J; Lee, Myung A; Lee, Yong B; Park, In H

2008-01-01

We document the protocols and methods for the production of immortalized cell lines of human neural stem cells from the human fetal central nervous system (CNS) cells by using a retroviral vector encoding v-myc oncogene. One of the human neural stem cell lines (HB1.F3) was found to express nestin and other specific markers for human neural stem cells, giving rise to three fundamental cell types of the CNS: neurons, astrocytes, and oligodendrocytes. After transplantation into the brain of mouse model of stroke, implanted human neural stem cells were observed to migrate extensively from the site of implantation into other anatomical sites and to differentiate into neurons and glial cells.

Risk-adapted monitoring is not inferior to extensive on-site monitoring: Results of the ADAMON cluster-randomised study.

PubMed

Brosteanu, Oana; Schwarz, Gabriele; Houben, Peggy; Paulus, Ursula; Strenge-Hesse, Anke; Zettelmeyer, Ulrike; Schneider, Anja; Hasenclever, Dirk

2017-12-01

Background According to Good Clinical Practice, clinical trials must protect rights and safety of patients and make sure that the trial results are valid and interpretable. Monitoring on-site has an important role in achieving these objectives; it controls trial conduct at trial sites and informs the sponsor on systematic problems. In the past, extensive on-site monitoring with a particular focus on formal source data verification often lost sight of systematic problems in study procedures that endanger Good Clinical Practice objectives. ADAMON is a prospective, stratified, cluster-randomised, controlled study comparing extensive on-site monitoring with risk-adapted monitoring according to a previously published approach. Methods In all, 213 sites from 11 academic trials were cluster-randomised between extensive on-site monitoring (104) and risk-adapted monitoring (109). Independent post-trial audits using structured manuals were performed to determine the frequency of major Good Clinical Practice findings at the patient level. The primary outcome measure is the proportion of audited patients with at least one major audit finding. Analysis relies on logistic regression incorporating trial and monitoring arm as fixed effects and site as random effect. The hypothesis was that risk-adapted monitoring is non-inferior to extensive on-site monitoring with a non-inferiority margin of 0.60 (logit scale). Results Average number of monitoring visits and time spent on-site was 2.1 and 2.7 times higher in extensive on-site monitoring than in risk-adapted monitoring, respectively. A total of 156 (extensive on-site monitoring: 76; risk-adapted monitoring: 80) sites were audited. In 996 of 1618 audited patients, a total of 2456 major audit findings were documented. Depending on the trial, findings were identified in 18%-99% of the audited patients, with no marked monitoring effect in any of the trials. The estimated monitoring effect is -0.04 on the logit scale with two-sided 95% confidence interval (-0.40; 0.33), demonstrating that risk-adapted monitoring is non-inferior to extensive on-site monitoring. At most, extensive on-site monitoring could reduce the frequency of major Good Clinical Practice findings by 8.2% compared with risk-adapted monitoring. Conclusion Compared with risk-adapted monitoring, the potential benefit of extensive on-site monitoring is small relative to overall finding rates, although risk-adapted monitoring requires less than 50% of extensive on-site monitoring resources. Clusters of findings within trials suggest that complicated, overly specific or not properly justified protocol requirements contributed to the overall frequency of findings. Risk-adapted monitoring in only a sample of patients appears sufficient to identify systematic problems in the conduct of clinical trials. Risk-adapted monitoring has a part to play in quality control. However, no monitoring strategy can remedy defects in quality of design. Monitoring should be embedded in a comprehensive quality management approach covering the entire trial lifecycle.

Risk-adapted monitoring is not inferior to extensive on-site monitoring: Results of the ADAMON cluster-randomised study

PubMed Central

Brosteanu, Oana; Schwarz, Gabriele; Houben, Peggy; Paulus, Ursula; Strenge-Hesse, Anke; Zettelmeyer, Ulrike; Schneider, Anja; Hasenclever, Dirk

2017-01-01

Background According to Good Clinical Practice, clinical trials must protect rights and safety of patients and make sure that the trial results are valid and interpretable. Monitoring on-site has an important role in achieving these objectives; it controls trial conduct at trial sites and informs the sponsor on systematic problems. In the past, extensive on-site monitoring with a particular focus on formal source data verification often lost sight of systematic problems in study procedures that endanger Good Clinical Practice objectives. ADAMON is a prospective, stratified, cluster-randomised, controlled study comparing extensive on-site monitoring with risk-adapted monitoring according to a previously published approach. Methods In all, 213 sites from 11 academic trials were cluster-randomised between extensive on-site monitoring (104) and risk-adapted monitoring (109). Independent post-trial audits using structured manuals were performed to determine the frequency of major Good Clinical Practice findings at the patient level. The primary outcome measure is the proportion of audited patients with at least one major audit finding. Analysis relies on logistic regression incorporating trial and monitoring arm as fixed effects and site as random effect. The hypothesis was that risk-adapted monitoring is non-inferior to extensive on-site monitoring with a non-inferiority margin of 0.60 (logit scale). Results Average number of monitoring visits and time spent on-site was 2.1 and 2.7 times higher in extensive on-site monitoring than in risk-adapted monitoring, respectively. A total of 156 (extensive on-site monitoring: 76; risk-adapted monitoring: 80) sites were audited. In 996 of 1618 audited patients, a total of 2456 major audit findings were documented. Depending on the trial, findings were identified in 18%–99% of the audited patients, with no marked monitoring effect in any of the trials. The estimated monitoring effect is −0.04 on the logit scale with two-sided 95% confidence interval (−0.40; 0.33), demonstrating that risk-adapted monitoring is non-inferior to extensive on-site monitoring. At most, extensive on-site monitoring could reduce the frequency of major Good Clinical Practice findings by 8.2% compared with risk-adapted monitoring. Conclusion Compared with risk-adapted monitoring, the potential benefit of extensive on-site monitoring is small relative to overall finding rates, although risk-adapted monitoring requires less than 50% of extensive on-site monitoring resources. Clusters of findings within trials suggest that complicated, overly specific or not properly justified protocol requirements contributed to the overall frequency of findings. Risk-adapted monitoring in only a sample of patients appears sufficient to identify systematic problems in the conduct of clinical trials. Risk-adapted monitoring has a part to play in quality control. However, no monitoring strategy can remedy defects in quality of design. Monitoring should be embedded in a comprehensive quality management approach covering the entire trial lifecycle. PMID:28786330

Characterization of aerosol composition and sources in the greater Atlanta area by aerosol mass spectrometry

NASA Astrophysics Data System (ADS)

Ng, N. L.; Xu, L.; Suresh, S.; Weber, R. J. J.; Baumann, K.; Edgerton, E. S.

2014-12-01

An important and uncertain aspect of biogenic secondary organic aerosol (SOA) formation is that it is often associated with anthropogenic pollution tracers. Prior studies in Atlanta suggested that 70-80% of the carbon in water-soluble organic carbon (WSOC) is modern, yet it is well-correlated with the anthropogenic CO. In this study, we deployed a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS) and an Aerosol Chemical Speciation Monitor (ACSM) at multiple sites in different seasons (May 2012-February 2013) to characterize the sources and chemical composition of aerosols in the greater Atlanta area. This area in the SE US is ideal to investigate anthropogenic-biogenic interactions due to high natural and anthropogenic emissions. These extensive field studies are part of the Southeastern Center for Air Pollution and Epidemiology study (SCAPE). The HR-ToF-AMS is deployed at four sites (~ 3 weeks each) in rotation: Jefferson Street (urban), Yorkville (rural), roadside site (near Highway 75/85), and Georgia Tech site (campus), with the urban and rural sites being part of the SEARCH network. We obtained seven HR-ToF-AMS datasets in total. During the entire measurement period, the ACSM is stationary at the GIT site and samples continuously. We perform positive matrix factorization (PMF) analysis on the HR-ToF-AMS and ACSM data to deconvolve the OA into different components. While the diurnal cycle of the total OA is flat as what have been previously observed, the OA factors resolved by PMF analysis show distinctively different diurnal trends. We find that the "more-oxidized oxygenated OA" (MO-OOA) constitutes a major fraction of OA at all sites. In summer, OA is dominated by SOA, e.g., isoprene-OA and OOA with different degrees of oxidation. In contrary, biomass burning OA is more prominent in winter data. By comparing HR-ToF-AMS and ACSM data during the same sampling periods, we find that the aerosol time series are highly correlated, indicating the regional nature of aerosols in the Atlanta area. Taken together, results from these extensive field studies provide invaluable insights into the sources and processing of aerosols in the greater Atlanta area. The effects of anthropogenic emissions on biogenic SOA formation at multiple sites in the region and in different seasons will be discussed.

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.

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

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

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE PAGES

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

2015-06-28

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Long-term community dynamics of small landbirds with and without exposure to extensive disturbance from military training activities.

PubMed

Rivers, James W; Gipson, Philip S; Althoff, Donald P; Pontius, Jeffrey S

2010-02-01

Military training activities are known to impact individual species, yet our understanding of how such activities influence animal communities is limited. In this study, we used long-term data in a case study approach to examine the extent to which the local small landbird community differed between a site in northeast Kansas that experienced intensive disturbance from military training activities (Ft. Riley Military Installation) and a similar, nearby site that experienced minimal human disturbance (Konza Prairie Biological Station). In addition, we characterized how the regional pool of potential colonizers influenced local community dynamics using Breeding Bird Survey data. From 1991 to 2001, most species of small terrestrial landbirds (73%) recorded during breeding surveys were found at both sites and the mean annual richness at Ft. Riley (39.0 +/- 2.86 [SD]) was very similar to that of Konza Prairie (39.4 +/- 2.01). Richness was maintained at relatively constant levels despite compositional changes because colonizations compensated local extinctions at both sites. These dynamics were driven primarily by woodland species that exhibited stochastic losses and gains and were present at a low local and regional abundance. Our results suggest that military training activities may mimic natural disturbances for some species in this area because the small landbird community did not differ markedly between sites with and sites without extensive human disturbance. Although our results suggest that military training is not associated with large changes in the avian community, additional studies are needed to determine if this pattern is found in other ecological communities.

Paired tree and soil instrumentation: what can we learn from two instrumented sites across various gradients in a forested catchment

NASA Astrophysics Data System (ADS)

Hartsough, P. C.; Roudneva, E.; Malazian, A. I.; Meadows, M. W.; Bales, R. C.; Hopmans, J. W.

2012-12-01

Extensive instrumentation both below and above ground across a forested catchment in the Southern Sierra Critical Zone Observatory (SSCZO) within the Kings River Experimental Watershed (KREW) begins to untangle the complex relationship between precipitation, water storage and transpiration as it relates to water availability from deeper sources. The first instrumented site (CZT-1) includes a White Fir (Abies concolor) situated on a flat ridge with access to deep soil moisture. Monitoring and modeling of shallow and deep soil regions confirm that there is significant soil water available from 100-400cm as the tree exhausts water from shallower depths. A root excavation and limited drilling show roots distributed from 30-150cm with limited roots available to access deeper soil water and water stored in the saprolite. At a second instrumented site, CZT-2, a Ponderosa Pine (Pinus ponderosa) was instrumented with a similar suite of sap flow and soil sensors. The CZT-2 site is on a slight slope and is characterized by shallow soils (<90cm) with extensive cobbles and bedrock outcrops with limited access to deeper soil or saprolite water. The second site also sits in the open while the first site is more protected in a closed forest. The two sites show different responses to changes in rain and snow loading from above as well as soil drainage and water depletion from below across a wet to dry transition. They also have different thresholds for transpiration shut down both due to late season water deficit and also during winter periods where air temperatures are high enough to permit photosynthesis. Sap flux and extensive soil water content and water potential measurements around both trees as well as evapotranspiration measurements from a 50m flux tower located adjacent to the two instrumented trees, show little water limitation during wet years and only moderate water limitation during a drought year. Access to deeper water storage pools is confirmed by modeling results across the soil/tree/atmosphere continuum.

Dust Aerosol, Clouds, and the Atmospheric Optical Depth Record over 5 Mars Years of the Mars Exploration Rover Mission

NASA Technical Reports Server (NTRS)

Lemmon, Mark T.; Wolff, Michael J.; Bell, James F., III; Smith, Michael D.; Cantor, Bruce A.; Smith, Peter H.

2014-01-01

Dust aerosol plays a fundamental role in the behavior and evolution of the Martian atmosphere. The first five Mars years of Mars Exploration Rover data provide an unprecedented record of the dust load at two sites. This record is useful for characterization of the atmosphere at the sites and as ground truth for orbital observations. Atmospheric extinction optical depths have been derived from solar images after calibration and correction for time-varying dust that has accumulated on the camera windows. The record includes local, regional, and globally extensive dust storms. Comparison with contemporaneous thermal infrared data suggests significant variation in the size of the dust aerosols, with a 1 micrometer effective radius during northern summer and a 2 micrometer effective radius at the onset of a dust lifting event. The solar longitude (L (sub s)) 20-136 degrees period is also characterized by the presence of cirriform clouds at the Opportunity site, especially near LS = 50 and 115 degrees. In addition to water ice clouds, a water ice haze may also be present, and carbon dioxide clouds may be present early in the season. Variations in dust opacity are important to the energy balance of each site, and work with seasonal variations in insolation to control dust devil frequency at the Spirit site.

75 FR 17050 - Enhancing Airline Passenger Protections: Extension of Compliance Date for Posting of Flight Delay...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-05

... Flight Delay Data on Web Sites AGENCY: Office of the Secretary (OST), Department of Transportation (DOT... information on their Web sites. This extension is in response to requests by several carrier associations for... on Web sites in view of the extensive changes to carriers' reporting systems that are necessitated by...

Advanced technologies for maintenance of electrical systems and equipment at the Savannah River Site Defense Waste Processing Facility

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

Husler, R.O.; Weir, T.J.

1991-01-01

An enhanced maintenance program is being established to characterize and monitor cables, components, and process response at the Savannah River Site, Defense Waste Processing Facility. This facility was designed and constructed to immobilize the radioactive waste currently stored in underground storage tanks and is expected to begin operation in 1993. The plant is initiating the program to baseline and monitor instrument and control (I C) and electrical equipment, remote process equipment, embedded instrument and control cables, and in-cell jumper cables used in the facility. This program is based on the electronic characterization and diagnostic (ECAD) system which was modified tomore » include process response analysis and to meet rigid Department of Energy equipment requirements. The system consists of computer-automated, state-of-the-art electronics. The data that are gathered are stored in a computerized database for analysis, trending, and troubleshooting. It is anticipated that the data which are gathered and trended will aid in life extension for the facility.« less

Advanced technologies for maintenance of electrical systems and equipment at the Savannah River Site Defense Waste Processing Facility

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

Husler, R.O.; Weir, T.J.

1991-12-31

An enhanced maintenance program is being established to characterize and monitor cables, components, and process response at the Savannah River Site, Defense Waste Processing Facility. This facility was designed and constructed to immobilize the radioactive waste currently stored in underground storage tanks and is expected to begin operation in 1993. The plant is initiating the program to baseline and monitor instrument and control (I&C) and electrical equipment, remote process equipment, embedded instrument and control cables, and in-cell jumper cables used in the facility. This program is based on the electronic characterization and diagnostic (ECAD) system which was modified to includemore » process response analysis and to meet rigid Department of Energy equipment requirements. The system consists of computer-automated, state-of-the-art electronics. The data that are gathered are stored in a computerized database for analysis, trending, and troubleshooting. It is anticipated that the data which are gathered and trended will aid in life extension for the facility.« less

Evaluation of field methods for vertical high resolution aquifer characterization

NASA Astrophysics Data System (ADS)

Vienken, T.; Tinter, M.; Rogiers, B.; Leven, C.; Dietrich, P.

2012-12-01

The delineation and characterization of subsurface (hydro)-stratigraphic structures is one of the challenging tasks of hydrogeological site investigations. The knowledge about the spatial distribution of soil specific properties and hydraulic conductivity (K) is the prerequisite for understanding flow and fluid transport processes. This is especially true for heterogeneous unconsolidated sedimentary deposits with a complex sedimentary architecture. One commonly used approach to investigate and characterize sediment heterogeneity is soil sampling and lab analyses, e.g. grain size distribution. Tests conducted on 108 samples show that calculation of K based on grain size distribution is not suitable for high resolution aquifer characterization of highly heterogeneous sediments due to sampling effects and large differences of calculated K values between applied formulas (Vienken & Dietrich 2011). Therefore, extensive tests were conducted at two test sites under different geological conditions to evaluate the performance of innovative Direct Push (DP) based approaches for the vertical high resolution determination of K. Different DP based sensor probes for the in-situ subsurface characterization based on electrical, hydraulic, and textural soil properties were used to obtain high resolution vertical profiles. The applied DP based tools proved to be a suitable and efficient alternative to traditional approaches. Despite resolution differences, all of the applied methods captured the main aquifer structure. Correlation of the DP based K estimates and proxies with DP based slug tests show that it is possible to describe the aquifer hydraulic structure on less than a meter scale by combining DP slug test data and continuous DP measurements. Even though correlations are site specific and appropriate DP tools must be chosen, DP is reliable and efficient alternative for characterizing even strongly heterogeneous sites with complex structured sedimentary aquifers (Vienken et al. 2012). References: Vienken, T., Leven, C., and Dietrich, P. 2012. Use of CPT and other direct push methods for (hydro-) stratigraphic aquifer characterization — a field study. Canadian Geotechnical Journal, 49(2): 197-206. Vienken, T., and Dietrich, P. 2011. Field evaluation of methods for determining hydraulic conductivity from grain size data. Journal of Hydrology, 400(1-2): 58-71.

Function and morphology correlates of rectal nerve mechanoreceptors innervating the guinea pig internal anal sphincter.

PubMed

Lynn, P A; Brookes, S J H

2011-01-01

Mechanoreceptors to the internal anal sphincter (IAS) contribute to continence and normal defecation, yet relatively little is known about their function or morphology. We investigated the function and structure of mechanoreceptors to the guinea pig IAS. Extracellular recordings from rectal nerve branches to the IAS in vitro, combined with anterograde labeling of recorded nerve trunks, were used to characterize extrinsic afferent nerve endings activated by circumferential distension. Slowly adapting, stretch-sensitive afferents were recorded in rectal nerves to the IAS. Ten of 11 were silent under basal conditions and responded to circumferential stretch in a saturating linear manner. Rectal nerve afferents responded to compression with von Frey hairs with low thresholds (0.3-0.5 mN) and 3.4 ± 0.5 discrete, elongated mechanosensitive fields of innervation aligned parallel to circular muscle bundles (length = 62 ± 16 mm, n = 10). Anterogradely labeled rectal nerve axons typically passed through sparse irregular myenteric ganglia adjacent to the IAS, before ending in extensive varicose arrays within the circular muscle and, to a lesser extent, the longitudinal muscle overlying the IAS. Few (8%) IAS myenteric ganglia contained intraganglionic laminar endings. In eight preparations, mechanotransduction sites were mapped in combination with successful anterograde fills. Mechanotransduction sites were strongly associated with extensive fine varicose arrays within the circular muscle (P < 0.05), and not with any other neural structures. Mechanotransduction sites for low-threshold, slowly adapting mechanoreceptors innervating the IAS are likely to correspond to extensive fine varicose arrays within the circular muscle. © 2010 Blackwell Publishing Ltd.

3-D Characterization of Seismic Properties at the Smart Weapons Test Range, YPG

NASA Astrophysics Data System (ADS)

Miller, Richard D.; Anderson, Thomas S.; Davis, John C.; Steeples, Don W.; Moran, Mark L.

2001-10-01

The Smart Weapons Test Range (SWTR) lies within the Yuma Proving Ground (YPG), Arizona. SWTR is a new facility constructed specifically for the development and testing of futuristic intelligent battlefield sensor networks. In this paper, results are presented for an extensive high-resolution geophysical characterization study at the SWTR site along with validation using 3-D modeling. In this study, several shallow seismic methods and novel processing techniques were used to generate a 3-D grid of earth seismic properties, including compressional (P) and shear (S) body-wave speeds (Vp and Vs), and their associated body-wave attenuation parameters (Qp, and Qs). These experiments covered a volume of earth measuring 1500 m by 300 m by 25 m deep (11 million cubic meters), centered on the vehicle test track at the SWTR site. The study has resulted in detailed characterizations of key geophysical properties. To our knowledge, results of this kind have not been previously achieved, nor have the innovative methods developed for this effort been reported elsewhere. In addition to supporting materiel developers with important geophysical information at this test range, the data from this study will be used to validate sophisticated 3-D seismic signature models for moving vehicles.

Rooting Depths of Red Maple (Acer Rubrum L.) on Various Sites in the Lake States

Treesearch

Carl L. Haag; James E. Johnson; Gayne G. Erdmann

1989-01-01

Rooting depth and habit of red maple were observed on 60 sites in northern Wisconsin and Michigan as part of a regional soil-site studay. Vertical woody root extension on dry, outwash sites averaged 174 cm, which was significantly greater than the extension on sites with fragipans (139 cm) and on wet sites (112 cm). Site index was higher on wet sites and non-woody...

Identification and characterization of conservative organic tracers for use as hydrologic tracers for the Yucca Mountain site characterization study. Final report

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

Stetzenbach, K.; Farnham, I.

1996-06-01

Extensive tracer testing is expected to take place at the C-well complex in the Nevada Test Site as part of the Yucca Mountain Site Characterization Project. The C-well complex consists of one pumping well, C3, and two injection wells, C1 and C2 into which tracer will be introduced. The goal of this research was to provide USGS with numerous tracers to completed these tests. Several classes of fluorinated organic acids have been evaluated. These include numerous isomers of fluorinated benzoic acids, cinnamic acids, and salicylic acids. Also several derivatives of 2-hydroxy nicotinic acid (pyridone) have been tested. The stability ofmore » these compounds was determined using batch and column tests. Ames testing (mutagenicity/carcinogenicity) was conducted on the fluorinated benzoic acids and a literature review of toxicity of the fluorobenzoates and three perfluoro aliphatic acids was prepared. Solubilities were measured and method development work was performed to optimize the detection of these compounds. A Quality Assurance (QA) Program was developed under existing DOE and USGS guidelines. The program includes QA procedures and technical standard operating procedures. A tracer test, using sodium iodide, was performed at the C-well complex. HRC chemists performed analyses on site, to provide real time data for the USGS hydrologists and in the laboratories at UNLV. Over 2,500 analyses were performed. This report provides the results of the laboratory experiments and literature reviews used to evaluate the potential tracers and reports on the results of the iodide C-well tracer test.« less

Carbohydrate recognition by the antiviral lectin cyanovirin-N

PubMed Central

Fujimoto, Yukiji K.; Green, David F.

2012-01-01

Cyanovirin-N is a cyanobacterial lectin with potent antiviral activity, and has been the focus of extensive pre-clinical investigation as a potential prophylactic for the prevention of the sexual transmission of the human immunodeficiency virus (HIV). Here we present a detailed analysis of carbohydrate recognition by this important protein, using a combination of computational methods, including extensive molecular dynamics simulations and Molecular-Mechanics/ Poisson–Boltzmann/Surface-Area (MM/PBSA) energetic analysis. The simulation results strongly suggest that the observed tendency of wildtype CVN to form domain-swapped dimers is the result of a previously unidentified cis-peptide bond present in the monomeric state. The energetic analysis additionally indicates that the highest-affinity ligand for CVN characterized to date (α-Man-(1,2)-α-Man-(1,2)-α-Man) is recognized asymmetrically by the two binding sites. Finally, we are able to provide a detailed map of the role of all binding site functional groups (both backbone and side chain) to various aspects of molecular recognition: general affinity for cognate ligands, specificity for distinct oligosaccharide targets and the asymmetric recognition of α-Man-(1,2)-α-Man-(1,2)-α-Man. Taken as a whole, these results complement past experimental characterization (both structural and thermodynamic) to provide the most complete understanding of carbohydrate recognition by CVN to date. The results also provide strong support for the application of similar approaches to the understanding of other protein–carbohydrate complexes. PMID:23057413

Topography and behavior of Sertoli cells in sparse culture during the transitional remodeling phase.

PubMed

Tung, P S; Choi, A H; Fritz, I B

1988-01-01

We report observations on the behavior of Sertoli cells in sparse culture during the period from the time of plating to the time of initial confluence (the transitional remodeling phase). Changes in shape, structure, and polarity of cells, as well as changes in migration patterns and cell-cell association patterns, have been followed during the transitional remodeling phase with the aid of topographical markers. These markers are based upon differences between ultrastructural features of the basolateral and apicolateral surfaces. The basolateral surface is characterized by plasmalemmal blebs, whereas the apicolateral surface is characterized by filopodial extensions. Structural differences observed in situ remain evident in Sertoli cells isolated by sequential enzymatic treatments that are described. Another marker is provided by laminin-binding sites, which are detected exclusively on the blebbed, basolateral surfaces of freshly prepared Sertoli cell aggregates. The orientation described is sustained during the initial radial migration of Sertoli cells explanted on uncoated glass coverslips. Under these conditions, blebs are detected only on the dorsal surfaces, and filopodial extensions are evident only on the ventral surfaces. In contrast, Sertoli cells sparsely plated on a reconstituted basement membrane (air-dried Matrigel) migrate rapidly, display an extraordinary capacity to form elaborate cytoplasmic extensions for cell-cell and cell-substratum contacts, and readily retract blebs and filopodial extensions. These cells do not form mosaic borders, whereas cells plated on uncoated glass do form a monolayer with mosaic-like borders. Cells sparsely seeded on gelated Matrigel migrate preferentially at gaps between adjacent cell explants, and develop a compact cell-cell association pattern. These cells display few, if any, cytoplasmic extensions. We compare the behavior of Sertoli cells sparsely plated on Matrigel with the behavior of Sertoli cells in situ during different stages of development.

Quantitative analysis of ribosome–mRNA complexes at different translation stages

PubMed Central

Shirokikh, Nikolay E.; Alkalaeva, Elena Z.; Vassilenko, Konstantin S.; Afonina, Zhanna A.; Alekhina, Olga M.; Kisselev, Lev L.; Spirin, Alexander S.

2010-01-01

Inhibition of primer extension by ribosome–mRNA complexes (toeprinting) is a proven and powerful technique for studying mechanisms of mRNA translation. Here we have assayed an advanced toeprinting approach that employs fluorescently labeled DNA primers, followed by capillary electrophoresis utilizing standard instruments for sequencing and fragment analysis. We demonstrate that this improved technique is not merely fast and cost-effective, but also brings the primer extension inhibition method up to the next level. The electrophoretic pattern of the primer extension reaction can be characterized with a precision unattainable by the common toeprint analysis utilizing radioactive isotopes. This method allows us to detect and quantify stable ribosomal complexes at all stages of translation, including initiation, elongation and termination, generated during the complete translation process in both the in vitro reconstituted translation system and the cell lysate. We also point out the unique advantages of this new methodology, including the ability to assay sites of the ribosomal complex assembly on several mRNA species in the same reaction mixture. PMID:19910372

Empirical evaluation of cross-site reproducibility in radiomic features for characterizing prostate MRI

NASA Astrophysics Data System (ADS)

Chirra, Prathyush; Leo, Patrick; Yim, Michael; Bloch, B. Nicolas; Rastinehad, Ardeshir R.; Purysko, Andrei; Rosen, Mark; Madabhushi, Anant; Viswanath, Satish

2018-02-01

The recent advent of radiomics has enabled the development of prognostic and predictive tools which use routine imaging, but a key question that still remains is how reproducible these features may be across multiple sites and scanners. This is especially relevant in the context of MRI data, where signal intensity values lack tissue specific, quantitative meaning, as well as being dependent on acquisition parameters (magnetic field strength, image resolution, type of receiver coil). In this paper we present the first empirical study of the reproducibility of 5 different radiomic feature families in a multi-site setting; specifically, for characterizing prostate MRI appearance. Our cohort comprised 147 patient T2w MRI datasets from 4 different sites, all of which were first pre-processed to correct acquisition-related for artifacts such as bias field, differing voxel resolutions, as well as intensity drift (non-standardness). 406 3D voxel wise radiomic features were extracted and evaluated in a cross-site setting to determine how reproducible they were within a relatively homogeneous non-tumor tissue region; using 2 different measures of reproducibility: Multivariate Coefficient of Variation and Instability Score. Our results demonstrated that Haralick features were most reproducible between all 4 sites. By comparison, Laws features were among the least reproducible between sites, as well as performing highly variably across their entire parameter space. Similarly, the Gabor feature family demonstrated good cross-site reproducibility, but for certain parameter combinations alone. These trends indicate that despite extensive pre-processing, only a subset of radiomic features and associated parameters may be reproducible enough for use within radiomics-based machine learning classifier schemes.

Kinetic analysis of bypass of abasic site by the catalytic core of yeast DNA polymerase eta.

PubMed

Yang, Juntang; Wang, Rong; Liu, Binyan; Xue, Qizhen; Zhong, Mengyu; Zeng, Hao; Zhang, Huidong

2015-09-01

Abasic sites (Apurinic/apyrimidinic (AP) sites), produced ∼ 50,000 times/cell/day, are very blocking and miscoding. To better understand miscoding mechanisms of abasic site for yeast DNA polymerase η, pre-steady-state nucleotide incorporation and LC-MS/MS sequence analysis of extension product were studied using pol η(core) (catalytic core, residues 1-513), which can completely eliminate the potential effects of the C-terminal C2H2 motif of pol η on dNTP incorporation. The extension beyond the abasic site was very inefficient. Compared with incorporation of dCTP opposite G, the incorporation efficiencies opposite abasic site were greatly reduced according to the order of dGTP > dATP > dCTP and dTTP. Pol η(core) showed no fast burst phase for any incorporation opposite G or abasic site, suggesting that the catalytic step is not faster than the dissociation of polymerase from DNA. LC-MS/MS sequence analysis of extension products showed that 53% products were dGTP misincorporation, 33% were dATP and 14% were -1 frameshift, indicating that Pol η(core) bypasses abasic site by a combined G-rule, A-rule and -1 frameshift deletions. Compared with full-length pol η, pol η(core) relatively reduced the efficiency of incorporation of dCTP opposite G, increased the efficiencies of dNTP incorporation opposite abasic site and the exclusive incorporation of dGTP opposite abasic site, but inhibited the extension beyond abasic site, and increased the priority in extension of A: abasic site relative to G: abasic site. This study provides further understanding in the mutation mechanism of abasic sites for yeast DNA polymerase η. Copyright © 2015 Elsevier B.V. All rights reserved.

An objective and reproducible landform and topography description approach based on digital terrain analysis used for soil profile site characteristics

NASA Astrophysics Data System (ADS)

Gruber, Fabian E.; Baruck, Jasmin; Hastik, Richard; Geitner, Clemens

2015-04-01

All major soil description and classification systems, including the World Reference Base (WRB) and the German Soil description guidelines (KA5), require the characterization of landform and topography for soil profile sites. This is commonly done at more than one scale, for instance at macro-, meso- and micro scale. However, inherent when humans perform such a task, different surveyors will reach different conclusions due to their subjective perception of landscape structure, based on their individual mind-model of soil-landscape structure, emphasizing different aspects and scales of the landscape. In this study we apply a work-flow using the GRASS GIS extension module r.geomorphon to make use of high resolution digital elevation models (DEMs) to characterize the landform elements and topography of soil profile sites at different scales, and compare the results with a large number of soil profile site descriptions performed during the course of forestry surveys in South and North Tyrol (Italy and Austria, respectively). The r.geomorphon extension module for the open source geographic information system GRASS GIS applies a pattern recognition algorithm to delineate landform elements based on an input DEM. For each raster cell it computes and characterizes the visible neighborhood using line-of-sight calculations and then applies a lookup-table to classify the raster cell into one of ten landform elements (flat, peak, ridge, shoulder, slope, spur, hollow, footslope, valley and pit). The input parameter search radius (L) represents the maximum number of pixels for line-of-sight calculation, resulting in landforms larger than L to be split into landform components. The use of these visibility calculations makes this landform delineation approach suitable for comparison with the landform descriptions of soil surveyors, as their spatial perception of the landscape surrounding a soil profile site certainly influences their classification of the landform on which the profile is situated (aided by additional information such as topographic maps and aerial images). Variation of the L-value furthermore presents the opportunity to mimic the different scales at which surveyors describe soil profile locations. We first illustrate the use of r.geomorphon for site descriptions using exemplary artificial elevation profiles resembling typic catenas at different scales (L-values). We then compare the results of a landform element map computed with r.geomorphon to the relief descriptions in the test dataset. We link the surveyors' landform classification to the computed landform elements. Using a multi-scale approach we characterize raster cell locations in a way similar to the micro-, meso- and macroscale definitions used in soil survey, resulting in so-called geomorphon-signatures, such as "pit (meso-scale) located on a ridge (macro-scale)". We investigate which ranges of L-values best represent the different observation-scales as noted by soil surveyors and discuss the impacts of using a large dataset of profile location descriptions performed by different surveyors. Issues that arise are possible individual differences in landscape structure perception, but also questions regarding the accuracy of position and resulting topographic measurements in soil profile site description.

The genomic structure of the human UFO receptor.

PubMed

Schulz, A S; Schleithoff, L; Faust, M; Bartram, C R; Janssen, J W

1993-02-01

Using a DNA transfection-tumorigenicity assay we have recently identified the UFO oncogene. It encodes a tyrosine kinase receptor characterized by the juxtaposition of two immunoglobulin-like and two fibronectin type III repeats in its extracellular domain. Here we describe the genomic organization of the human UFO locus. The UFO receptor is encoded by 20 exons that are distributed over a region of 44 kb. Different isoforms of UFO mRNA are generated by alternative splicing of exon 10 and differential usage of two imperfect polyadenylation sites resulting in the presence or absence of 1.5-kb 3' untranslated sequences. Primer extension and S1 nuclease analyses revealed multiple transcriptional initiation sites including a major site 169 bp upstream of the translation start site. The promoter region is GC rich, lacks TATA and CAAT boxes, but contains potential recognition sites for a variety of trans-acting factors, including Sp1, AP-2 and the cyclic AMP response element-binding protein. Proto-UFO and its oncogenic counterpart exhibit identical cDNA and promoter regions sequences. Possible modes of UFO activation are discussed.

Adverse health effects in Canada geese (Branta canadensis) associated with waste from zinc and lead mines in the Tri-State Mining District (Kansas, Oklahoma, and Missouri, USA).

PubMed

van der Merwe, Deon; Carpenter, James W; Nietfeld, Jerome C; Miesner, John F

2011-07-01

Lead and zinc poisoning have been recorded in a variety of bird species, including migrating waterfowl such as Canada Geese (Branta canadensis), at sites contaminated with mine waste from lead and zinc mines in the Tri-State Mining District, Kansas, Oklahoma, and Missouri, USA. The adverse health impacts from mine waste on these birds may, however, be more extensive than is apparent from incidental reports of clinical disease. To characterize health impacts from mine waste on Canada Geese that do not have observable signs of poisoning, four to eight apparently healthy birds per site were collected from four contaminated sites and an uncontaminated reference site, and examined for physical and physiologic evidence of metals poisoning. Tissue concentrations of silver, aluminum, arsenic, barium, cadmium, cobalt, chromium, copper, iron, magnesium, manganese, molybdenum, nickel, lead, selenium, thallium, vanadium, and zinc were determined by inductively coupled plasma mass spectroscopy. Adverse health effects due to lead were characterized by assessing blood δ-aminolevulinic acid dehydratase (ALAD) enzyme activity. Adverse effects associated with zinc poisoning were determined from histologic examination of pancreas tissues. Elevated tissue lead concentrations and inhibited blood ALAD enzyme activities were consistently found in birds at all contaminated sites. Histopathologic signs of zinc poisoning, including fibrosis and vacuolization, were associated with elevated pancreatic zinc concentrations at one of the study sites. Adverse health effects associated with other analyzed elements, or tissue concentrations indicating potentially toxic exposure levels to these elements, were not observed.

An Online Resource Site for Extension Master Gardener Coordinators

ERIC Educational Resources Information Center

Langellotto, Gail Ann; Dorn, Sheri

2016-01-01

Developing an online resource site for Extension master gardener (EMG) coordinators is an ongoing project for Extension collaborators. Begun in 2014, the website includes peer-reviewed resources focused on best practices in volunteer management and program administration. The website is organized according to nine resource categories (e.g.,…

A multi-residue method for characterization and determination of atmospheric pesticides measured at two French urban and rural sampling sites.

PubMed

Baraud, Laurent; Tessier, Didier; Aaron, Jean-Jacques; Quisefit, Jean-Paul; Pinart, Johann

2003-12-01

The extensive use of pesticides to protect agricultural crops can result in the transfer of these compounds into the atmosphere and their diffusion towards urban areas. Precise evaluation of the geographic impact of this type of pollution is important environmentally. In this paper, analytical methods for the sampling, characterization, and determination of agricultural pesticides in air were developed; the methods were then applied in the Paris and Champagne regions. Sixteen pesticides belonging to nine chemical families were monitored. Sampling was carried out in urban (Paris) and rural (Aube district) sites, utilizing either a high-volume pump (12.5 m3 h(-1)) (urban site) or a low-volume pump (2.3 m3 h(-1)) for the rural site. Quartz filters and polyurethane foams (PUF) were used for sampling in all cases. After extracting the samples and concentrating the recovered solutions, high-performance liquid chromatography (HPLC) analysis with UV detection was performed. Identification of the pesticides was confirmed by applying to the HPLC measurements a novel UV-detection procedure based on the normalized absorbance variation with wavelength (Noravawa procedure). The presence of metsulfuron methyl, isoproturon, linuron, deltamethrin (and/or malathion), and chlorophenoxy acids (2,4-D and MCPP) was found at the urban sampling site at levels ranging from about 1 to 1130 ng m(-3) of air, depending on the compound and sampling period. On the rural sampling site residues of isoproturon, deltamethrin (and/or malathion), MCPP, and 2,4-D were generally detected at higher levels (19-5130 ng m(-3)) than on the urban site, as expected. The effects of the weather conditions and agricultural activity on the atmospheric concentrations of pesticides are discussed, as are long-range atmospheric transfer processes for these pesticides.

Uncertainty quantification and experimental design based on unsupervised machine learning identification of contaminant sources and groundwater types using hydrogeochemical data

NASA Astrophysics Data System (ADS)

Vesselinov, V. V.

2017-12-01

Identification of the original groundwater types present in geochemical mixtures observed in an aquifer is a challenging but very important task. Frequently, some of the groundwater types are related to different infiltration and/or contamination sources associated with various geochemical signatures and origins. The characterization of groundwater mixing processes typically requires solving complex inverse models representing groundwater flow and geochemical transport in the aquifer, where the inverse analysis accounts for available site data. Usually, the model is calibrated against the available data characterizing the spatial and temporal distribution of the observed geochemical species. Numerous geochemical constituents and processes may need to be simulated in these models which further complicates the analyses. As a result, these types of model analyses are typically extremely challenging. Here, we demonstrate a new contaminant source identification approach that performs decomposition of the observation mixtures based on Nonnegative Matrix Factorization (NMF) method for Blind Source Separation (BSS), coupled with a custom semi-supervised clustering algorithm. Our methodology, called NMFk, is capable of identifying (a) the number of groundwater types and (b) the original geochemical concentration of the contaminant sources from measured geochemical mixtures with unknown mixing ratios without any additional site information. We also demonstrate how NMFk can be extended to perform uncertainty quantification and experimental design related to real-world site characterization. The NMFk algorithm works with geochemical data represented in the form of concentrations, ratios (of two constituents; for example, isotope ratios), and delta notations (standard normalized stable isotope ratios). The NMFk algorithm has been extensively tested on synthetic datasets; NMFk analyses have been actively performed on real-world data collected at the Los Alamos National Laboratory (LANL) groundwater sites related to Chromium and RDX contamination.

Assessing background ground water chemistry beneath a new unsewered subdivision

USGS Publications Warehouse

Wilcox, J.D.; Bradbury, K.R.; Thomas, C.L.; Bahr, J.M.

2005-01-01

Previous site-specific studies designed to assess the impacts of unsewered subdivisions on ground water quality have relied on upgradient monitoring wells or very limited background data to characterize conditions prior to development. In this study, an extensive monitoring program was designed to document ground water conditions prior to construction of a rural subdivision in south-central Wisconsin. Previous agricultural land use has impacted ground water quality; concentrations of chloride, nitrate-nitrogen, and atrazine ranged from below the level of detection to 296 mg/L, 36 mg/L, and 0.8 ??g/L, respectively, and were highly variable from well to well and through time. Seasonal variations in recharge, surface topography, aquifer heterogeneities, surficial loading patterns, and well casing depth explain observed variations in ground water chemistry. This variability would not have been detected if background conditions were determined from only a few monitoring wells or inferred from wells located upgradient of the subdivision site. This project demonstrates the importance of characterizing both ground water quality and chemical variability prior to land-use change to detect any changes once homes are constructed. Copyright ?? 2005 National Ground Water Association.

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.

Genetic structure and variability of virus populations in cross-protected grapevines superinfected by Grapevine fanleaf virus.

PubMed

Vigne, Emmanuelle; Marmonier, Aurélie; Komar, Véronique; Lemaire, Olivier; Fuchs, Marc

2009-09-01

Recombination was assessed in a vineyard site in which grapevines cross-protected with mild strains GHu of Grapevine fanleaf virus (GFLV) or Ta of Arabis mosaic virus (ArMV) were superinfected with GFLV field isolates following transmission by the nematode vector Xiphinema index. The genetic structure and variability within RNA2 of isolates from grapevines co-infected with GFLV field isolates and either GFLV-GHu or ArMV-Ta were characterized to identify intra- and interspecies recombinants. Sequence analysis and phylogenetic relationships inferred intraspecies recombination among GFLV field isolates but not between field isolates and GFLV-GHu. SISCAN analysis confirmed a mosaic structure for two GFLV field isolates for which recombination sites were located in the movement protein and coat protein genes. One of the recombinants was found in eight grapevines that were in close spatial proximity within the vineyard site, suggesting its transmission by X. index. No interspecies recombination was detected between GFLV field isolates and ArMV-Ta. Altogether, our findings suggest that mild protective strains GFLV-GHu and ArMV-Ta did not assist the emergence of viable recombinants to detectable level during a 12-year cross-protection trial. To our knowledge, this is the first extensive characterization of the genetic structure and variability of virus isolates in cross-protected plants.

N- and O-Glycosylation in the Murine Synaptosome*

PubMed Central

Trinidad, Jonathan C.; Schoepfer, Ralf; Burlingame, Alma L.; Medzihradszky, Katalin F.

2013-01-01

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues. PMID:23816992

N- and O-glycosylation in the murine synaptosome.

PubMed

Trinidad, Jonathan C; Schoepfer, Ralf; Burlingame, Alma L; Medzihradszky, Katalin F

2013-12-01

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues.

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups

PubMed Central

Leung, Marcus H. Y.; Wilkins, David; Lee, Patrick K. H.

2015-01-01

Many studies have characterized microbiomes of western individuals. However, studies involving non-westerners are scarce. This study characterizes the skin microbiomes of Chinese individuals. Skin-associated genera, including Propionibacterium, Corynebacterium, Staphylococcus, and Enhydrobacter were prevalent. Extensive inter-individual microbiome variations were detected, with core genera present in all individuals constituting a minority of genera detected. Species-level analyses presented dominance of potential opportunistic pathogens in respective genera. Host properties including age, gender, and household were associated with variations in community structure. For all sampled sites, skin microbiomes within an individual is more similar than that of different co-habiting individuals, which is in turn more similar than individuals living in different households. Network analyses highlighted general and skin-site specific relationships between genera. Comparison of microbiomes from different population groups revealed race-based clustering explained by community membership (Global R = 0.968) and structure (Global R = 0.589), contributing to enlargement of the skin pan-microbiome. This study provides the foundation for subsequent in-depth characterization and microbial interactive analyses on the skin and other parts of the human body in different racial groups, and an appreciation that the human skin pan-microbiome can be much larger than that of a single population. PMID:26177982

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

Chemistry and Properties of Imide Oligomers from Phenylethynyl-Containing Diamines

NASA Technical Reports Server (NTRS)

Smith, J. G., Jr.; Connell, J. W.

2000-01-01

As an extension of work on pendent phenylethynlyl-containing imide oligomer, three new diamines containing pendent phenylethynyl groups were prepared and characterized. These diamines were used to prepare pendent and pendent and terminal phenylethynyl imide oliogomers via the amide acid route in N-methyl-2-pyrrolidinone at a calculated number average molecular weight of 5000 g mol (exp -1). The pendent phenylethynyl groups were randomly distributed along the oliogomer backbone and provided a means of controlling the distance between reactive sites. The imide oligomers were characterized and thermally cured, and the cured polymers evaluated as thin films and compared with materials of similar composition prepared from 3,5-diamino-4'-phenylethynylbenzophenone. This work was performed as part of a continuing research effort to develop structural resins for potential aeronautical applications.

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

PubMed Central

Shen, Yingjia; Ji, Guoli; Haas, Brian J.; Wu, Xiaohui; Zheng, Jianti; Reese, Greg J.; Li, Qingshun Quinn

2008-01-01

The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3′-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5′-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites. PMID:18411206

N- and O-glycosylation Analysis of Human C1-inhibitor Reveals Extensive Mucin-type O-Glycosylation.

PubMed

Stavenhagen, Kathrin; Kayili, H Mehmet; Holst, Stephanie; Koeleman, Carolien A M; Engel, Ruchira; Wouters, Diana; Zeerleder, Sacha; Salih, Bekir; Wuhrer, Manfred

2018-06-01

Human C1-inhibitor (C1-Inh) is a serine protease inhibitor and the major regulator of the contact activation pathway as well as the classical and lectin complement pathways. It is known to be a highly glycosylated plasma glycoprotein. However, both the structural features and biological role of C1-Inh glycosylation are largely unknown. Here, we performed for the first time an in-depth site-specific N - and O -glycosylation analysis of C1-Inh combining various mass spectrometric approaches, including C18-porous graphitized carbon (PGC)-LC-ESI-QTOF-MS/MS applying stepping-energy collision-induced dissociation (CID) and electron-transfer dissociation (ETD). Various proteases were applied, partly in combination with PNGase F and exoglycosidase treatment, in order to analyze the (glyco)peptides. The analysis revealed an extensively O -glycosylated N-terminal region. Five novel and five known O -glycosylation sites were identified, carrying mainly core1-type O -glycans. In addition, we detected a heavily O -glycosylated portion spanning from Thr 82 -Ser 121 with up to 16 O -glycans attached. Likewise, all known six N -glycosylation sites were covered and confirmed by this site-specific glycosylation analysis. The glycoforms were in accordance with results on released N -glycans by MALDI-TOF/TOF-MS/MS. The comprehensive characterization of C1-Inh glycosylation described in this study will form the basis for further functional studies on the role of these glycan modifications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Benthic habitat characterization and distribution from two representative sites of the deep-water SML Coral Province (Mediterranean)

NASA Astrophysics Data System (ADS)

Vertino, A.; Savini, A.; Rosso, A.; Di Geronimo, I.; Mastrototaro, F.; Sanfilippo, R.; Gay, G.; Etiope, G.

2010-03-01

Two sites (MS04 and MS06) from the Santa Maria di Leuca (SML) Coral Province were analyzed by a video and acoustic survey during the National Italian Project Apulian Plateau Bank Ecosystem Study (APLABES). Site MS04 (Atlantis Mound) is characterized by a sub-conical mound, 500 m wide and 25 m high, located at a water depth of about 650 m. Site MS06 (Yellow Chain) comprises several elongated reliefs (NNW-SSE-oriented), up to 25 m high and 500 m in maximum lateral extent, located at a depth of between 490 and 540 m. At both sites, two main mesohabitats (mound and intermound) containing several coral-bearing and -barren macrohabitats were observed in recorded videos and detected in side-scan sonographs. The coral-rich macrohabitats, characterized by densely packed colonies of the scleractinians Madrepora oculata and, secondarily, Lophelia pertusa ( M/ L), are typically restricted to the mound areas. The mud-dominated ones, almost devoid of M/L colonies, are more common within the intermound mesohabitat. However, on the most extensive mounds, both macrohabitat typologies exist. They are heterogeneously distributed on the mound surface, often showing a clear differentiation along two opposite flanks of the same topographic feature. M/ L-rich macrohabitats are preferentially located on top and along the mound northeastern flank, showing a typical step-like distribution, probably reflecting the arrangement of hard substrate outcrops. Along this flank, fan-shaped Madrepora colonies and sponges are often oriented NNW-SSE, implying, together with other evidence, a primary southwestern current flow. The hard-bottom macrohabitats of the southwestern mound flank are generally restricted to sparse exposed, subvertical to overhanging scarps as well as to heterometric boulders located at the scarp base. Their fauna is mainly characterized by small-sized organisms (such as sponges and solitary scleractinians) although m-sized boulders may locally host very large antipatharian colonies ( Leiopathes glaberrima). The heterogeneous distribution of the observed benthic macrohabitats seems to be strictly related to the local topography, the main current flow (and consequently larvae/food supply per unit of time), and the substrate typology (hard- vs. soft-bottom).

Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer.

PubMed

Ross, Breyan; Krapp, Stephan; Augustin, Martin; Kierfersauer, Reiner; Arciniega, Marcelino; Geiss-Friedlander, Ruth; Huber, Robert

2018-02-13

Dipeptidyl peptidases 8 and 9 are intracellular N-terminal dipeptidyl peptidases (preferentially postproline) associated with pathophysiological roles in immune response and cancer biology. While the DPP family member DPP4 is extensively characterized in molecular terms as a validated therapeutic target of type II diabetes, experimental 3D structures and ligand-/substrate-binding modes of DPP8 and DPP9 have not been reported. In this study we describe crystal and molecular structures of human DPP8 (2.5 Å) and DPP9 (3.0 Å) unliganded and complexed with a noncanonical substrate and a small molecule inhibitor, respectively. Similar to DPP4, DPP8 and DPP9 molecules consist of one β-propeller and α/β hydrolase domain, forming a functional homodimer. However, they differ extensively in the ligand binding site structure. In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding. As vestiges of this helix are also seen in one of the copies of the unliganded form, conformational selection may contributes to ligand binding. Molecular dynamics simulations support increased flexibility of the R-helix in the unliganded state. Consistently, enzyme kinetics assays reveal a cooperative allosteric mechanism. DPP8 and DPP9 are closely similar and display few opportunities for targeted ligand design. However, extensive differences from DPP4 provide multiple cues for specific inhibitor design and development of the DPP family members as therapeutic targets or antitargets.

Characterization of local polarity and hydrophobic binding sites of beta-lactoglobulin by using N-terminal specific fluorescence labeling.

PubMed

Dong, Su-Ying; Zhao, Zhen-Wen; Ma, Hui-Min

2006-01-01

Because of wide ligand-binding ability and significant industrial interest of beta-lactoglobulin (beta-LG), its binding properties have been extensively studied. However, there still exists a controversy as to where a ligand binds, since at least two potential hydrophobic binding sites in beta-LG have been postulated for ligand binding: an internal one (calyx) and an external one (near the N-terminus). In this work, the local polarity and hydrophobic binding sites of beta-LG have been characterized by using N-terminal specific fluorescence labeling combined with a polarity-sensitive fluorescent probe 3-(4-chloro-6-hydrazino- 1,3,5-triazinylamino)-7-(dimethylamino)-2-methylphenazine (CHTDP). The polarity within the calyx is found to be extremely low, which is explained in terms of superhydrophobicity possibly resulting from its nanostructure, and the polarity is increased with the destruction of the calyx by heat treatment. However, the polarity of the N-terminal domain in native beta-LG is decreased after thermal denaturation. This polarity trend toward decreasing instead of increasing shows that beta-LG may have no definite external hydrophobic binding site. The hydrophobic binding of a ligand such as CHTDP at the surface of the protein is probably achieved via appropriate assembling of corresponding hydrophobic residues rather than via a fixed external hydrophobic binding site. Also, the ligand-binding location in beta-LG is found to be relevant to not only experimental conditions (pH < or = 6.2 or pH > 7.1) but also binding mechanisms (hydrophobic affinity or electrostatic interaction).

76 FR 65508 - Extension of the Public Comment Period for the Draft Site-Wide Environmental Impact Statement for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-21

... DEPARTMENT OF ENERGY National Nuclear Security Administration Extension of the Public Comment... Department of Energy/National Nuclear Security Administration Nevada National Security Site and Off-Site Locations in the State of Nevada AGENCY: National Nuclear Security Administration, U.S. Department of Energy...

Yucca Mountain Project Subsurface Facilities Design

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

A. Linden; R.S. Saunders; R.J. Boutin

2002-11-19

Four units of the Topopah Springs formation (volcanic tuff) are considered for the proposed repository: the upper lithophysal, the middle non-lithophysal, the lower lithophysal, and the lower non-lithophysal. Yucca Mountain was recently designated the site for a proposed repository to dispose of spent nuclear fuel and high-level radioactive waste. Work is proceeding to advance the design of subsurface facilities to accommodate emplacing waste packages in the proposed repository. This paper summarized recent progress in the design of subsurface layout of the proposed repository. The original Site Recommendation (SR) concept for the subsurface design located the repository largely within the lowermore » lithophysal zone (approximately 73%) of the Topopah The Site Recommendation characterized area suitable for emplacement consisted of the primary upper block, the lower block and the southern upper block extension. The primary upper block accommodated the mandated 70,000 metric tons of heavy metal (MTHM) at a 1.45 kW/m hear heat load. Based on further study of the Site Recommendation concept, the proposed repository siting area footprint was modified to make maximum use of available site characterization data, and thus, reduce uncertainties associated with performance assessment. As a result of this study, a modified repository footprint has been proposed and is presently being review for acceptance by the DOE. A panel design concept was developed to reduce overall costs and reduce the overall emplacement schedule. This concept provides flexibility to adjust the proposed repository subsurface layout with time, as it makes it unnecessary to ''commit'' to development of a large single panel at the earliest stages of construction. A description of the underground layout configuration and influencing factors that affect the layout configuration are discussed in the report.« less

Algal diversity in North American desert soils

NASA Astrophysics Data System (ADS)

Flechtner, Valerie R.; Ng, Rainer A.; Johansen, Jeffrey R.; Antionio, Sheri

2005-09-01

Clonal isolates of cyanophytes were collected from several study sites in the Dugway Proving Ground and San Rafael Sell Overlook in Utah. We identified 32 taxa belonging to 24 cyanobacterial genera. Some taxa were widely distributed, occurring in all sites. For example, the members of the filamentous cyanobacterial genera Leptolyngbya, Microcoleus, Nostoc and Trichocoleus and members of the coccoid genus Aphanocapsa were common to all sites. On the other hand, members of the cyanobacterial genus Calothrix were rarely encountered at the Dugway site but were recovered frequently from the San Rafael site. We were able to compare disturbed and undisturbed sites located close together in the San Rafael Overlook. We found that the genera Spirirestis and Cyanosarcina, were found exclusively in the undisturbed site. A number of the taxa recovered could be identified only to the genus level because they did not match previously published species descriptions. Since we have recovered both prokaryotic eukaryotic taxa new to science in our previous work, it is quite likely that some of these isolates do indeed represent new cyanobacterial species. This study is the most extensive characterization of cyanobacteria from soil crusts in a semi-arid North American deserts. It expands our knowledge of the diversity of the cyanobacterial components of North American soil crusts.

Performance-enhancing drugs on the web: a growing public-health issue.

PubMed

Brennan, Brian P; Kanayama, Gen; Pope, Harrison G

2013-01-01

Today's Internet provides extensive "underground" guidelines for obtaining and using illicit substances, including especially anabolic-androgenic steroids (AAS) and other appearance- and performance-enhancing drugs (APEDs). We attempted to qualitatively characterize APED-related Internet sites. We used relevant Internet search terms (eg, "steroids bodybuilding" and "buy steroids online") to assess (i) the numbers of site visitors; (ii) offers of drugs for sale; and (iii) the quality of online medical information. We also chose the examples of (iv) "site-enhancing oils" and (v) "cattle implants" to illustrate the volume of available Internet information as compared with that in the medical literature. We found thousands of sites involving AAS and other APEDs. Most sites presented an unabashedly pro-drug position, often openly questioning the qualifications and motivations of mainstream medical practitioners. Offers of AAS and other APEDs for sale, together with medical advice of varying legitimacy, was widespread across sites. Importantly, many sites provided detailed guidelines for exotic forms of APED use, some likely associated with serious health risks, which are probably unknown to most practicing clinicians. It seems important for practitioners to be aware of the extent of this "underground literature," which may strongly influence their patients' decisions about use and abuse of APEDs. Copyright © American Academy of Addiction Psychiatry.

THM large spatial-temporal model to simulate the past 2 Ma hydrogeological evolution of Paris Basin including natural tracer transport as part of site characterization for radwaste repository project Cigéo - France

NASA Astrophysics Data System (ADS)

Benabderrahmane, A., Sr.

2017-12-01

Hydrogeological site characterization for deep geological high level and intermediate level long lived radioactive waste repository cover a large time scale needed for safety analysis and calculation. Hydrogeological performance of a site relies also on the effects of geodynamic evolution as tectonic uplift, erosion/sedimentation and climate including glaciation on the groundwater flow and solute and heat transfer. Thermo-Hydro-Mechanical model of multilayered aquifer system of Paris Basin is developed to reproduce the present time flow and the natural tracer (Helium) concentration profiles based on the last 2 Ma of geodynamic evolution. Present time geological conceptual model consist of 27 layers at Paris Basin (Triassic-Tertiary) with refinement at project site scale (29 layers from Triassic to Portlandian). Target layers are the clay host formation of Callovo-Oxfrodian age (160 Ma) and the surrounding aquifer layers of Oxfordian and Dogger. Modelled processes are: groundwater flow, heat and solutes (natural tracers) transport, freezing and thawing of groundwater (expansion and retreat of permafrost), deformation of the multilayered aquifer system induced by differential tectonic uplift and the hydro-mechanical stress effect as caused by erosion of the outcropping layers. Numerical simulation considers a period from 2 Ma BP and up to the present. Transient boundary conditions are governed by geodynamic processes: (i) modification of the geometry of the basin and (ii) temperatures along the topography will change according to a series of 15 identical climate cycles with multiple permafrost (glaciation) periods. Numerical model contains 71 layers and 18 million cells. The solution procedure solves three coupled systems of equations, head, temperature and concentrations, by the use of a finite difference method, and by applying extensive parallel processing. The major modelling results related to the processes of importance for site characterization as hydraulic head distribution, flow velocity, heat and natural tracer transport impacted by geodynamic past evolution are discussed.

Performance of ground-penetrating radar on granitic regoliths with different mineral composition

USGS Publications Warehouse

Breiner, J.M.; Doolittle, James A.; Horton, Radley M.; Graham, R.C.

2011-01-01

Although ground-penetrating radar (GPR) is extensively used to characterize the regolith, few studies have addressed the effects of chemical and mineralogical compositions of soils and bedrock on its performance. This investigation evaluated the performance of GPR on two different granitic regoliths of somewhat different mineralogical composition in the San Jacinto Mountains of southern California. Radar records collected at a site where soils are Alfisols were more depth restricted than the radar record obtained at a site where soils are Entisols. Although the Alfisols contain an argillic horizon, and the Entisols have no such horizon of clay accumulation, the main impact on GPR effectiveness is related to mineralogy. The bedrock at the Alfisol site, which contains more mafic minerals (5% hornblende and 20% biotite), is more attenuating to GPR than the bedrock at the Entisol site, where mafic mineral content is less (<1% hornblende and 10% biotite). Thus, a relatively minor variation in bedrock mineralogy, specifically the increased biotite content, severely restricts the performance of GPR. Copyright ?? 2011 by Lippincott Williams & Wilkins.

DNA Motion Capture Reveals the Mechanical Properties of DNA at the Mesoscale

PubMed Central

Price, Allen C.; Pilkiewicz, Kevin R.; Graham, Thomas G.W.; Song, Dan; Eaves, Joel D.; Loparo, Joseph J.

2015-01-01

Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length. PMID:25992731

Conceptual Model of Uranium in the Vadose Zone for Acidic and Alkaline Wastes Discharged at the Hanford Site Central Plateau

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

Truex, Michael J.; Szecsody, James E.; Qafoku, Nikolla

2014-09-01

Historically, uranium was disposed in waste solutions of varying waste chemistry at the Hanford Site Central Plateau. The character of how uranium was distributed in the vadose zone during disposal, how it has continued to migrate through the vadose zone, and the magnitude of potential impacts on groundwater are strongly influenced by geochemical reactions in the vadose zone. These geochemical reactions can be significantly influenced by the disposed-waste chemistry near the disposal location. This report provides conceptual models and supporting information to describe uranium fate and transport in the vadose zone for both acidic and alkaline wastes discharged at amore » substantial number of waste sites in the Hanford Site Central Plateau. The conceptual models include consideration of how co-disposed acidic or alkaline fluids influence uranium mobility in terms of induced dissolution/precipitation reactions and changes in uranium sorption with a focus on the conditions near the disposal site. This information, when combined with the extensive information describing uranium fate and transport at near background pH conditions, enables focused characterization to support effective fate and transport estimates for uranium in the subsurface.« less

Colloidal gold-labeled insulin complex. Characterization and binding to adipocytes.

PubMed

Moll, U M; Thun, C; Pfeiffer, E F

1986-01-01

Biologically active insulin gold complex was used as an ultrastructural marker to study insulin binding sites, uptake, and internalization in isolated rat adipocytes. The preparation conditions for monodispersed particles, ca. 16 nm in diameter and loaded with approximately 100 insulin molecules, are reported. The complex is stable for at least six weeks. Single particles or small clusters were scattered across the cell membrane. The distribution of unbound receptors seemed to be independent of the extensive system of pre-existing surface connected vesicles in adipocytes. The uptake of particles took place predominantly via non-coated pinocytotic invaginations; clathrin-coated pits did not seem to be important for this process. Lysosome-like structures contained aggregates of 10-15 particles. These data suggest that insulin gold complex is a useful marker for the specific labeling of insulin binding sites.

Extensive rill erosion and gullying on abandoned pit mining sites in Lusatia, Germany

NASA Astrophysics Data System (ADS)

Kunth, Franziska; Kaiser, Andreas; Vláčilová, Markéta; Schindewolf, Marcus; Schmidt, Jürgen

2015-04-01

As the major economic driver in the province of Lusatia, Eastern Germany, the large open-cast lignite mining sites characterize the landscape and leave vast areas of irreversible changed post-mining landscapes behind. Cost-intensive renaturation projects have been implemented in order to restructure former mine sites into stabile self-sustaining ecosystems and local recreation areas. With considerable expenditure the pits are stabilized, flooded and surrounding areas are restructured. Nevertheless, heavy soil erosion, extensive gullying and slope instability are challenges for the restructuring and renaturation of the abandoned open-cast mining sites. The majority of the sites remain inaccessible to the public due to instable conditions resulting in uncontrolled slides and large gullies. In this study a combined approach of UAV-based aerial imagery, 3D multi-vision surface reconstruction and physically-based soil erosion modelling is carried out in order to document, quantify and better understand the causes of erosion processes on mining sites. Rainfall simulations have been carried out in lausatian post mining areas to reproduce soil detachment processes and observe the responsible mechanisms for the considerable erosion rates. Water repellency and soil sealing by biological crusts were hindering infiltration and consequently increasing runoff rates despite the mainly sandy soil texture. On non-vegetated experimental plots runoff coefficients up to 87 % were measured. In a modelling routine for a major gully catchment regarding a 50 years rainfall event, simulation results reveal runoff coefficients of up to 84% and erosion rates of 118 Mg*ha^-1. At the sediment pass over point 450Mg of sediments enter the surface water bodies. A system response of this order of magnitude were unexpected by the authorities. By applying 3D multi-vision surface reconstruction a model validation is now possible and further may illustrate the great importance of soil conservation measures under the described conditions.

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches.

PubMed

Hassenrück, Christiane; Fink, Artur; Lichtschlag, Anna; Tegetmeyer, Halina E; de Beer, Dirk; Ramette, Alban

2016-05-01

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. © FEMS 2016.

GPR impedance inversion for imaging and characterization of buried archaeological remains: A case study at Mudu city cite in Suzhou, China

NASA Astrophysics Data System (ADS)

Liu, Yu; Shi, Zhanjie; Wang, Bangbing; Yu, Tianxiang

2018-01-01

As a method with high resolution, GPR has been extensively used in archaeological surveys. However, conventional GPR profile can only provide limited geometry information, such as the shape or location of the interface, but can't give the distribution of physical properties which could help identify the historical remains more directly. A common way for GPR to map parameter distribution is the common-midpoint velocity analysis, but it provides limited resolution. Another research hotspot, the full-waveform inversion, is unstable and relatively dependent on the initial model. Coring method could give direct information in drilling site, while the accurate result is only limited in several boreholes. In this paper, we propose a new scheme to enhance imaging and characterization of archaeological targets by fusion of GPR and coring data. The scheme mainly involves the impedance inversion of conventional common-offset GPR data, which uses well log to compensate GPR data and finally obtains a high-resolution estimation of permittivity. The core analysis result also contributes to interpretation of the inversion result. To test this method, we did a case study at Mudu city site in Suzhou, China. The results provide clear images of the ancient city's moat and wall subsurface and improve the characterization of archaeological targets. It is shown that this method is effective and feasible for archaeological exploration.

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

Maheras, Steven J.; Best, Ralph E.; Ross, Steven B.

A preliminary evaluation of removing spent nuclear fuel (SNF) from 13 shutdown nuclear power reactor sites was conducted. At these shutdown sites the nuclear power reactors have been permanently shut down and the sites have been decommissioned or are undergoing decommissioning. The shutdown sites were Maine Yankee, Yankee Rowe, Connecticut Yankee, Humboldt Bay, Big Rock Point, Rancho Seco, Trojan, La Crosse, Zion, Crystal River, Kewaunee, San Onofre, and Vermont Yankee. The evaluation was divided into four components: (1) characterization of the SNF and greater-than-Class C low-level radioactive waste (GTCC waste) inventory, (2) a description of the on-site infrastructure and conditionsmore » relevant to transportation of SNF and GTCC waste, (3) an evaluation of the near-site transportation infrastructure and experience relevant to shipping transportation casks containing SNF and GTCC waste, including identification of gaps in information, and (4) an evaluation of the actions necessary to prepare for and remove SNF and GTCC waste. Every site was found to have at least one off-site transportation mode option for removing its SNF and GTCC waste; some have multiple options. Experience removing large components during reactor decommissioning provided an important source of information used to identify the transportation mode options for the sites. Especially important in conducting the evaluation were site visits, through which information was obtained that would not have been available otherwise. Extensive photographs taken during the site visits proved to be particularly useful in documenting the current conditions at or near the sites. It is expected that additional site visits will be conducted to add to the information presented in the evaluation.« less

A new metal binding domain involved in cadmium, cobalt and zinc transport

DOE PAGES

Smith, Aaron T.; Barupala, Dulmini; Stemmler, Timothy L.; ...

2015-07-20

The P 1B-ATPases, which couple cation transport across membranes to ATP hydrolysis, are central to metal homeostasis in all organisms. An important feature of P 1B-ATPases is the presence of soluble metal binding domains (MBDs) that regulate transport activity. Only one type of MBD has been characterized extensively, but bioinformatics analyses indicate that a diversity of MBDs may exist in nature. In this paper, we report the biochemical, structural and functional characterization of a new MBD from the Cupriavidus metallidurans P 1B-4-ATPase CzcP (CzcP MBD). The CzcP MBD binds two Cd 2+, Co 2+ or Zn 2+ ions in distinctmore » and unique sites and adopts an unexpected fold consisting of two fused ferredoxin-like domains. Both in vitro and in vivo activity assays using full-length CzcP, truncated CzcP and several variants indicate a regulatory role for the MBD and distinct functions for the two metal binding sites. Finally, taken together, these findings elucidate a previously unknown MBD and suggest new regulatory mechanisms for metal transport by P 1B-ATPases.« less

Site-specific microtubule-associated protein 4 dephosphorylation causes microtubule network densification in pressure overload cardiac hypertrophy.

PubMed

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F; Bethard, Jennifer R; Menick, Donald R; Kuppuswamy, Dhandapani; Cooper, George

2010-07-09

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac alpha- and beta-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 --> Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality.

Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

PubMed

Häger, K P; Wind, C

1997-06-15

Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

Performance-Enhancing Drugs on the Web: A Growing Public-Health Issue

PubMed Central

Brennan, Brian P.; Kanayama, Gen; Pope, Harrison G.

2012-01-01

Background and Objectives Today’s Internet provides extensive “underground” guidelines for obtaining and using illicit substances, including especially anabolic-androgenic steroids (AAS) and other appearance- and performance-enhancing drugs (APEDs). We attempted to qualitatively characterize APED-related Internet sites. Methods We used relevant Internet search terms (e.g., “steroids bodybuilding” and “buy steroids online”), to assess 1) the numbers of site visitors; 2) offers of drugs for sale; and 3) the quality of online medical information. We also chose the examples of 4) “site-enhancing oils” and 5) “cattle implants” to illustrate the volume of available Internet information as compared with that in the medical literature. Results We found thousands of sites involving AAS and other APEDs. Most sites presented an unabashedly pro-drug position, often openly questioning the qualifications and motivations of mainstream medical practitioners. Offers of AAS and other APEDs for sale, together with medical advice of varying legitimacy, was widespread across sites. Importantly, many sites provided detailed guidelines for exotic forms of APED use, some likely associated with serious health risks, which are probably unknown to most practicing clinicians. Conclusions and Scientific Significance It seems important for practitioners to be aware of the extent of this “underground literature,” which may strongly influence their patients’ decisions about use and abuse of APEDs. PMID:23414502

Gene Expression-Based Survival Prediction in Lung Adenocarcinoma: A Multi-Site, Blinded Validation Study

PubMed Central

Shedden, Kerby; Taylor, Jeremy M.G.; Enkemann, Steve A.; Tsao, Ming S.; Yeatman, Timothy J.; Gerald, William L.; Eschrich, Steve; Jurisica, Igor; Venkatraman, Seshan E.; Meyerson, Matthew; Kuick, Rork; Dobbin, Kevin K.; Lively, Tracy; Jacobson, James W.; Beer, David G.; Giordano, Thomas J.; Misek, David E.; Chang, Andrew C.; Zhu, Chang Qi; Strumpf, Dan; Hanash, Samir; Shepherd, Francis A.; Ding, Kuyue; Seymour, Lesley; Naoki, Katsuhiko; Pennell, Nathan; Weir, Barbara; Verhaak, Roel; Ladd-Acosta, Christine; Golub, Todd; Gruidl, Mike; Szoke, Janos; Zakowski, Maureen; Rusch, Valerie; Kris, Mark; Viale, Agnes; Motoi, Noriko; Travis, William; Sharma, Anupama

2009-01-01

Although prognostic gene expression signatures for survival in early stage lung cancer have been proposed, for clinical application it is critical to establish their performance across different subject populations and in different laboratories. Here we report a large, training-testing, multi-site blinded validation study to characterize the performance of several prognostic models based on gene expression for 442 lung adenocarcinomas. The hypotheses proposed examined whether microarray measurements of gene expression either alone or combined with basic clinical covariates (stage, age, sex) can be used to predict overall survival in lung cancer subjects. Several models examined produced risk scores that substantially correlated with actual subject outcome. Most methods performed better with clinical data, supporting the combined use of clinical and molecular information when building prognostic models for early stage lung cancer. This study also provides the largest available set of microarray data with extensive pathological and clinical annotation for lung adenocarcinomas. PMID:18641660

Remote detection of geobotanical anomalies associated with hydrocarbon microseepage

NASA Technical Reports Server (NTRS)

Rock, B. N.

1985-01-01

As part of the continuing study of the Lost River, West Virginia NASA/Geosat Test Case Site, an extensive soil gas survey of the site was conducted during the summer of 1983. This soil gas survey has identified an order of magnitude methane, ethane, propane, and butane anomaly that is precisely coincident with the linear maple anomaly reported previously. This and other maple anomalies were previously suggested to be indicative of anaerobic soil conditions associated with hydrocarbon microseepage. In vitro studies support the view that anomalous distributions of native tree species tolerant of anaerobic soil conditions may be useful indicators of methane microseepage in heavily vegetated areas of the United States characterized by deciduous forest cover. Remote sensing systems which allow discrimination and mapping of native tree species and/or species associations will provide the exploration community with a means of identifying vegetation distributional anomalies indicative of microseepage.

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

Jensen, Michael; Kollias, Pavlos; Giangrande, Scott

The Mid-latitude Continental Convective Clouds Experiment (MC3E) took place from April 22 through June 6, 2011, centered at the ARM Southern Great Plains site (http://www.arm.gov/sites/sgp) in northcentral Oklahoma. MC3E was a collaborative effort between the ARM Climate Research Facility and the National Aeronautics and Space Administration’s (NASA’s) Global Precipitation Measurement (GPM) mission Ground Validation (GV) program. The campaign leveraged the largest ground-based observing infrastructure available in the central United States, including recent upgrades through the American Recovery and Reinvestment Act of 2009, combined with an extensive sounding array, remote sensing and in situ aircraft observations, and additional radar and inmore » situ precipitation instrumentation. The overarching goal of the campaign was to provide a three-dimensional characterization of convective clouds and precipitation for the purpose of improving the representation of convective lifecycle in atmospheric models and the reliability of satellite-based retrievals of precipitation.« less

Sediment Transport from Urban, Urbanizing, and Rural Areas in Johnson County, Kansas, 2006-08

USGS Publications Warehouse

Lee, Casey J.

2013-01-01

1. Studies have commonly illustrated that erosion and sediment transport from construction sites is extensive, typically 10-100X that of background levels. 2. However, to our knowledge, the affects of construction and urbanization have rarely been assessed (1) since erosion and sediment controls have been required at construction sites, and (2) at watershed (5-65 mi2) scales. This is primarily because of difficulty characterizing sediment loads in small basins. Studies (such as that illustrated from Timble, 1999) illustrated how large changes in surface erosion may not result in substantive changes in downstream sediment loads (b/c of sediment deposition on land-surfaces, floodplains, and in stream channels). 3. Improved technology (in-situ turbidity) sensors provide a good application b/c they provide an independent surrogate of sediment concentration that is more accurate at estimating sediment concentrations and loads that instantaneous streamflow.

Intercalation of Coordinatively Unsaturated Fe(III) Ion within Interpenetrated Metal-Organic Framework MOF-5.

PubMed

Holmberg, Rebecca J; Burns, Thomas; Greer, Samuel M; Kobera, Libor; Stoian, Sebastian A; Korobkov, Ilia; Hill, Stephen; Bryce, David L; Woo, Tom K; Murugesu, Muralee

2016-06-01

Coordinatively unsaturated Fe(III) metal sites were successfully incorporated into the iconic MOF-5 framework. This new structure, Fe(III) -iMOF-5, is the first example of an interpenetrated MOF linked through intercalated metal ions. Structural characterization was performed with single-crystal and powder XRD, followed by extensive analysis by spectroscopic methods and solid-state NMR, which reveals the paramagnetic ion through its interaction with the framework. EPR and Mössbauer spectroscopy confirmed that the intercalated ions were indeed Fe(III) , whereas DFT calculations were employed to ascertain the unique pentacoordinate architecture around the Fe(III) ion. Interestingly, this is also the first crystallographic evidence of pentacoordinate Zn(II) within the MOF-5 SBU. This new MOF structure displays the potential for metal-site addition as a framework connector, thus creating further opportunity for the innovative development of new MOF materials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Morphological size evaluation of the mid-substance insertion areas and the fan-like extension fibers in the femoral ACL footprint.

PubMed

Suruga, Makoto; Horaguchi, Takashi; Iriuchishima, Takanori; Yahagi, Yoshiyuki; Iwama, Genki; Tokuhashi, Yasuaki; Aizawa, Shin

2017-08-01

The purpose of this study was to evaluate the detailed anatomy of the femoral anterior cruciate ligament (ACL) insertion site, with special attention given to the morphology of the mid-substance insertion areas and the fan-like extension fibers. Twenty-three non-paired human cadaver knees were used (7 Males, 16 Females, median age 83, range 69-96). All soft tissues around the knee were resected except the ligaments. The ACL was divided into antero-medial (AM) and postero-lateral (PL) bundles according to the difference in macroscopic tension patterns. The ACL was carefully dissected and two outlines were made of the periphery of each bundle insertion site: those which included and those which excluded the fan-like extension fibers. An accurate lateral view of the femoral condyle was photographed with a digital camera, and the images were downloaded to a personal computer. The area of each bundle, including and excluding the fan-like extension fibers, was measured with Image J software (National Institution of Health). The width and length of the mid-substance insertion sites were also evaluated using same image. The femoral ACL footprint was divided into four regions (mid-substance insertion sites of the AM and PL bundles, and fan-like extensions of the AM and PL bundles). The measured areas of the mid-substance insertion sites of the AM and PL bundles were 35.5 ± 12.5, and 32.4 ± 13.8 mm 2 , respectively. Whole width and length of the mid-substance insertion sites were 5.3 ± 1.4, and 15.5 ± 2.9 mm, respectively. The measured areas of the fan-like extensions of the AM and PL bundles were 27 ± 11.5, and 29.5 ± 12.4 mm 2 , respectively. The femoral ACL footprint was divided into quarters of approximately equal size (mid-substance insertion sites of the AM and PL bundles, and fan-like extensions of the AM and PL bundles). For clinical relevance, to perform highly reproducible anatomical ACL reconstruction, the presence of the fan-like extension fibers should be taken into consideration.

Characterizing structures on borehole images and logging data of the Nankai trough accretionary prism: new insights

NASA Astrophysics Data System (ADS)

Jurado, Maria Jose

2016-04-01

IODP has extensively used the D/V Chikyu to drill the Kumano portion of the Nankai Trough, including two well sites within the Kumano Basin. IODP Expeditions 338 and 348 drilled deep into the inner accretionary prism south of the Kii Peninsula collecting a suite of LWD data, including natural gamma ray, electrical resistivity logs and borehole images, suitable to characterize structures (fractures and faults) inside the accretionary prism. Structural interpretation and analysis of logging-while-drilling data in the deep inner prism revealed intense deformation of a generally homogenous lithology characterized by bedding that dips steeply (60-90°) to the NW, intersected by faults and fractures. Multiple phases of deformation are characterized. IODP Expedition borehole images and LWD data acquired in the last decade in previous and results of NantroSEIZE IODP Expeditions (314, 319) were also analyzed to investigate the internal geometries and structures of the Nankai Trough accretionary prism. This study focused mainly on the characterization of the different types of structures and their specific position within the accretionary prism structures. New structural constraints and methodologies as well as a new approach to the characterization of study of active structures inside the prism will be presented.

Least Disturbed Condition for European Mediterranean rivers.

PubMed

Feio, M J; Aguiar, F C; Almeida, S F P; Ferreira, J; Ferreira, M T; Elias, C; Serra, S R Q; Buffagni, A; Cambra, J; Chauvin, C; Delmas, F; Dörflinger, G; Erba, S; Flor, N; Ferréol, M; Germ, M; Mancini, L; Manolaki, P; Marcheggiani, S; Minciardi, M R; Munné, A; Papastergiadou, E; Prat, N; Puccinelli, C; Rosebery, J; Sabater, S; Ciadamidaro, S; Tornés, E; Tziortzis, I; Urbanič, G; Vieira, C

2014-04-01

The present report describes a three-step approach that was used to characterize and define thresholds for the Least Disturbed Condition in Mediterranean streams of four different types, regarding organic pollution and nutrients, hydrological and morphological alterations, and land use. For this purpose, a common database composed of national reference sites (929 records) from seven countries, sampled for invertebrates, diatoms and macrophytes was used. The analyses of reference sites showed that small (catchment <100 km(2)) siliceous and non-siliceous streams were mainly affected by channelization, bank alteration and hydropeaking. Medium-sized siliceous rivers were the most affected by stressors: 25-43% of the samples showed at least slight alterations regarding channelization, connectivity, upstream dam influence, hydropeaking and degradation of riparian vegetation. Temporary streams were the least affected by hydromorphological changes, but they were nevertheless affected by alterations in riparian vegetation. There were no major differences between all permanent stream types regarding water quality, but temporary streams showed lower values for oxygenation (DO) and wider ranges for other variables, such as nitrates. A lower threshold value for DO (60%) was determined for this stream type and can be attributed to the streams' natural characteristics. For all other river types, common limits were found for the remaining variables (ammonium, nitrate, phosphate, total P, % of artificial areas, % of intensive and extensive agriculture, % of semi-natural areas in the catchment). These values were then used to select the list of reference sites. The biological communities were characterized, revealing the existence of nine groups of Mediterranean invertebrate communities, six for diatoms and five for macrophytes: each group was characterized by specific indicator taxa that highlighted the differences between groups. Copyright © 2013 Elsevier B.V. All rights reserved.

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...

Water dissociating on rigid Ni(100): A quantum dynamics study on a full-dimensional potential energy surface

NASA Astrophysics Data System (ADS)

Liu, Tianhui; Chen, Jun; Zhang, Zhaojun; Shen, Xiangjian; Fu, Bina; Zhang, Dong H.

2018-04-01

We constructed a nine-dimensional (9D) potential energy surface (PES) for the dissociative chemisorption of H2O on a rigid Ni(100) surface using the neural network method based on roughly 110 000 energies obtained from extensive density functional theory (DFT) calculations. The resulting PES is accurate and smooth, based on the small fitting errors and the good agreement between the fitted PES and the direct DFT calculations. Time dependent wave packet calculations also showed that the PES is very well converged with respect to the fitting procedure. The dissociation probabilities of H2O initially in the ground rovibrational state from 9D quantum dynamics calculations are quite different from the site-specific results from the seven-dimensional (7D) calculations, indicating the importance of full-dimensional quantum dynamics to quantitatively characterize this gas-surface reaction. It is found that the validity of the site-averaging approximation with exact potential holds well, where the site-averaging dissociation probability over 15 fixed impact sites obtained from 7D quantum dynamics calculations can accurately approximate the 9D dissociation probability for H2O in the ground rovibrational state.

Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

PubMed

Patron, Nicola J; Orzaez, Diego; Marillonnet, Sylvestre; Warzecha, Heribert; Matthewman, Colette; Youles, Mark; Raitskin, Oleg; Leveau, Aymeric; Farré, Gemma; Rogers, Christian; Smith, Alison; Hibberd, Julian; Webb, Alex A R; Locke, James; Schornack, Sebastian; Ajioka, Jim; Baulcombe, David C; Zipfel, Cyril; Kamoun, Sophien; Jones, Jonathan D G; Kuhn, Hannah; Robatzek, Silke; Van Esse, H Peter; Sanders, Dale; Oldroyd, Giles; Martin, Cathie; Field, Rob; O'Connor, Sarah; Fox, Samantha; Wulff, Brande; Miller, Ben; Breakspear, Andy; Radhakrishnan, Guru; Delaux, Pierre-Marc; Loqué, Dominique; Granell, Antonio; Tissier, Alain; Shih, Patrick; Brutnell, Thomas P; Quick, W Paul; Rischer, Heiko; Fraser, Paul D; Aharoni, Asaph; Raines, Christine; South, Paul F; Ané, Jean-Michel; Hamberger, Björn R; Langdale, Jane; Stougaard, Jens; Bouwmeester, Harro; Udvardi, Michael; Murray, James A H; Ntoukakis, Vardis; Schäfer, Patrick; Denby, Katherine; Edwards, Keith J; Osbourn, Anne; Haseloff, Jim

2015-10-01

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The Ionosphere's Pocket Litter: Exploiting Crowd-Sourced Observations

NASA Astrophysics Data System (ADS)

Miller, E. S.; Frissell, N. A.; Kaeppler, S. R.; Demajistre, R.; Knuth, A. A.

2015-12-01

One of the biggest challenges faced in developing and testing our understanding of the ionosphere is acquiring data that characterizes the latitudinal and longitudinal variability of the ionosphere. While there are extensive networks of ground sites that sample the vertical distribution, we have rather poor coverage over the oceans and in parts of the southern hemisphere. Our ability to validate the ionospheric models is limited by the lack of point measurements and those measurements that essentially constitute characterization of horizontal gradients. In this talk, we discuss and demonstrate the use of various types of crowd-sourced information that enables us to extend our coverage over these regions. We will discuss new sources of these data, concepts for new experiments and the use of these data in assimilative models. We note that there are new, low cost options for obtaining data that broaden the participation beyond the aeronomy/ionospheric community.

Multi-Relational Characterization of Dynamic Social Network Communities

NASA Astrophysics Data System (ADS)

Lin, Yu-Ru; Sundaram, Hari; Kelliher, Aisling

The emergence of the mediated social web - a distributed network of participants creating rich media content and engaging in interactive conversations through Internet-based communication technologies - has contributed to the evolution of powerful social, economic and cultural change. Online social network sites and blogs, such as Facebook, Twitter, Flickr and LiveJournal, thrive due to their fundamental sense of "community". The growth of online communities offers both opportunities and challenges for researchers and practitioners. Participation in online communities has been observed to influence people's behavior in diverse ways ranging from financial decision-making to political choices, suggesting the rich potential for diverse applications. However, although studies on the social web have been extensive, discovering communities from online social media remains challenging, due to the interdisciplinary nature of this subject. In this article, we present our recent work on characterization of communities in online social media using computational approaches grounded on the observations from social science.

Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.

PubMed

Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J

2016-02-26

G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Correlation Between Hot Spots and 3-d Defect Structure in Single and Polycrystalline High-explosive Materials

NASA Astrophysics Data System (ADS)

Hawkins, Cameron; Tschuaner, Oliver; Fussell, Zachary; Smith, Jesse

2017-06-01

A novel approach that spatially identifies inhomogeneities from microscale (defects, con-formational disorder) to mesoscale (voids, inclusions) is developed using synchrotron x-ray methods: tomography, Lang topography, and micro-diffraction mapping. These techniques pro-vide a non-destructive method for characterization of mm-sized samples prior to shock experiments. These characterization maps can be used to correlate continuum level measurements in shock compression experiments to the mesoscale and microscale structure. Specifically examined is a sample of C4. We show extensive conformational disorder in gamma-RDX, which is the main component. Further, we observe that the minor HMX-component in C4 contains at least two different phases: alpha- and beta-HMX. This work supported by National Security Technologies, LLC, under Contract No. DE-AC52-06NA25946 with the U.S. Department of Energy and by the Site-Directed Research and Development Program. DOE/NV/25946-3071.

Rural Housing Site Planning in North Carolina. Agricultural Extension Publication 105.

ERIC Educational Resources Information Center

Hester, Randolph T., Jr.; And Others

Addressing the problems of rural housing site selection and development in North Carolina, this guide is designed for cooperative and coordinated use by: technical assistance personnel employed by the Farmers Home Administration; local lending institutions; Health Departments; the Agricultural Extension Service; the Soil Conservation Service; and…

Structure of choline oxidase in complex with the reaction product glycine betaine.

PubMed

Salvi, Francesca; Wang, Yuan-Fang; Weber, Irene T; Gadda, Giovanni

2014-02-01

Choline oxidase from Arthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose-methanol-choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand-enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250-255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.

Extension joints: a tool to infer the active stress field orientation (case study from southern Italy)

NASA Astrophysics Data System (ADS)

De Guidi, Giorgio; Caputo, Riccardo; Scudero, Salvatore; Perdicaro, Vincenzo

2013-04-01

An intense tectonic activity in eastern Sicily and southern Calabria is well documented by the differential uplift of Late Quaternary coastlines and by the record of the strong historical earthquakes. The extensional belt that crosses this area is dominated by a well established WNW-ESE-oriented extensional direction. However, this area is largely lacking of any structural analysis able to define the tectonics at a more local scale. In the attempt to fill this gap of knowledge, we carried out a systematic analysis of extension joint sets. In fact, the systematic field collection of these extensional features, coupled with an appropriate inversion technique, allows to determine the characteristic of the causative tectonic stress field. Joints are defined as outcrop-scale mechanical discontinuities showing no evidence of shear motion and being originated as purely extensional fractures. Such tectonic features are one of the most common deformational structures in every tectonic environment and particularly abundant in the study area. A particular arrangement of joints, called "fracture grid-lock system", and defined as an orthogonal joint system where mutual abutting and crosscutting relationships characterize two geologically coeval joint sets, allow to infer the direction and the magnitude of the tectonic stress field. We performed the analyses of joints only on Pleistocene deposits of Eastern Sicily and Southern Calabria. Moreover we investigated only calcarenite sediments and cemented deposits, avoiding claysh and loose matrix-supported clastic sediments where the deformation is generally accomodated in a distributed way through the relative motion between the single particles. In the selection of the sites, we also took into account the possibility to clearly observe the geometric relationships among the joints. For this reason we chose curvilinear road cuts or cliffs, wide coastal erosional surfaces and quarries. The numerical inversions show a similar stress tensors at all the investigated sites. Indeed, the maximum principal stress axis σ1 is vertical or subvertical, while the intermediate and the least axes (σ2 and σ3) lie on the horizontal plane or show low plunging values. The main direction of extension (σ3) at each site is in general agreement with the first-order regional stress field (WNW-ESE) even though some local perturbations have been recognized. These are interpreted as due to interferences between large active faults and their particular geometrical arrangement. In particular local stress deflections and stress swaps systematically occur in zones characterized by two overlapping fault segments or close to their tips.

Differential DNA methylation patterns of polycystic ovarian syndrome in whole blood of Chinese women.

PubMed

Li, Shuxia; Zhu, Dongyi; Duan, Hongmei; Ren, Anran; Glintborg, Dorte; Andersen, Marianne; Skov, Vibe; Thomassen, Mads; Kruse, Torben; Tan, Qihua

2017-03-28

As a universally common endocrinopathy in women of reproductive age, the polycystic ovarian syndrome is characterized by composite clinical phenotypes reflecting the contributions of reproductive impact of ovarian dysfunction and metabolic abnormalities with widely varying symptoms resulting from interference of the genome with the environment through integrative biological mechanisms including epigenetics. We have performed a genome-wide DNA methylation analysis on polycystic ovarian syndrome and identified a substantial number of genomic sites differentially methylated in the whole blood of PCOS patients and healthy controls (52 sites, false discovery rate < 0.05 and corresponding p value < 5.68e-06), highly consistently replicating biological pathways extensively implicated in immunity and immunity-related inflammatory disorders (false discovery rate < 0.05) that were reportedly regulated in the DNA methylome from ovarian tissue under PCOS condition. Most importantly, our genome-wide profiling focusing on PCOS patients revealed a large number of DNA methylation sites and their enriched functional pathways significantly associated with diverse clinical features (levels of prolactin, estradiol, progesterone and menstrual cycle) that could serve as novel molecular basis of the clinical heterogeneity observed in PCOS women.

X-ray diffraction and Raman spectroscopy study of white decorations on tricolored ceramics from Northwestern Argentina

NASA Astrophysics Data System (ADS)

Freire, E.; Acevedo, V.; Halac, E. B.; Polla, G.; López, M.; Reinoso, M.

2016-03-01

White virgules, commas, and dot designs on tricolored ceramics are sporadically found in different archaeological sites located in Northwestern Argentina area, as Puna and Quebrada de Humahuaca. This decorating style has been reported in several articles, but few previous archaeometric studies have been carried out on the pigment composition. Fragments from Puna and Quebrada archaeological sites, belonging to Regional Development Period (900-1430 AD), were analyzed by X-ray diffraction and Raman spectroscopy in order to characterize the pigments employed. Red and black pigments are based on iron and manganese oxides, as it has been extensively reported for the NW Argentina area. White pigments from white virgules, comma, and dot designs have shown different composition. Hydroxyapatite was found in samples from Doncellas site (North Puna region), and calcium and calcium-magnesium containing compounds, as vaterite and dolomite, along with titanium containing compounds were detected on samples from Abralaite (Central Puna region) and Gasoducto (Quebrada de Humahuaca region). It has been concluded that pigment composition is not characteristic of a unique region.

X-ray diffraction and Raman spectroscopy study of white decorations on tricolored ceramics from Northwestern Argentina.

PubMed

Freire, E; Acevedo, V; Halac, E B; Polla, G; López, M; Reinoso, M

2016-03-15

White virgules, commas, and dot designs on tricolored ceramics are sporadically found in different archaeological sites located in Northwestern Argentina area, as Puna and Quebrada de Humahuaca. This decorating style has been reported in several articles, but few previous archaeometric studies have been carried out on the pigment composition. Fragments from Puna and Quebrada archaeological sites, belonging to Regional Development Period (900-1430 AD), were analyzed by X-ray diffraction and Raman spectroscopy in order to characterize the pigments employed. Red and black pigments are based on iron and manganese oxides, as it has been extensively reported for the NW Argentina area. White pigments from white virgules, comma, and dot designs have shown different composition. Hydroxyapatite was found in samples from Doncellas site (North Puna region), and calcium and calcium-magnesium containing compounds, as vaterite and dolomite, along with titanium containing compounds were detected on samples from Abralaite (Central Puna region) and Gasoducto (Quebrada de Humahuaca region). It has been concluded that pigment composition is not characteristic of a unique region. Copyright © 2015 Elsevier B.V. All rights reserved.

Soil contamination by heavy metals: measurements from a closed unlined landfill.

PubMed

Kasassi, A; Rakimbei, P; Karagiannidis, A; Zabaniotou, A; Tsiouvaras, K; Nastis, A; Tzafeiropoulou, K

2008-12-01

The aim of the present study was the characterization of soil samples of a closed unlined landfill located northwest of Thessaloniki, North Greece, in relation to heavy metals values. Samples were obtained by drilling in different depths (2.5-17.5m). Then they were analyzed by atomic absorption spectrophotometry for Cd, Cr, Cu, Ni, Pb and Zn investigation. The chemical analysis showed that the metal values varied over a wide range: from 0.50 to 18.75mg/kg for Cd, 3.88-171.88mg/kg for Cr, 8.13-356.25mg/kg for Cu, 5.63-63.75mg/kg for Ni, 2.50-92.50mg/kg for Pb and 6.38-343.75mg/kg for Zn. The highest values found in three of the six drillings, in depths over 2.5m. Although the area is heavily industrialized, the presented results indicated that local industries have not constituted an extensive metal pollution source for the site. Finally, after all necessary preparatory operations of site cleaning and flattening, surface planting selected and applied as a phytoremediation rehabilitation method of the site.

DNA motion capture reveals the mechanical properties of DNA at the mesoscale.

PubMed

Price, Allen C; Pilkiewicz, Kevin R; Graham, Thomas G W; Song, Dan; Eaves, Joel D; Loparo, Joseph J

2015-05-19

Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Long-term analysis of Zostera noltei: A retrospective approach for understanding seagrasses' dynamics.

PubMed

Calleja, Felipe; Galván, Cristina; Silió-Calzada, Ana; Juanes, José A; Ondiviela, Bárbara

2017-09-01

Long-term studies are necessary to establish trends and to understand seagrasses' spatial and temporal dynamic. Nevertheless, this type of research is scarce, as the required databases are often unavailable. The objectives of this study are to create a method for mapping the seagrass Zostera noltei using remote sensing techniques, and to apply it to the characterization of the meadows' extension trend and the potential drivers of change. A time series was created using a novel method based on remote sensing techniques that proved to be adequate for mapping the seagrass in the emerged intertidal. The meadows seem to have a decreasing trend between 1984 and the early 2000s, followed by an increasing tendency that represents a recovery in the extension area of the species. This 30-year analysis demonstrated the Z. noltei's recovery in the study site, similar to that in other estuaries nearby and contrary to the worldwide decreasing behavior of seagrasses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evidence for preferential flow through sandstone aquifers in Southern Wisconsin

USGS Publications Warehouse

Swanson, S.K.; Bahr, J.M.; Bradbury, K.R.; Anderson, K.M.

2006-01-01

Sandstones often escape extensive hydrogeologic characterization due to their high primary porosity and perceived homogeneity of permeability. This study provides evidence for laterally extensive, high permeability zones in the Tunnel City Group, an undeformed, Cambrian-aged sandstone unit that exists in the subsurface throughout much of central and southern Wisconsin, USA. Several discrete high-permeability zones were identified in boreholes using flow logging and slug tests, and the interconnectedness of the features was tested using a site-specific numerical model for springs in the region. Explicit incorporation of a high-permeability layer leads to improvements in the flux calibration over simulations that lack the features, thus supporting the hydraulic continuity of high-permeability zones in the sandstone aquifer over tens of kilometers. The results suggest that stratigraphically controlled heterogeneities like contrasts in lithology or bedding-plane fractures, which have been shown to strongly influence the flow of groundwater in more heterogeneous sedimentary rocks, may also deserve close examination in sandstone aquifers. ?? 2005 Elsevier B.V. All rights reserved.

A grammar inference approach for predicting kinase specific phosphorylation sites.

PubMed

Datta, Sutapa; Mukhopadhyay, Subhasis

2015-01-01

Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.

Solar Field Optical Characterization at Stillwater Geothermal/Solar Hybrid Plant

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

Zhu, Guangdong; Turchi, Craig

Concentrating solar power (CSP) can provide additional thermal energy to boost geothermal plant power generation. For a newly constructed solar field at a geothermal power plant site, it is critical to properly characterize its performance so that the prediction of thermal power generation can be derived to develop an optimum operating strategy for a hybrid system. In the past, laboratory characterization of a solar collector has often extended into the solar field performance model and has been used to predict the actual solar field performance, disregarding realistic impacting factors. In this work, an extensive measurement on mirror slope error andmore » receiver position error has been performed in the field by using the optical characterization tool called Distant Observer (DO). Combining a solar reflectance sampling procedure, a newly developed solar characterization program called FirstOPTIC and public software for annual performance modeling called System Advisor Model (SAM), a comprehensive solar field optical characterization has been conducted, thus allowing for an informed prediction of solar field annual performance. The paper illustrates this detailed solar field optical characterization procedure and demonstrates how the results help to quantify an appropriate tracking-correction strategy to improve solar field performance. In particular, it is found that an appropriate tracking-offset algorithm can improve the solar field performance by about 15%. The work here provides a valuable reference for the growing CSP industry.« less

Solar Field Optical Characterization at Stillwater Geothermal/Solar Hybrid Plant

DOE PAGES

Zhu, Guangdong; Turchi, Craig

2017-01-27

Concentrating solar power (CSP) can provide additional thermal energy to boost geothermal plant power generation. For a newly constructed solar field at a geothermal power plant site, it is critical to properly characterize its performance so that the prediction of thermal power generation can be derived to develop an optimum operating strategy for a hybrid system. In the past, laboratory characterization of a solar collector has often extended into the solar field performance model and has been used to predict the actual solar field performance, disregarding realistic impacting factors. In this work, an extensive measurement on mirror slope error andmore » receiver position error has been performed in the field by using the optical characterization tool called Distant Observer (DO). Combining a solar reflectance sampling procedure, a newly developed solar characterization program called FirstOPTIC and public software for annual performance modeling called System Advisor Model (SAM), a comprehensive solar field optical characterization has been conducted, thus allowing for an informed prediction of solar field annual performance. The paper illustrates this detailed solar field optical characterization procedure and demonstrates how the results help to quantify an appropriate tracking-correction strategy to improve solar field performance. In particular, it is found that an appropriate tracking-offset algorithm can improve the solar field performance by about 15%. The work here provides a valuable reference for the growing CSP industry.« less

Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.

PubMed

Addy, Christine; Ohara, Masato; Kawai, Fumihiro; Kidera, Akinori; Ikeguchi, Mitsunori; Fuchigami, Sotaro; Osawa, Masanori; Shimada, Ichio; Park, Sam-Yong; Tame, Jeremy R H; Heddle, Jonathan G

2007-02-01

Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.

CO2 sequestration in two mediterranean dune areas subjected to a different level of anthropogenic disturbance

NASA Astrophysics Data System (ADS)

Bonito, Andrea; Ricotta, Carlo; Iberite, Mauro; Gratani, Loretta; Varone, Laura

2017-09-01

Coastal sand dunes are among the most threatened habitats, especially in the Mediterranean Basin, where the high levels of human pressure impair the presence of plant species, putting at risk the maintenance of the ecosystem services, such as CO2 sequestration provided by these habitats. The aim of this study was to analyze how disturbance-induced changes in plant species abundance patterns account for variations in annual CO2 sequestration flow (CS) of Mediterranean sand dune areas. Two sites characterized by a high (site HAD) and a lower (site LAD) anthropogenic disturbance level were selected. At both sites, plant species number, cover, height and CS based on net photosynthesis measurements were sampled. At the plant species level, our results highlighted that Ammophila arenaria and Pancratium maritimum, had a key role in CS. Moreover, the results revealed a patchy species assemblage in both sites. In particular, HAD was characterized by a higher extension of the anthropogenic aphytoic zone (64% of the total transect length) than LAD. In spite of the observed differences in plant species composition, there were not significant differences between HAD and LAD in structural and functional traits, such as plant height and net photosynthesis. As a consequence, HAD and LAD had a similar CS (443 and 421 Mg CO2 ha-1 y-1, respectively). From a monetary point of view, our estimates based on the social costs of carbon revealed that the flow of sequestered CO2 valued on an average 3181 ± 114 ha-1 year-1 (mean value for the two sites). However, considering also the value of the CO2 negative flow related to loss of vegetated area, the annual net benefit arising from CO2 sequestration amounted to 1641 and 1772 for HAD and LAD, respectively. Overall, the results highlighted the importance to maximize the efforts to preserve dune habitats by applying an effective management policy, which could allow maintaining also a regulatory ecosystem service such as CO2 sequestration.

An overview of AmeriFlux data products and methods for data acquisition, processing, and publication

NASA Astrophysics Data System (ADS)

Pastorello, G.; Poindexter, C.; Agarwal, D.; Papale, D.; van Ingen, C.; Torn, M. S.

2014-12-01

The AmeriFlux network encompasses independently managed field sites measuring ecosystem carbon, water, and energy fluxes across the Americas. In close coordination with ICOS in Europe, a new set of fluxes data and metadata products is being produced and released at the FLUXNET level, including all AmeriFlux sites. This will enable continued releases of global standardized set of flux data products. In this release, new formats, structures, and ancillary information are being proposed and adopted. This presentation discusses these aspects, detailing current and future solutions. One of the major revisions was to the BADM (Biological, Ancillary, and Disturbance Metadata) protocols. The updates include structure and variable changes to address new developments in data collection related to flux towers and facilitate two-way data sharing. In particular, a new organization of templates is now in place, including changes in templates for biomass, disturbances, instrumentation, soils, and others. New variables and an extensive addition to the vocabularies used to describe BADM templates allow for a more flexible and comprehensible coverage of field sites and the data collection methods and results. Another extensive revision is in the data formats, levels, and versions for fluxes and micrometeorological data. A new selection and revision of data variables and an integrated new definition for data processing levels allow for a more intuitive and flexible notation for the variety of data products. For instance, all variables now include positional information that is tied to BADM instrumentation descriptions. This allows for a better characterization of spatial representativeness of data points, e.g., individual sensors or the tower footprint. Additionally, a new definition for data levels better characterizes the types of processing and transformations applied to the data across different dimensions (e.g., spatial representativeness of a data point, data quality checks applied, and differentiation between measured data and data from models that use process knowledge). We also present an expanded approach to versions of data and data processing software, with stable and immutable data releases, but also pre-release versions to allow evaluation and feedback prior to a stable release.

The peregrine falcon in Arizona: Habitat utilization and management recommendations

USGS Publications Warehouse

Ellis, D.H.

1982-01-01

The peregrine falcon once bred in significant numbers in Arizona. Good documentation is available for specific breeding sites and an additional 20 general locations. This report, based on the published literature, an extensive personal contact survey, an aerial habitat inventory (over 124 hours air time), and ground visits to over 300 locations, provides information on habitat preferences and management practices which can contribute to the bird's survival. In seeking to identify the habitat preferences of the falcon, many site description factors were examined. Those traits which appeared common to most recent Arizona sites (and therefore most useful in evaluating habitat) were: elevation less than 9,000 feet, cliffs tall or very tall, cliffs extensive, topographic relief high, and surface water readily available. All recent sites are in extensive canyon systems or in extensive mountain ranges. Using a habitat evaluation key derived from the traits common to known breeding sites, all cliff regions in Arizona and the Navajo Indian Reservation were flown and evaluated for suitability. Nineteen falcon eyries located in subsequent ground visits were all in areas previously ranked acceptable or better. Many management alternatives are discussed: management of information on breeding sites, habitat preservation, controlling disruptive human activities, and enhancing productivity through the creation of suitable breeding ledges, providing pesticide free prey, or direct reintroductions. Given their privacy (and an increasingly pesticide free environment) the peregrine falcon will likely exist indefinitely in suitable areas across Arizona.

Co-Conserved MAPK Features Couple D-Domain Docking Groove to Distal Allosteric Sites via the C-Terminal Flanking Tail

PubMed Central

Nguyen, Tuan; Ruan, Zheng; Oruganty, Krishnadev; Kannan, Natarajan

2015-01-01

Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors. PMID:25799139

Genomic structure of the human D-site binding protein (DBP) gene

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

Shutler, G.; Glassco, T.; Kang, Xiaolin

1996-06-15

The human gene for the D-Site Binding Protein (DBP) has been sequenced and characterized. This gene is a member of the b/ZIP family of transcription factors and is one of three genes forming the PAR sub-family. DBP has been implicated in the diurnal regulation of a variety of liver-specific genes. Examination of the genomic structure of DBP reveals that the gene is divided into four exons and is contained within a relatively compact region of approximately 6 kb. These exons appear to correspond to functional divisions the DBP protein. Exon 1 contains a long 5{prime} UTR, and conservation between themore » rat and the human genes of the presence of small open reading frames within this region suggests that is may play a role in translational control. Exon 2 contains a limited region of similarity to the other PAR domain genes, which may be part of a potential activation domain. Exon 3 contains the PAR domain and differs by only 1 of 71 amino acids between rat and human. Exon 4, containing both the basic and the leucine zipper domains, is likewise highly conserved. The overall degree of homology between the rat and the human cDNA sequences is 82% for the nucleic acid sequence and 92% for the protein sequence. comparison of the rat and human proximal promoters reveals extensive sequence conservation, with two previously characterized DNA binding sites being conserved at the functional and sequence levels. 31 refs., 4 figs.« 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 ...

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

Characterization of the glucansucrase GTF180 W1065 mutant enzymes producing polysaccharides and oligosaccharides with altered linkage composition.

PubMed

Meng, Xiangfeng; Pijning, Tjaard; Tietema, Martin; Dobruchowska, Justyna M; Yin, Huifang; Gerwig, Gerrit J; Kralj, Slavko; Dijkhuizen, Lubbert

2017-02-15

Exopolysaccharides produced by lactic acid bacteria are extensively used for food applications. Glucansucrase enzymes of lactic acid bacteria use sucrose to catalyze the synthesis of α-glucans with different linkage compositions, size and physico-chemical properties. Crystallographic studies of GTF180-ΔN show that at the acceptor binding sites +1 and +2, residue W1065 provides stacking interactions to the glucosyl moiety. However, the detailed functional roles of W1065 have not been elucidated. We performed random mutagenesis targeting residue W1065 of GTF180-ΔN, resulting in the generation of 10 mutant enzymes that were characterized regarding activity and product specificity. Characterization of mutant enzymes showed that residue W1065 is critical for the activity of GTF180-ΔN. Using sucrose, and sucrose (donor) plus maltose (acceptor) as substrates, the mutant enzymes synthesized polysaccharides and oligosaccharides with changed linkage composition. The stacking interaction of an aromatic residue at position 1065 is essential for polysaccharide synthesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Summary of IODP Expedition 344, CRISP-A2, offshore the Osa Peninsula, Costa Rica

NASA Astrophysics Data System (ADS)

Harris, R. N.; Sakaguchi, A.; Petronotis, K. E.

2013-12-01

The Costa Rica Seismogenesis Project (CRISP) is designed to elucidate the processes that control nucleation and seismic rupture of large earthquakes at erosional subduction zones. The CRISP study area is located offshore the Osa Peninsula where the incoming Cocos Ridge has lifted the seismogenic zone to within reach of scientific drilling. The incoming plate is characterized by low sediment supply, a fast convergence rate, abundant plate interface seismicity, and a change in subducting plate relief along strike. In addition to elucidating processes at erosional convergent margins, this project is complementary to other IODP deep fault drilling projects (e.g., NanTroSEIZE and J-FAST). Expedition 344 (23 October - 11 December, 2012) is the second expedition of CRISP Program A (Integrated Ocean Drilling Program Proposal 537A-Full5) that focused on the shallow lithologic, hydrologic, stress, and thermal conditions that lead to unstable slip in the seismogenic zone. With the exception of not reaching the décollement and the underthrust sediment at the toe site (U1412), Expedition 344 exceeded expectations. Material was recovered from the incoming Cocos plate (Sites U1381 and U1414), the toe of the margin (Site U1412), the mid-slope region (Site U1380), and the upper-slope region (Site U1413). Input sites U1381 and U1414 are characterized by anomalously high heat flow and the flow of fluids. These sites contained abundant ash that will be used to assess the impact of Cocos Ridge subduction on the evolution of the Central American volcanic arc. Although toe Site U1412 did not cross the décollement we did penetrate terrigenous sediments interrupted by a Miocene ooze that may reflect accretion of a frontal prism sliver. Mid-slope Site U1380 yielded a major result in that the upper plate material is not a mélange of oceanic material or the offshore extension of the Caribbean large igneous complex, but forearc basin material consisting of lithic sedimentary units. Upper-slope Site U1413 consists of a terrestrially sourced upper slope sequence consistent with high sediment accumulation rates. Preliminary biostratigraphic and paleomagnetic ages from Sites U1380 and U1413, the midslope and upper slope, respectively, yield sediment accumulation rates between ~290 and 590 m/m.y., an order of magnitude greater than estimated offshore the Nicoya Peninsula.

Characterization of Conserved Tandem Donor Sites and Intronic Motifs Required for Alternative Splicing in Corticosteroid Receptor Genes

PubMed Central

Qian, Xiaoxiao; Matthews, Laura; Lightman, Stafford; Ray, David; Norman, Michael

2015-01-01

Alternative splicing events from tandem donor sites result in mRNA variants coding for additional amino acids in the DNA binding domain of both the glucocorticoid (GR) and mineralocorticoid (MR) receptors. We now show that expression of both splice variants is extensively conserved in mammalian species, providing strong evidence for their functional significance. An exception to the conservation of the MR tandem splice site (an A at position +5 of the MR+12 donor site in the mouse) was predicted to decrease U1 small nuclear RNA binding. In accord with this prediction, we were unable to detect the MR+12 variant in this species. The one exception to the conservation of the GR tandem splice site, an A at position +3 of the platypus GRγ donor site that was predicted to enhance binding of U1 snRNA, was unexpectedly associated with decreased expression of the variant from the endogenous gene as well as a minigene. An intronic pyrimidine motif present in both GR and MR genes was found to be critical for usage of the downstream donor site, and overexpression of TIA1/TIAL1 RNA binding proteins, which are known to bind such motifs, led to a marked increase in the proportion of GRγ and MR+12. These results provide striking evidence for conservation of a complex splicing mechanism that involves processes other than stochastic spliceosome binding and identify a mechanism that would allow regulation of variant expression. PMID:19819975

Crystal structure of a lipoxygenase from Cyanothece sp. may reveal novel features for substrate acquisition[S

PubMed Central

Newie, Julia; Andreou, Alexandra; Neumann, Piotr; Einsle, Oliver; Feussner, Ivo; Ficner, Ralf

2016-01-01

In eukaryotes, oxidized PUFAs, so-called oxylipins, are vital signaling molecules. The first step in their biosynthesis may be catalyzed by a lipoxygenase (LOX), which forms hydroperoxides by introducing dioxygen into PUFAs. Here we characterized CspLOX1, a phylogenetically distant LOX family member from Cyanothece sp. PCC 8801 and determined its crystal structure. In addition to the classical two domains found in plant, animal, and coral LOXs, we identified an N-terminal helical extension, reminiscent of the long α-helical insertion in Pseudomonas aeruginosa LOX. In liposome flotation studies, this helical extension, rather than the β-barrel domain, was crucial for a membrane binding function. Additionally, CspLOX1 could oxygenate 1,2-diarachidonyl-sn-glycero-3-phosphocholine, suggesting that the enzyme may act directly on membranes and that fatty acids bind to the active site in a tail-first orientation. This binding mode is further supported by the fact that CspLOX1 catalyzed oxygenation at the n-10 position of both linoleic and arachidonic acid, resulting in 9R- and 11R-hydroperoxides, respectively. Together these results reveal unifying structural features of LOXs and their function. While the core of the active site is important for lipoxygenation and thus highly conserved, peripheral domains functioning in membrane and substrate binding are more variable. PMID:26667668

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...

Fish community-based measures of estuarine ecological quality and pressure-impact relationships

NASA Astrophysics Data System (ADS)

Fonseca, Vanessa F.; Vasconcelos, Rita P.; Gamito, Rita; Pasquaud, Stéphanie; Gonçalves, Catarina I.; Costa, José L.; Costa, Maria J.; Cabral, Henrique N.

2013-12-01

Community-based responses of fish fauna to anthropogenic pressures have been extensively used to assess the ecological quality of estuarine ecosystems. Several methodologies have been developed recently combining metrics reflecting community structure and function. A fish community facing significant environmental disturbances will be characterized by a simplified structure, with lower diversity and complexity. However, estuaries are naturally dynamic ecosystems exposed to numerous human pressures, making it difficult to distinguish between natural and anthropogenic-induced changes to the biological community. In the present work, the variability of several fish metrics was assessed in relation to different pressures in estuarine sites. The response of a multimetric index (Estuarine Fish Assessment Index) was also analysed. Overall, fish metrics and the multimetric index signalled anthropogenic stress, particularly environmental chemical pollution. The fish assemblage associated with this type of pressure was characterized by lower species diversity, lower number of functional guilds, lower abundance of marine migrants and of piscivorous individuals, and higher abundance of estuarine resident species. A decreased ecological quality status, based on the EFAI, was also determined for sites associated with this pressure group. Ultimately, the definition of each pressure groups favoured a stressor-specific analysis, evidencing pressure patterns and accounting for multiple factors in a highly dynamic environment.

Identification and characterization of 20 immunocompetent patients with simultaneous varicella zoster and herpes simplex virus infection.

PubMed

Giehl, K A; Müller-Sander, E; Rottenkolber, M; Degitz, K; Volkenandt, M; Berking, C

2008-06-01

It has been shown that varicella zoster virus (VZV) and herpes simplex virus (HSV) can co-localize to the same sensory ganglion. However, only a few case reports on VZV/HSV co-infections exist. Objective To identify and characterize patients with concurrent VZV and HSV infection at the same body site. In 1718 patients, the presence of VZV and HSV in suspicious skin lesions was investigated by polymerase chain reaction analysis. Clinical characteristics of co-infected patients were compared with matched control patients infected with either VZV or HSV. The data are discussed in the context of an extensive review of the literature. Twenty (1.2%) of 1718 patients were infected with both VZV and HSV at the same body site. The mean age was 54 years (range, 2-83). The clinical diagnosis was zoster in 65%, herpes simplex in 20%, varicella in 10% and erythema multiforme in 5% of cases. The trigeminus region was affected in 60% and the trunk in 25%. Involvement of the head was most commonly associated with a severe course of disease and with older age. Simultaneous VZV/HSV infection is rare but can occur in immunocompetent patients, which is often overlooked. The majority of cases is localized to the trigeminus region and affects elderly people.

Rockfall risk evaluation using geotechnical survey, remote sensing data, and GIS: a case study from western Greece

NASA Astrophysics Data System (ADS)

Nikolakopoulos, Konstantinos; Depountis, Nikolaos; Vagenas, Nikolaos; Kavoura, Katerina; Vlaxaki, Eleni; Kelasidis, George; Sabatakakis, Nikolaos

2015-06-01

In this paper a specific example of the synergistic use of geotechnical survey, remote sensing data and GIS for rockfall risk evaluation is presented. The study area is located in Western Greece. Extensive rockfalls have been recorded along Patras - Ioannina highway just after the cable-stayed bridge of Rio-Antirrio, at Klokova site. The rockfalls include medium- sized limestone boulders with volume up to 1.5m3. A detailed engineering geological survey was conducted including rockmass characterization, laboratory testing and geological - geotechnical mapping. Many Rockfall trajectory simulations were done. Rockfall risk along the road was estimated using spatial analysis in a GIS environment.

Magnetometry and Ground-Penetrating Radar Studies in the Sihuas Valley, Peru

NASA Astrophysics Data System (ADS)

Wisnicki, E.; Papadimitrios, K.; Bank, C.

2013-12-01

The Quillcapampa la Antigua site in Peru's Sihuas Valley is a settlement from Peru's Middle Horizon (600-100 A.D.). Archaeological interest in the area stems from the question of whether ancient civilizations were able to have extensive state control of distant groups, or whether state influence occurred through less direct ties (e.g., marriage, religion, or trade). Our geophysical surveys are preliminary to archaeological digging in the area. Ground-penetrating radar and magnetometry attempt to locate areas of interest for focused archaeological excavation, characterize the design of architectural remains and burial mounds in the area, and allow archaeologists to interpret the amount of influence the Wari civilization had on the local residents.

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...

Global Impact of Oncogenic Src on a Phosphotyrosine Proteome

PubMed Central

Luo, Weifeng; Slebos, Robbert J.; Hill, Salisha; Li, Ming; Brábek, Jan; Amanchy, Ramars; Chaerkady, Raghothama; Pandey, Akhilesh; Ham, Amy-Joan L.; Hanks, Steven K.

2008-01-01

Elevated activity of Src, the first characterized protein-tyrosine kinase, is associated with progression of many human cancers, and Src has attracted interest as a therapeutic target. Src is known to act in various receptor signaling systems to impact cell behavior, yet it remains likely that the spectrum of Src protein substrates relevant to cancer is incompletely understood. To better understand the cellular impact of deregulated Src kinase activity, we extensively applied a mass spectrometry shotgun phosphotyrosine (pTyr) proteomics strategy to obtain global pTyr profiles of Src-transformed mouse fibroblasts as well as their nontransformed counterparts. A total of 867 peptides representing 563 distinct pTyr sites on 374 different proteins were identified from the Src-transformed cells, while 514 peptides representing 275 pTyr sites on 167 proteins were identified from nontransformed cells. Distinct characteristics of the two profiles were revealed by spectral counting, indicative of pTyr site relative abundance, and by complementary quantitative analysis using stable isotope labeling with amino acids in cell culture (SILAC). While both pTyr profiles are replete with sites on signaling and adhesion/cytoskeletal regulatory proteins, the Src-transformed profile is more diverse with enrichment in sites on metabolic enzymes and RNA and protein synthesis and processing machinery. Forty-three pTyr sites (32 proteins) are predicted as major biologically relevant Src targets on the basis of frequent identification in both cell populations. This select group, of particular interest as diagnostic biomarkers, includes well-established Src sites on signaling/adhesion/cytoskeletal proteins, but also uncharacterized sites of potential relevance to the transformed cell phenotype. PMID:18563927

Insulator function and topological domain border strength scale with architectural protein occupancy

PubMed Central

2014-01-01

Background Chromosome conformation capture studies suggest that eukaryotic genomes are organized into structures called topologically associating domains. The borders of these domains are highly enriched for architectural proteins with characterized roles in insulator function. However, a majority of architectural protein binding sites localize within topological domains, suggesting sites associated with domain borders represent a functionally different subclass of these regulatory elements. How topologically associating domains are established and what differentiates border-associated from non-border architectural protein binding sites remain unanswered questions. Results By mapping the genome-wide target sites for several Drosophila architectural proteins, including previously uncharacterized profiles for TFIIIC and SMC-containing condensin complexes, we uncover an extensive pattern of colocalization in which architectural proteins establish dense clusters at the borders of topological domains. Reporter-based enhancer-blocking insulator activity as well as endogenous domain border strength scale with the occupancy level of architectural protein binding sites, suggesting co-binding by architectural proteins underlies the functional potential of these loci. Analyses in mouse and human stem cells suggest that clustering of architectural proteins is a general feature of genome organization, and conserved architectural protein binding sites may underlie the tissue-invariant nature of topologically associating domains observed in mammals. Conclusions We identify a spectrum of architectural protein occupancy that scales with the topological structure of chromosomes and the regulatory potential of these elements. Whereas high occupancy architectural protein binding sites associate with robust partitioning of topologically associating domains and robust insulator function, low occupancy sites appear reserved for gene-specific regulation within topological domains. PMID:24981874

ARRA-funded VS30 measurements using multi-technique approach at strong-motion stations in California and central-eastern United States

USGS Publications Warehouse

Yong, Alan; Martin, Antony; Stokoe, Kenneth; Diehl, John

2013-01-01

Funded by the 2009 American Recovery and Reinvestment Act (ARRA), we conducted geophysical site characterizations at 191 strong-motion stations: 187 in California and 4 in the Central-Eastern United States (CEUS). The geophysical methods used at each site included passive and active surface-wave and body-wave techniques. Multiple techniques were used at most sites, with the goal of robustly determining VS (shear-wave velocity) profiles and VS30 (the time-averaged shear-wave velocity in the upper 30 meters depth). These techniques included: horizontal-to-vertical spectral ratio (HVSR), two-dimensional (2-D) array microtremor (AM), refraction microtremor (ReMi™), spectral analysis of surface wave (SASW), multi-channel analysis of surface waves (Rayleigh wave: MASRW; and Love wave: MASLW), and compressional- and shear-wave refraction. Of the selected sites, 47 percent have crystalline, volcanic, or sedimentary rock at the surface or at relatively shallow depth, and 53 percent are of Quaternary sediments located in either rural or urban environments. Calculated values of VS30 span almost the full range of the National Earthquake Hazards Reduction Program (NEHRP) Site Classes, from D (stiff soils) to B (rock). The NEHRP Site Classes based on VS30 range from being consistent with the Class expected from analysis of surficial geology, to being one or two Site Classes below expected. In a few cases where differences between the observed and expected Site Class occurred, it was the consequence of inaccurate or coarse geologic mapping, as well as considerable degradation of the near-surface rock. Additionally, several sites mapped as rock have Site Class D (stiff soil) velocities, which is due to the extensive weathering of the surficial rock.

Variation in characteristics of ambient particulate matter at eight locations in the Netherlands - The RAPTES project

NASA Astrophysics Data System (ADS)

Strak, Maciej; Steenhof, Maaike; Godri, Krystal J.; Gosens, Ilse; Mudway, Ian S.; Cassee, Flemming R.; Lebret, Erik; Brunekreef, Bert; Kelly, Frank J.; Harrison, Roy M.; Hoek, Gerard; Janssen, Nicole A. H.

2011-08-01

Numerous epidemiological studies have shown health effects related to short- and long-term exposure to elevated levels of ambient particulate matter (PM). It is not clear however which specific characteristics (e.g., size, components) or sources of PM are responsible for the observed effects. The aim of RAPTES (Risk of Airborne Particles: a Toxicological-Epidemiological hybrid Study) was to investigate which specific physical, chemical or oxidative characteristics of ambient PM are associated with adverse effects of PM on health. This was done by performing experimental exposure of human volunteers to air pollution at several real-world settings that had high contrast and low correlation between several PM characteristics. For this goal, eight sites in the Netherlands that differed in local PM emission sources were chosen for extensive air pollution characterization. Measurement sites included an underground train station, three different road traffic sites, an animal farm, a sea harbor, a site located in the vicinity of steelworks, and an urban background site. Five- to six-hours average concentration measurements at each site were made between June 2007 and October 2009. We measured PM 10, PM 2.5, particle number concentration (PNC), oxidative potential of PM, absorbance, endotoxin content, as well as elemental and chemical composition of PM, and gaseous pollutants concentrations. This paper presents a detailed characterization of particulate air pollution at the sampling sites. We found significant differences in all PM characteristics between the sites. The underground train station, compared to each outdoor location, had substantially higher concentrations of nearly all PM characteristics. The average PM 10 and PM 2.5 mass concentrations at the underground train station were 394 μg m -3 and 137 μg m -3, respectively, which was 14.1 and 7.6 times higher than the urban background. The sum of the concentrations of trace metals in fine and coarse PM was nearly 20 times above the outdoor levels. Elemental carbon (EC) was elevated at the underground site in the fine but also in the coarse mode, in contrast to the traffic sites where EC was predominantly found in fine PM. The highest concentrations and contrasts in PNC were at the traffic sites (between 45,000 and 80,000 particles cm -3), which was several times higher than measured at any other site. Correlations of PNC with metals, PM 10, PM 2.5 and absorbance were low to moderate, while correlations between PM 10, PM 2.5 and the metals Cu and Fe were high. After excluding the underground train station data, correlations between PM10, EC and metals decreased whereas the correlation between PNC and EC increased. We conclude that we were able to successfully identify and characterize real-world situations with very different particle characteristics. High contrast and low correlations between PM characteristics, as well as consistency of these differences across sampling campaigns, provide a good basis for identifying health relevant PM characteristics in the upcoming analysis.

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.

Tyrosine411 and Arginine410 of Human Serum Albumin Play an Important Role in the Binding of Sodium 4-Phenylbutyrate to Site II.

PubMed

Enokida, Taisuke; Yamasaki, Keishi; Okamoto, Yuko; Taguchi, Kazuaki; Ishiguro, Takako; Maruyama, Toru; Seo, Hakaru; Otagiri, Masaki

2016-06-01

Sodium 4-phenylbutyrate (PB) has many pharmacological activities; therefore extending its clinical use to the treatment of a wider variety of diseases would be desirable. However, our knowledge of the binding of PB to plasma proteins is not extensive. To address this issue in more detail, we characterized the protein binding of PB. Binding experiments showed that PB mainly binds to human serum albumin (HSA) in plasma. PB was also found to bind to a single site on HSA, which was identified as site II by fluorescent probe displacement experiment. Furthermore, an appropriate alkyl chain length and a carboxylic group in the PB structure were required for PB binding to HSA, suggesting that hydrophobic (and van der Waals) and electrostatic interactions are involved as binding modes. The contributions of hydrogen bonding and/or van der Waals interactions were also indicated by thermodynamic analyses. Tyrosine411 and arginine410 were identified as being involved in the binding of PB to site II, based on binding experiments using chemically modified- and mutant-HSA preparations. In conclusion, the available evidence indicates that PB binds to site II of HSA with assistance by multiple forces and that tyrosine411 and arginine410 both play important roles in this phenomenon. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum.

PubMed

Chen, Zhuo; Luo, Ling; Chen, Runfa; Hu, Hanhua; Pan, Yufang; Jiang, Haibo; Wan, Xia; Jin, Hu; Gong, Yangmin

2018-03-01

N ε -lysine acetylation represents a highly dynamic and reversibly regulated post-translational modification widespread in almost all organisms, and plays important roles for regulation of protein function in diverse metabolic pathways. However, little is known about the role of lysine acetylation in photosynthetic eukaryotic microalgae. We integrated proteomic approaches to comprehensively characterize the lysine acetylome in the model diatom Phaeodactylum tricornutum In total, 2324 acetylation sites from 1220 acetylated proteins were identified, representing the largest data set of the lysine acetylome in plants to date. Almost all enzymes involved in fatty acid synthesis were found to be lysine acetylated. Six putative lysine acetylation sites were identified in a plastid-localized long-chain acyl-CoA synthetase. Site-directed mutagenesis and site-specific incorporation of N-acetyllysine in acyl-CoA synthetase show that acetylation at K407 and K425 increases its enzyme activity. Moreover, the nonenzymatically catalyzed overall hyperacetylation of acyl-CoA synthetase by acetyl-phosphate can be effectively deacetylated and reversed by a sirtuin-type NAD + -dependent deacetylase with subcellular localization of both the plastid and nucleus in Phaeodactylum This work indicates the regulation of acyl-CoA synthetase activity by site-specific lysine acetylation and highlights the potential regulation of fatty acid metabolism by lysine actetylation in the plastid of the diatom Phaeodactylum . © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

ALS Multicenter Cohort Study of Oxidative Stress (ALS COSMOS): study methodology, recruitment, and baseline demographic and disease characteristics.

PubMed

Mitsumoto, Hiroshi; Factor-Litvak, Pam; Andrews, Howard; Goetz, Raymond R; Andrews, Leslie; Rabkin, Judith G; McElhiney, Martin; Nieves, Jeri; Santella, Regina M; Murphy, Jennifer; Hupf, Jonathan; Singleton, Jess; Merle, David; Kilty, Mary; Heitzman, Daragh; Bedlack, Richard S; Miller, Robert G; Katz, Jonathan S; Forshew, Dallas; Barohn, Richard J; Sorenson, Eric J; Oskarsson, Bjorn; Fernandes Filho, J Americo M; Kasarskis, Edward J; Lomen-Hoerth, Catherine; Mozaffar, Tahseen; Rollins, Yvonne D; Nations, Sharon P; Swenson, Andrea J; Shefner, Jeremy M; Andrews, Jinsy A; Koczon-Jaremko, Boguslawa A

2014-06-01

Abstract In a multicenter study of newly diagnosed ALS patients without a reported family history of ALS, we are prospectively investigating whether markers of oxidative stress (OS) are associated with disease progression. Methods utilize an extensive structured telephone interview ascertaining environmental, lifestyle, dietary and psychological risk factors associated with OS. Detailed assessments were performed at baseline and at 3-6 month intervals during the ensuing 30 months. Our biorepository includes DNA, plasma, urine, and skin. Three hundred and fifty-five patients were recruited. Subjects were enrolled over a 36-month period at 16 sites. To meet the target number of subjects, the recruitment period was prolonged and additional sites were included. Results showed that demographic and disease characteristics were similar between 477 eligible/non-enrolled and enrolled patients, the only difference being type of health insurance among enrolled patients. Sites were divided into three groups by the number of enrolled subjects. Comparing these three groups, the Columbia site had fewer 'definite ALS' diagnoses. This is the first prospective, interdisciplinary, in-depth, multicenter epidemiological investigation of OS related to ALS progression and has been accomplished by an aggressive recruitment process. The baseline demographic and disease features of the study sample are now fully characterized.

The Brazilian Experience with Agroecological Extension: A Critical Analysis of Reform in a Pluralistic Extension System

ERIC Educational Resources Information Center

Diesel, Vivien; Miná Dias, Marcelo

2016-01-01

Purpose: To analyze the Brazilian experience in designing and implementing a recent extension policy reform based on agroecology, and reflect on its wider theoretical implications for extension reform literature. Design/methodology/approach: Using a critical public analysis we characterize the evolution of Brazilian federal extension policy…

Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.

PubMed

Narczyk, Marta; Bertoša, Branimir; Papa, Lucija; Vuković, Vedran; Leščić Ašler, Ivana; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Luić, Marija; Štefanić, Zoran

2018-04-01

Even with decades of research, purine nucleoside phosphorylases (PNPs) are enzymes whose mechanism is yet to be fully understood. This is especially true in the case of hexameric PNPs, and is probably, in part, due to their complex oligomeric nature and a whole spectrum of active site conformations related to interactions with different ligands. Here we report an extensive structural characterization of the apo forms of hexameric PNP from Helicobacter pylori (HpPNP), as well as its complexes with phosphate (P i ) and an inhibitor, formycin A (FA), together with kinetic, binding, docking and molecular dynamics studies. X-ray structures show previously unseen distributions of open and closed active sites. Microscale thermophoresis results indicate that a two-site model describes P i binding, while a three-site model is needed to characterize FA binding, irrespective of P i presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with P i and FA shows, however, that P i binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that P i moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. Altogether, these findings show some unique features of HpPNP and provide new insights into the functioning of the active sites, with implications for understanding the complex mechanism of catalysis of this enzyme. The atomic coordinates and structure factors have been deposited in the Protein Data Bank: with accession codes 6F52 (HpPNPapo_1), 6F5A (HpPNPapo_2), 6F5I (HpPNPapo_3), 5LU0 (HpPNP_PO4), 6F4W (HpPNP_FA) and 6F4X (HpPNP_PO4_FA). Purine nucleoside orthophosphate ribosyl transferase, EC2.4.2.1, UniProtID: P56463. © 2018 Federation of European Biochemical Societies.

Correlation of Spatio-Temporal Contaminant Distribution, Land Use, and Hydrogeological Factors in the Karst Aquifers of Northern Puerto Rico

NASA Astrophysics Data System (ADS)

Torres Torres, N. I.; Padilla, I. Y.

2015-12-01

Karst aquifers are characterized by caves, springs, and sinkholes, and typified by interconnected fissures, fractures and conduits. These characteristics make these aquifers highly productive, and vulnerable to contamination. Previous studies in the northern karst aquifers of Puerto Rico have shown significant distribution of contaminants, including volatile organic compounds, phthalates and other contaminants of emerging concern, beyond demarked sources of contamination. This study develops spatial-temporal distributions of phthalate contaminants in the karst system of northern Puerto Rico and assesses statistical correlations between hydrogeologic factors and groundwater contamination with phthalates. Geographic Information Systems (GIS) tools and technologies, and statistical models are applied to attain these objectives. Results show that there is an extensive contamination with phthalates that varies with time. Contamination is present in the confined and shallow aquifers. Di-(2-ethylhexyl) phthalate (DEHP) is the most detected contaminant (20.6% of the sites). Diethyl phthalate and and dibutyl phthalate are also detected in 6.7% and 8.24% of the sites, respectively. Phthalates detected as mixtures components are significantly detected in areas of high urban and industrial development. They are also detected in areas within 5 miles of superfund sites and landfills. The results indicate that phthalate contamination is highly related to land use. Statistical models show that the hydraulic conductivity of the aquifers, sinkholes density, and time are significantly related to the presence of phthalates in groundwater. The extensive spatio-temporal contamination suggests that contaminants can persist in the environment for long periods of time, and that land use and hydrogeological factors are important factors contributing to the presence of emerging contaminants in karst systems.

Structural analysis of secretory phospholipase A2 from Clonorchis sinensis: therapeutic implications for hepatic fibrosis.

PubMed

Hariprasad, Gururao; Kaur, Punit; Srinivasan, Alagiri; Singh, Tej Pal; Kumar, Manoj

2012-07-01

Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an attractive drug target in the light of extensive structural characterization of this class of enzyme. In this study, the structure of the enzyme was modeled based on its sequence homology to the group III bee venom PLA(2). On analysis, the overall structure essentially is comprised of three helices, two sets of β-wings and an elongated C-terminal extension. The structure is stabilized by four disulfide bonds. The structure is comprised of a calcium binding loop, active site and a substrate binding hydrophobic channel. The active site of the enzyme shows the classical features of PLA(2) with the participation of the three residues: histidine-aspartic acid-tyrosine in hydrogen bond formation. This is an interesting variation from the house keeping group III PLA(2) enzyme of human which has a histidine-aspartic acid and phenylalanine arrangement at the active site. This difference is therefore an important structural parameter that can be exploited to design specific inhibitor molecules against the pathogen PLA(2). Likewise, there are certain unique structural features in the hydrophobic channel and the putative membrane binding surface of the PLA(2) from Clonorchis sinensis that not only help understand the mechanism of action but also provide knowledge for a targeted therapy of liver fibrosis caused by the parasite.

Cloning and characterization of the novel D-aspartyl endopeptidase, paenidase, from Paenibacillus sp. B38.

PubMed

Nirasawa, Satoru; Nakahara, Kazuhiko; Takahashi, Saori

2018-02-27

Paenidase is the first microorganism-derived D-aspartyl endopeptidase that specifically recognizes an internal D-Asp residue to cleave [D-Asp]-X peptide bonds. Using peptide sequences obtained from the protein, we performed PCR with degenerate primers to amplify the paenidase I-encoding gene. Nucleotide sequencing revealed that mature paenidase I consists of 322 amino acid residues and that the protein is encoded as a pro-protein with a 197-amino-acid N-terminal extension compared to the mature protein. Paenidase I exhibits amino acid sequence similarity to several penicillin-binding proteins. In addition, paenidase I was classified into peptidase family S12 based on a MEROPS database search. Family S12 contains serine-type D-Ala-D-Ala carboxypeptidases that have three active site residues (Ser, Lys, and Tyr) in the conserved motifs Ser-Xaa-Thr-Lys and Tyr-Xaa-Asn. These motifs were conserved in the primary structure of paenidase I, and the role of these residues was confirmed by site-directed mutagenesis.

Current status of coral reefs in the United Arab Emirates: Distribution, extent, and community structure with implications for management.

PubMed

Grizzle, Raymond E; Ward, Krystin M; AlShihi, Rashid M S; Burt, John A

2016-04-30

Coral reefs of the United Arab Emirates were once extensive, but have declined dramatically in recent decades. Marine management and policy have been hampered by outdated and inaccurate habitat maps and habitat quality information. We combined existing recent datasets with our newly mapped coral habitats to provide a current assessment of nation-wide extent, and performed quantitative surveys of communities at 23 sites to assess coral cover and composition. Over 132 km(2) of coral habitat was mapped, averaging 28.6 ± 3.8% live coral cover at surveyed sites. In the Arabian Gulf low cover, low richness Porites dominated communities characterized western Abu Dhabi, while reefs northeast of Abu Dhabi city generally contained higher richness and cover, and were dominated by merulinids (formerly faviids). Distinct communities occur in the Sea of Oman, where cover and richness were low. We provide management recommendations to enhance conservation of vulnerable coral reefs in the UAE. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

FY02 Final Report on Phytoremediation of Chlorinated Ethenes in Southern Sector Sediments of the Savannah River Site

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

Brigmon, R..L.

This final report details the operations and results of a 3-year Seepline Phytoremediation Project performed adjacent to Tims Branch, which is located in the Southern Sector of the Savannah River Site (SRS) A/M Area. Phytoremediation is a process where interactions between vegetation, associated microorganisms, and the host substrate combine to effectively degrade contaminated soils, sediments, and groundwater. Phytoremediation is a rapidly developing technology that shows promise for the effective and safe cleanup of certain hazardous wastes. It has the potential to remediate numerous volatile organic compounds (VOCs). Extensive characterization work has demonstrated that two VOCs, tetrachloroethylene (PCE) and trichloroethylene (TCE)more » are the major components of the VOC-contaminated groundwater that is migrating through the Southern Sector and Tims Branch seepline area (WSRC, 1999). The PCE and TCE are chlorinated ethenes (CE), and have been detected in seepline soils and ground water adjacent to the ecologically-sensitive Tims Branch seepline area.« less

Site-specific Microtubule-associated Protein 4 Dephosphorylation Causes Microtubule Network Densification in Pressure Overload Cardiac Hypertrophy*

PubMed Central

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F.; Bethard, Jennifer R.; Menick, Donald R.; Kuppuswamy, Dhandapani; Cooper, George

2010-01-01

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac α- and β-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 → Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality. PMID:20436166

F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations

PubMed Central

Mancini, Giordano; Zazza, Costantino

2015-01-01

The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization. PMID:26415031

F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations.

PubMed

Mancini, Giordano; Zazza, Costantino

2015-01-01

The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization.

Unique DNA methylome profiles in CpG island methylator phenotype colon cancers

PubMed Central

Xu, Yaomin; Hu, Bo; Choi, Ae-Jin; Gopalan, Banu; Lee, Byron H.; Kalady, Matthew F.; Church, James M.; Ting, Angela H.

2012-01-01

A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to be hypermethylated in CIMP tumors only; and importantly, 80% of these sites were located in CpG islands. These data demonstrate on a genome-wide level that the additional hypermethylation seen in CIMP tumors occurs almost exclusively at CpG islands and support definitively that these tumors were appropriately named. When these sites were examined more closely, we found that 25% were adjacent to sites that were also hypermethylated in non-CIMP tumors. Thus, CIMP is also characterized by more extensive methylation of sites that are already prone to be hypermethylated in colon cancer. These observations indicate that CIMP tumors have specific defects in controlling both DNA methylation seeding and spreading and serve as an important first step in delineating molecular mechanisms that control these processes. PMID:21990380

Multi-Scale Mass Transfer Processes Controlling Natural Attenuation and Engineered Remediation: An IFRC Focused on Hanford’s 300 Area Uranium Plume

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

Zachara, John M.; Bjornstad, Bruce N.; Christensen, John N.

2010-02-01

The Integrated Field-Scale Subsurface Research Challenge (IFRC) at the Hanford Site 300 Area uranium (U) plume addresses multi-scale mass transfer processes in a complex hydrogeologic setting where groundwater and riverwater interact. A series of forefront science questions on mass transfer are posed for research which relate to the effect of spatial heterogeneities; the importance of scale; coupled interactions between biogeochemical, hydrologic, and mass transfer processes; and measurements and approaches needed to characterize and model a mass-transfer dominated system. The project was initiated in February 2007, with CY 2007 and CY 2008 progress summarized in preceding reports. The site has 35more » instrumented wells, and an extensive monitoring system. It includes a deep borehole for microbiologic and biogeochemical research that sampled the entire thickness of the unconfined 300 A aquifer. Significant, impactful progress has been made in CY 2009 with completion of extensive laboratory measurements on field sediments, field hydrologic and geophysical characterization, four field experiments, and modeling. The laboratory characterization results are being subjected to geostatistical analyses to develop spatial heterogeneity models of U concentration and chemical, physical, and hydrologic properties needed for reactive transport modeling. The field experiments focused on: (1) physical characterization of the groundwater flow field during a period of stable hydrologic conditions in early spring, (2) comprehensive groundwater monitoring during spring to characterize the release of U(VI) from the lower vadose zone to the aquifer during water table rise and fall, (3) dynamic geophysical monitoring of salt-plume migration during summer, and (4) a U reactive tracer experiment (desorption) during the fall. Geophysical characterization of the well field was completed using the down-well Electrical Resistance Tomography (ERT) array, with results subjected to robust, geostatistically constrained inversion analyses. These measurements along with hydrologic characterization have yielded 3D distributions of hydraulic properties that have been incorporated into an updated and increasingly robust hydrologic model. Based on significant findings from the microbiologic characterization of deep borehole sediments in CY 2008, down-hole biogeochemistry studies were initiated where colonization substrates and spatially discrete water and gas samplers were deployed to select wells. The increasingly comprehensive field experimental results, along with the field and laboratory characterization, are leading to a new conceptual model of U(VI) flow and transport in the IFRC footprint and the 300 Area in general, and insights on the microbiological community and associated biogeochemical processes. A significant issue related to vertical flow in the IFRC wells was identified and evaluated during the spring and fall field experimental campaigns. Both upward and downward flows were observed in response to dynamic Columbia River stage. The vertical flows are caused by the interaction of pressure gradients with our heterogeneous hydraulic conductivity field. These impacts are being evaluated with additional modeling and field activities to facilitate interpretation and mitigation. The project moves into CY 2010 with ambitious plans for a drilling additional wells for the IFRC well field, additional experiments, and modeling. This research is part of the ERSP Hanford IFRC at Pacific Northwest National Laboratory.« less

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...

Teacher Factors Associated with Innovative Curriculum Goals and Pedagogical Practices: Differences between Extensive and Non-Extensive ICT-Using Science Teachers

ERIC Educational Resources Information Center

Voogt, J.

2010-01-01

Second Information Technology in Education Study (SITES) 2006 was an international study about pedagogical practices and the use of information and communication technology (ICT) in math and science classrooms. One of the findings of SITES 2006 was that--across educational systems--a proportion of the math and science teachers in the 22 countries…

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...

Site characterization report for the basalt waste isolation project. Volume II

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

None

1982-11-01

The reference location for a repository in basalt for the terminal storage of nuclear wastes on the Hanford Site and the candidate horizons within this reference repository location have been identified and the preliminary characterization work in support of the site screening process has been completed. Fifteen technical questions regarding the qualification of the site were identified to be addressed during the detailed site characterization phase of the US Department of Energy-National Waste Terminal Storage Program site selection process. Resolution of these questions will be provided in the final site characterization progress report, currently planned to be issued in 1987,more » and in the safety analysis report to be submitted with the License Application. The additional information needed to resolve these questions and the plans for obtaining the information have been identified. This Site Characterization Report documents the results of the site screening process, the preliminary site characterization data, the technical issues that need to be addressed, and the plans for resolving these issues. Volume 2 contains chapters 6 through 12: geochemistry; surface hydrology; climatology, meteorology, and air quality; environmental, land-use, and socioeconomic characteristics; repository design; waste package; and performance assessment.« less

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...

Site classification for northern forest species

Treesearch

Willard H. Carmean

1977-01-01

Summarizes the extensive literature for northern forest species covering site index curves, site index species comparisons, growth intercepts, soil-site studies, plant indicators, physiographic site classifications, and soil survey studies. The advantages and disadvantages of each are discussed, and suggestions are made for future research using each of these methods....

iss012e16633

NASA Image and Video Library

2006-01-28

ISS012-E-16633 (28 Jan. 2006) --- Savannah River Site, South Carolina is featured in this image photographed by an Expedition 12 crew member on the International Space Station. Situated between the South Carolina piedmont and the Atlantic Ocean, the Savannah River Site is an important part of the US Department of Energy’s nuclear program. Construction of the site – originally called the Savannah River Plant – began in 1951 for the purpose of generating radioactive materials, primarily the hydrogen isotope tritium and plutonium-239, necessary for nuclear weapons production during the Cold War. A total of five nuclear reactors occupy the central portion of the site and operated throughout 1953-1992. Following the end of the Cold War in 1991 activities at the Savannah River Site are now focused on disposal of nuclear wastes, environmental cleanup of the site itself, and development of advanced remediation technologies. The Savannah River Site is located in the Sand Hills region of South Carolina and includes an area of 800 square kilometers (300 square miles). The southern half of the Site (building clusters with reflective white rooftops) is shown. The nearby Savannah River and its tributary creeks provided a ready source of water for the nuclear reactors; to this end, two artificial lakes (“L” Lake and Par Pond) were constructed. The meandering channel of the River and its floodplain, characterized by grey-brown sediments, extends from northwest to southeast across the left portion of the image. The proximity of the River, and the permeable nature of the geological materials under laying the site (sand, clay, gravel, and carbonate rocks), necessitate extensive and ongoing environmental monitoring and cleanup efforts to reduce potential contamination of local water sources. According to NASA scientists, final remediation of wastes posing threats to surface and groundwater is scheduled to occur by 2025.

Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition

PubMed Central

Kulp, John L.; Cloudsdale, Ian S.; Kulp, John L.

2017-01-01

Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition. PMID:28837642

Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition.

PubMed

Kulp, John L; Cloudsdale, Ian S; Kulp, John L; Guarnieri, Frank

2017-01-01

Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.

A molecular Debye-Huckel theory of solvation in polar fluids: An extension of the Born model

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

Xiao, Tiejun; Song, Xueyu

A dielectric response theory of solvation beyond the conventional Born model for polar fluids is presented. The dielectric response of a polar fluid is described by a Born response mode and a linear combination of Debye-Hückel-like response modes that capture the nonlocal response of polar fluids. The Born mode is characterized by a bulk dielectric constant, while a Debye-Hückel mode is characterized by its corresponding Debye screening length. Both the bulk dielectric constant and the Debye screening lengths are determined from the bulk dielectric function of the polar fluid. The linear combination coefficients of the response modes are evaluated inmore » a self-consistent way and can be used to evaluate the electrostatic contribution to the thermodynamic properties of a polar fluid. In conclusion, our theory is applied to a dipolar hard sphere fluid as well as interaction site models of polar fluids such as water, where the electrostatic contribution to their thermodynamic properties can be obtained accurately.« less

A molecular Debye-Huckel theory of solvation in polar fluids: An extension of the Born model

DOE PAGES

Xiao, Tiejun; Song, Xueyu

2017-12-06

A dielectric response theory of solvation beyond the conventional Born model for polar fluids is presented. The dielectric response of a polar fluid is described by a Born response mode and a linear combination of Debye-Hückel-like response modes that capture the nonlocal response of polar fluids. The Born mode is characterized by a bulk dielectric constant, while a Debye-Hückel mode is characterized by its corresponding Debye screening length. Both the bulk dielectric constant and the Debye screening lengths are determined from the bulk dielectric function of the polar fluid. The linear combination coefficients of the response modes are evaluated inmore » a self-consistent way and can be used to evaluate the electrostatic contribution to the thermodynamic properties of a polar fluid. In conclusion, our theory is applied to a dipolar hard sphere fluid as well as interaction site models of polar fluids such as water, where the electrostatic contribution to their thermodynamic properties can be obtained accurately.« less

A molecular Debye-Hückel theory of solvation in polar fluids: An extension of the Born model

NASA Astrophysics Data System (ADS)

Xiao, Tiejun; Song, Xueyu

2017-12-01

A dielectric response theory of solvation beyond the conventional Born model for polar fluids is presented. The dielectric response of a polar fluid is described by a Born response mode and a linear combination of Debye-Hückel-like response modes that capture the nonlocal response of polar fluids. The Born mode is characterized by a bulk dielectric constant, while a Debye-Hückel mode is characterized by its corresponding Debye screening length. Both the bulk dielectric constant and the Debye screening lengths are determined from the bulk dielectric function of the polar fluid. The linear combination coefficients of the response modes are evaluated in a self-consistent way and can be used to evaluate the electrostatic contribution to the thermodynamic properties of a polar fluid. Our theory is applied to a dipolar hard sphere fluid as well as interaction site models of polar fluids such as water, where the electrostatic contribution to their thermodynamic properties can be obtained accurately.

A molecular Debye-Hückel theory of solvation in polar fluids: An extension of the Born model.

PubMed

Xiao, Tiejun; Song, Xueyu

2017-12-07

A dielectric response theory of solvation beyond the conventional Born model for polar fluids is presented. The dielectric response of a polar fluid is described by a Born response mode and a linear combination of Debye-Hückel-like response modes that capture the nonlocal response of polar fluids. The Born mode is characterized by a bulk dielectric constant, while a Debye-Hückel mode is characterized by its corresponding Debye screening length. Both the bulk dielectric constant and the Debye screening lengths are determined from the bulk dielectric function of the polar fluid. The linear combination coefficients of the response modes are evaluated in a self-consistent way and can be used to evaluate the electrostatic contribution to the thermodynamic properties of a polar fluid. Our theory is applied to a dipolar hard sphere fluid as well as interaction site models of polar fluids such as water, where the electrostatic contribution to their thermodynamic properties can be obtained accurately.

Shedding new light on opsin evolution

PubMed Central

Porter, Megan L.; Blasic, Joseph R.; Bok, Michael J.; Cameron, Evan G.; Pringle, Thomas; Cronin, Thomas W.; Robinson, Phyllis R.

2012-01-01

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function. PMID:22012981

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

Cheng, J.; Liu, C.; Koopman, W.J.

Ligation of the Fas cell-surface molecule induces apoptosis. Defective Fas-mediated apoptosis has been associated with spontaneous autoimmunity in mice. Using human Fas/Apo-1 cDNA as a probe, the authors have molecularly cloned and characterized the human Fas chromosomal gene. The gene consists of nine exons and spans more than 26 kilobases of DNA. The lengths of introns vary from > 14 kilobases at the 5` end of the gene to 152 base pairs upstream of the exon encoding the transmembrane domain. The domain structure of the human Fas is encoded by an exon or a set of exons. Primer extension analysismore » revealed three major transcription initiation sites. The promoter region lacked canonical {open_quotes}TATA{close_quotes} and {open_quotes}CAAT{close_quotes} boxes but was a {open_quotes}GC-rich{close_quotes} sequence, and contained consensus sequences for AP-1, GF-1, NY-Y, CP-2, EBP20, and c-myb. These data provide the first characterization of the human Fas gene and insight into its regulatory region. 54 refs., 3 figs., 1 tab.« less

Characterization and Epidemiology of Pigeon Paramyxovirus Type-1 Viruses (PPMV-1) Isolated in Macedonia.

PubMed

Dodovski, A; Cvetkovikj, I; Krstevski, K; Naletoski, I; Savić, Vladimir

2017-06-01

We have characterized in this study 10 PPMV-1 isolated from domestic pigeons and one PPMV-1 isolated from a feral pigeon in the period 2007-2012, using both classical methods (HI test and ICPI test) and molecular methods (RT-qPCR, RT-PCR, and nucleotide sequencing). Using phylogenetic analysis of partial fusion gene sequences, these viruses clustered with recent European PPMV-1 isolates (EU/re) within the genotype VIb/1. All isolates possessed virulent cleavage site motifs with variable morbidity and mortality in pigeons. The intracerebral pathogenecity indices of the five isolates ranged from 0.59 to 1.53. The repetitive isolation of PPMV-1 viruses for several consecutive years led toward establishing enzootic presence of the disease in pigeons. A high nucleotide sequence homology between the Macedonian isolates and EU/re isolates was shown. Co-circulation of different isolates in the same holdings was detected. This is the first study to extensively describe the molecular epidemiology of PPMV-1 isolated in Macedonia.

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

DOE PAGES

Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S.; ...

2016-02-09

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. Thismore » “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.« less

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

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

Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S.

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. Thismore » “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.« less

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.

Post-analysis report on Chesapeake Bay data processing. [spectral analysis and recognition computer signature extension

NASA Technical Reports Server (NTRS)

Thomson, F.

1972-01-01

The additional processing performed on data collected over the Rhode River Test Site and Forestry Site in November 1970 is reported. The techniques and procedures used to obtain the processed results are described. Thermal data collected over three approximately parallel lines of the site were contoured, and the results color coded, for the purpose of delineating important scene constituents and to identify trees attacked by pine bark beetles. Contouring work and histogram preparation are reviewed and the important conclusions from the spectral analysis and recognition computer (SPARC) signature extension work are summarized. The SPARC setup and processing records are presented and recommendations are made for future data collection over the site.

Structural and Biochemical Characterization of a Novel Aminopeptidase from Human Intestine

DOE PAGES

Tykvart, Jan; Bařinka, Cyril; Svoboda, Michal; ...

2015-03-09

N-acetylated α-linked acidic dipeptidase-like protein (NAALADase L), encoded by the NAALADL1 gene, is a close homolog of glutamate carboxypeptidase II, a metallopeptidase that has been intensively studied as a target for imaging and therapy of solid malignancies and neuropathologies. However, neither the physiological functions nor structural features of NAALADase L are known at present. In this paper, we report a thorough characterization of the protein product of the human NAALADL1 gene, including heterologous overexpression and purification, structural and biochemical characterization, and analysis of its expression profile. By solving the NAALADase L x-ray structure, we provide the first experimental evidence thatmore » it is a zinc-dependent metallopeptidase with a catalytic mechanism similar to that of glutamate carboxypeptidase II yet distinct substrate specificity. A proteome-based assay revealed that the NAALADL1 gene product possesses previously unrecognized aminopeptidase activity but no carboxy- or endopeptidase activity. These findings were corroborated by site-directed mutagenesis and identification of bestatin as a potent inhibitor of the enzyme. Analysis of NAALADL1 gene expression at both the mRNA and protein levels revealed the small intestine as the major site of protein expression and points toward extensive alternative splicing of the NAALADL1 gene transcript. Taken together, our data imply that the NAALADL1 gene product's primary physiological function is associated with the final stages of protein/peptide digestion and absorption in the human digestive system. Finally, based on these results, we suggest a new name for this enzyme: human ileal aminopeptidase (HILAP).« less

Compartmentalized self-replication under fast PCR cycling conditions yields Taq DNA polymerase mutants with increased DNA-binding affinity and blood resistance.

PubMed

Arezi, Bahram; McKinney, Nancy; Hansen, Connie; Cayouette, Michelle; Fox, Jeffrey; Chen, Keith; Lapira, Jennifer; Hamilton, Sarah; Hogrefe, Holly

2014-01-01

Faster-cycling PCR formulations, protocols, and instruments have been developed to address the need for increased throughput and shorter turn-around times for PCR-based assays. Although run times can be cut by up to 50%, shorter cycle times have been correlated with lower detection sensitivity and increased variability. To address these concerns, we applied Compartmentalized Self Replication (CSR) to evolve faster-cycling mutants of Taq DNA polymerase. After five rounds of selection using progressively shorter PCR extension times, individual mutations identified in the fastest-cycling clones were randomly combined using ligation-based multi-site mutagenesis. The best-performing combinatorial mutants exhibit 35- to 90-fold higher affinity (lower Kd ) for primed template and a moderate (2-fold) increase in extension rate compared to wild-type Taq. Further characterization revealed that CSR-selected mutations provide increased resistance to inhibitors, and most notably, enable direct amplification from up to 65% whole blood. We discuss the contribution of individual mutations to fast-cycling and blood-resistant phenotypes.

Modeling species occurrence dynamics with multiple states and imperfect detection

USGS Publications Warehouse

MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

2009-01-01

Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics. ?? 2009 by the Ecological Society of America.

Dynamic models for problems of species occurrence with multiple states

USGS Publications Warehouse

MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

2009-01-01

Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture?recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.

Cellular projections from sensory hair cells form polarity-specific scaffolds during synaptogenesis

PubMed Central

Dow, Eliot; Siletti, Kimberly

2015-01-01

The assembly of a nervous system requires the extension of axons and dendrites to specific regions where they are matched with appropriate synaptic targets. Although the cues that guide long-range outgrowth have been characterized extensively, additional mechanisms are required to explain short-range guidance in neural development. Using a complementary combination of time-lapse imaging by fluorescence confocal microscopy and serial block-face electron microscopy, we identified a novel type of presynaptic projection that participates in the assembly of the vertebrate nervous system. Synapse formation by each hair cell of the zebrafish's lateral line occurs during a particular interval after the cell's birth. During the same period, projections emerge from the cellular soma, extending toward a specific subpopulation of mature hair cells and interacting with polarity-specific afferent nerve terminals. The terminals then extend along the projections to reach appropriately matched presynaptic sites, after which the projections recede. Our results suggest that presynaptic projections act as transient scaffolds for short-range partner matching, a mechanism that may occur elsewhere in the nervous system. PMID:25995190

LesionTracker: Extensible Open-Source Zero-Footprint Web Viewer for Cancer Imaging Research and Clinical Trials.

PubMed

Urban, Trinity; Ziegler, Erik; Lewis, Rob; Hafey, Chris; Sadow, Cheryl; Van den Abbeele, Annick D; Harris, Gordon J

2017-11-01

Oncology clinical trials have become increasingly dependent upon image-based surrogate endpoints for determining patient eligibility and treatment efficacy. As therapeutics have evolved and multiplied in number, the tumor metrics criteria used to characterize therapeutic response have become progressively more varied and complex. The growing intricacies of image-based response evaluation, together with rising expectations for rapid and consistent results reporting, make it difficult for site radiologists to adequately address local and multicenter imaging demands. These challenges demonstrate the need for advanced cancer imaging informatics tools that can help ensure protocol-compliant image evaluation while simultaneously promoting reviewer efficiency. LesionTracker is a quantitative imaging package optimized for oncology clinical trial workflows. The goal of the project is to create an open source zero-footprint viewer for image analysis that is designed to be extensible as well as capable of being integrated into third-party systems for advanced imaging tools and clinical trials informatics platforms. Cancer Res; 77(21); e119-22. ©2017 AACR . ©2017 American Association for Cancer Research.

The folding transition state of Protein L is extensive with non-native interactions (and not small and polarized)

PubMed Central

Yoo, Tae Yeon; Adhikari, Aashish; Xia, Zhen; Huynh, Tien; Freed, Karl F.; Zhou, Ruhong; Sosnick, Tobin R.

2012-01-01

Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data are required that can be meaningfully compared to simulations. According to standard mutational φ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by φ analysis also occurs for acyl phosphatase1, ubiquitin2 and BdpA3. The carboxy terminal hairpin in the transition state of Protein L is found to be non-native, a significant result that agrees with our PDB-based backbone sampling and all-atom simulations. The non-native character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states. PMID:22522126

An Orchestrated Intron Retention Program in Meiosis Controls Timely Usage of Transcripts during Germ Cell Differentiation.

PubMed

Naro, Chiara; Jolly, Ariane; Di Persio, Sara; Bielli, Pamela; Setterblad, Niclas; Alberdi, Antonio J; Vicini, Elena; Geremia, Raffaele; De la Grange, Pierre; Sette, Claudio

2017-04-10

Global transcriptome reprogramming during spermatogenesis ensures timely expression of factors in each phase of male germ cell differentiation. Spermatocytes and spermatids require particularly extensive reprogramming of gene expression to switch from mitosis to meiosis and to support gamete morphogenesis. Here, we uncovered an extensive alternative splicing program during this transmeiotic differentiation. Notably, intron retention was largely the most enriched pattern, with spermatocytes showing generally higher levels of retention compared with spermatids. Retained introns are characterized by weak splice sites and are enriched in genes with strong relevance for gamete function. Meiotic intron-retaining transcripts (IRTs) were exclusively localized in the nucleus. However, differently from other developmentally regulated IRTs, they are stable RNAs, showing longer half-life than properly spliced transcripts. Strikingly, fate-mapping experiments revealed that IRTs are recruited onto polyribosomes days after synthesis. These studies reveal an unexpected function for regulated intron retention in modulation of the timely expression of select transcripts during spermatogenesis. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

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...

Geological Investigation Program for the Site of a New Nuclear Power Plant in Hungary

NASA Astrophysics Data System (ADS)

Gerstenkorn, András; Trosits, Dalma; Chikán, Géza; János Katona, Tamás

2015-04-01

Comprehensive site evalaution program is implemented for the new Nuclear Power Plant to be constructed at Paks site in Hungary with the aim of confirmation of acceptability of the site and definition of site-related design basis data. Most extensive part of this program is to investigate geological-tectonical features of the site with particular aim on the assessment of the capability of faults at and around the site, characterization of site seismic hazard, and definition of the design basis earthquake. A brief description of the scope and methodology of the geological, seismological, geophysical, geotechnical and hydrogeological investigations will be given on the poster. Main focus of the presentation is to show the graded structure and extent of the geological investigations that follow the needs and scale of the geological modeling, starting with the site and its vicinity, as well as on the near regional and the regional scale. Geological inverstigations includes several boreholes up-to the base-rock, plenty of boreholes discovering the Pannonian and large number of shallow boreholes for investigation of more recent development. The planning of the geological investigations is based on the 3D seismic survey performed around the site, that is complemented by shallow-seimic survey at and in the vicinity of the site. The 3D geophysical imaging provides essential geodynamic information to assess the capability of near site faults and for the seismic hazard analysis, as well as for the hydrogeological modeling. The planned seismic survey gives a unique dataset for understanding the spatial relationship between individual fault segments. Planning of the research (trenching, etc.) for paleoseismic manifestations is also based on the 3D seismic survey. The seismic survey and other geophysical data (including data of space geodesy) allow the amendment of the understanding and the model of the tectonic evolution of the area and geological events. As it is known from earlier studies, seismic sources in the near regional area are the dominating contributors to the site seimic hazard. Therefore a 3D geological model will be developed for the 50 km region around the site in order to consider different geological scenarios. Site-scale investigations are aimed on the characterization of local geotechnical and hydrogeological conditions. The geotechnical investigations provide data for the evaluation of site response, i.e. the free-field ground motion response spectra, assessment of the liquefaction hazard and foundation design. Important element of the hydrogeological survey is numerical groundwater modeling. The aim of hydrogeological modeling is the summary of hydrogeological data in a numeric system, the description, simulation of underground water flow and transport conditions.

The Savannah River Site`s Groundwater Monitoring Program, third quarter 1991

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

Not Available

The Environmental Protection Department/Environmental Monitoring Section (EPD/EMS) administers the Savannah River Site`s (SRS) Groundwater Monitoring Program. During third quarter 1991, EPD/EMS conducted extensive sampling of monitoring wells. Analytical results from third quarter 1991 are listed in this report.

A potential Italian CCS site: site characterization and monitoring of Sulcis Basin (Sardinia).

NASA Astrophysics Data System (ADS)

Chiara Tartarello, Maria; Bigi, Sabina; Beaubien, Stanley Eugene; De Angelis, Davide; Graziani, Stefano; Lombardi, Salvatore; Sacco, Pietro; Ruggiero, Livio

2017-04-01

The Sulcis Basin is an area situated in SW Sardinia (Italy) and is a potential site for the implementation of CCS in Italy. In fact, in the last years many studies were conducted to characterize the area and to define the baseline. The "Miliolitico" has been identified as the potential reservoir and is composed by fractured carbonate, while the "Produttivo Fm.", a sequence of clay, coal and marl, is the caprock. Above the "Produttivo Fm." there is a thick volcanic sequence (more than 800 m) that could be considered also a secondary caprock. In the area of Matzaccara, the "Miliolitico" is below an alluvial plain and it is estimates that could reach a depth of more than 800 m. To characterize the reservoir-caprock system there were conducted an extensive structural-geological survey, and more in detail a fracture analysis on all the Formation at the outcrop. With regard to the faults, it has been examined their architecture, and in particular the conduit-barrier behaviors. Moreover, to evaluate the theoretical capacity of the potential reservoir, we built a Discrete Fracture Model, using the fracture data collected at outcrop. So, we estimate a secondary porosity of about 3%. As regards to the definition of geochemical baseline, it has been conducted both discontinuous and continuous monitoring of CO2 and other gases. More in details, there were carried out a regional and a detailed survey, measuring the concentration and the flux of CO2. in that manner, it has been possible to identify potential migration pathways along faults and to define the position of continuous monitoring station. We developed small, low-power consuming, low-cost pCO2 "GasPro", to measure the CO2 both in soil and water. In the next months, it is planned to extend the monitoring network and to inject a little quantity of CO2 along a fault in the Matzaccara plain.

Measuring the Impact of Wildfire on Active Layer Thickness in a Discontinuous Permafrost region using Interferometric Synthetic Aperture Radar (InSAR)

NASA Astrophysics Data System (ADS)

Michaelides, R. J.; Schaefer, K. M.; Zebker, H. A.; Liu, L.; Chen, J.; Parsekian, A.

2017-12-01

In permafrost regions, the active layer is defined as the uppermost portion of the permafrost table that is subject to annual freeze/thaw cycles. The active layer plays a crucial role in surface processes, surface hydrology, and vegetation succession; furthermore, trapped methane, carbon dioxide, and other greenhouse gases in permafrost are released into the atmosphere as permafrost thaws. A detailed understanding of active layer dynamics is therefore critical towards understanding the interactions between permafrost surface processes, freeze/thaw cycles, and climate-especially in regions across the Arctic subject to long-term permafrost degradation. The Yukon-Kuskokwim (YK) delta in southwestern Alaska is a region of discontinuous permafrost characterized by surface lakes, wetlands, and thermokarst depressions. Furthermore, extensive wildfires have burned across the YK delta in 2006, 2007, and 2015, impacting vegetation cover, surface soil moisture, and the active layer. Using data from the ALOS PALSAR, ALOS-2 PALSAR-2, and Sentinel-1A/B space borne synthetic aperture radar (SAR) systems, we generate a series of interferograms over a study site in the YK delta spanning 2007-2011, and 2014-present. Using the ReSALT (Remotely-Sensed Active Layer Thickness) technique, we demonstrate that active layer can be characterized over most of the site from the relative interferometric phase difference due to ground subsidence and rebound associated with the seasonal active layer freeze/thaw cycle. Additionally, we show that this technique successfully discriminates between burned and unburned regions, and can resolve increases in active layer thickness in burned regions on the order of 10's of cms. We use the time series of interferograms to discuss permafrost recovery following wildfire burn, and compare our InSAR observations with GPR and active layer probing data from a 2016 summer field campaign to the study site. Finally, we compare the advantages and disadvantages of the ALOS, ALOS-2, and Sentinel systems for characterizing permafrost dynamics.

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

Afraid to Start Because the Outcome is Uncertain?: Social Site Characterization as a Tool for Informing Public Engagement Efforts

USGS Publications Warehouse

Wade, S.; Greenberg, S.

2009-01-01

This paper introduces the concept of social site characterization as a parallel effort to technical site characterization to be used in evaluating and planning carbon dioxides capture and storage (CCS) projects. Social site characterization, much like technical site characterization, relies on a series of iterative investigations into public attitudes towards a CCS project and the factors that will shape those views. This paper also suggests ways it can be used to design approaches for actively engaging stakeholders and communities in the deployment of CCS projects. This work is informed by observing the site selection process for FutureGen and the implementation of research projects under the Regional Carbon Sequestration Partnership Program. ?? 2009 Elsevier Ltd. All rights reserved.

Scleredema adultorum of Buschke presenting as periorbital edema: a diagnostic challenge.

PubMed

Ioannidou, Despina I; Krasagakis, Konstantin; Stefanidou, Maria P; Karampekios, Spyros; Panayiotidis, John; Tosca, Androniki D

2005-02-01

Scleredema adultorum is a rare sclerotic disorder characterized by diffuse swelling and nonpitting induration of the skin. Its occurrence has been documented in association with infections, diabetes mellitus, paraproteinemia, multiple myeloma, and monoclonal gammopathy. We report an unusual case of a 48-year-old man with an asymptomatic bilateral eyelid edema of sudden onset. During a period of 6 months, the condition slowly progressed to extensive nonpitting edematous swelling restricted to the periorbital sites. The presumptive diagnosis of scleredema adultorum was confirmed by the presence of typical histologic findings. This case is unique in that the periorbital swelling remained as the sole clinical manifestation of scleredema during the 5-year follow-up and was complicated with partial vision blockage.

Robust one-Tube Ω-PCR Strategy Accelerates Precise Sequence Modification of Plasmids for Functional Genomics

PubMed Central

Chen, Letian; Wang, Fengpin; Wang, Xiaoyu; Liu, Yao-Guang

2013-01-01

Functional genomics requires vector construction for protein expression and functional characterization of target genes; therefore, a simple, flexible and low-cost molecular manipulation strategy will be highly advantageous for genomics approaches. Here, we describe a Ω-PCR strategy that enables multiple types of sequence modification, including precise insertion, deletion and substitution, in any position of a circular plasmid. Ω-PCR is based on an overlap extension site-directed mutagenesis technique, and is named for its characteristic Ω-shaped secondary structure during PCR. Ω-PCR can be performed either in two steps, or in one tube in combination with exonuclease I treatment. These strategies have wide applications for protein engineering, gene function analysis and in vitro gene splicing. PMID:23335613

Inactivation of phosphorylase b by potassium ferrate. Identification of a tyrosine residue involved in the binding of adenosine 5'-monophosphate.

PubMed

Lee, Y M; Benisek, W F

1978-08-10

The site of reaction of potassium ferrate (K2FeO4) with rabbit muscle phosphorylase b has been further characterized in an extension of previously published studies (Lee, Y. M., and Benisek, W. F. (1976) J. Biol, Chem. 251, 1553-1560) reporting inactivation of the enzyme by this reagent. The tryptic peptide composed of residues 70 to 80 of the enzyme's polypeptide chain was shown to contain a tyrosine residue which is chemically modified by ferrate and which is protected by 5'-AMP. The sequence of this peptide obtained from both untreated and ferrate-treated phosphorylase b was determined, and the results showed that tyrosine-75 was the residue with which ferrate reacts.

Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

PubMed

Watters, Kyle E; Lucks, Julius B

2016-01-01

Mapping RNA structure with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry has proven to be a versatile method for characterizing RNA structure in a variety of contexts. SHAPE reagents covalently modify RNAs in a structure-dependent manner to create adducts at the 2'-OH group of the ribose backbone at nucleotides that are structurally flexible. The positions of these adducts are detected using reverse transcriptase (RT) primer extension, which stops one nucleotide before the modification, to create a pool of cDNAs whose lengths reflect the location of SHAPE modification. Quantification of the cDNA pools is used to estimate the "reactivity" of each nucleotide in an RNA molecule to the SHAPE reagent. High reactivities indicate nucleotides that are structurally flexible, while low reactivities indicate nucleotides that are inflexible. These SHAPE reactivities can then be used to infer RNA structures by restraining RNA structure prediction algorithms. Here, we provide a state-of-the-art protocol describing how to perform in vitro RNA structure probing with SHAPE chemistry using next-generation sequencing to quantify cDNA pools and estimate reactivities (SHAPE-Seq). The use of next-generation sequencing allows for higher throughput, more consistent data analysis, and multiplexing capabilities. The technique described herein, SHAPE-Seq v2.0, uses a universal reverse transcription priming site that is ligated to the RNA after SHAPE modification. The introduced priming site allows for the structural analysis of an RNA independent of its sequence.

Extensive geographic and ontogenetic variation characterizes the trophic ecology of a temperate reef fish on southern California (USA) rocky reefs

PubMed Central

Hamilton, Scott L.; Caselle, Jennifer E.; Lantz, Coulson A.; Egloff, Tiana L.; Kondo, Emi; Newsome, Seth D.; Loke-Smith, Kerri; Pondella, Daniel J.; Young, Kelly A.; Lowe, Christopher G.

2015-01-01

Interactions between predator and prey act to shape the structure of ecological communities, and these interactions can differ across space. California sheephead Semicossyphus pulcher are common predators of benthic invertebrates in kelp beds and rocky reefs in southern California, USA. Through gut content and stable isotope (δ13C and †15N) analyses, we investigated geographic and ontogenetic variation in trophic ecology across 9 populations located at island and mainland sites throughout southern California. We found extensive geographic variation in California sheephead diet composition over small spatial scales. Populations differed in the proportion of sessile filter/suspension feeders or mobile invertebrates in the diet. Spatial variation in diet was highly correlated with other life history and demographic traits (e.g. growth, survivorship, reproductive condition, and energy storage), in addition to proxies of prey availability from community surveys. Multivariate descriptions of the diet from gut contents roughly agreed with the spatial groupings of sites based on stable isotope analysis of both California sheephead and their prey. Ontogenetic changes in diet occurred consistently across populations, despite spatial differences in size structure. As California sheephead increase in size, diets shift from small filter feeders, like bivalves, to larger mobile invertebrates, such as sea urchins. Our results indicate that locations with large California sheephead present, such as many marine reserves, may experience increased predation pressure on sea urchins, which could ultimately affect kelp persistence. PMID:26246648

How do land use intensity, experimentally increased temperature and water level affect methane and nitrous oxide emissions from a drained fen peatland?

NASA Astrophysics Data System (ADS)

Heinichen, Jan; Eickenscheidt, Tim; Drösler, Matthias

2014-05-01

Rewetting and extensification of peatlands is widely discussed and practiced to reduce losses of CO2 and N2O from drained peat soils. But rewetting is known to carry the risk of increased CH4 emissions. Up to now it is not completely clear how the predicted temperature increase in the face of climate change will alter the N2O and CH4 exchange of grasslands on drained peatland soils in the temperate zone. Therefore we investigated the effects of land use intensity, increased groundwater level, increased temperature and the combination of warming and increased groundwater level on CH4 and N2O exchange of two grassland sites (intensive and extensive grassland) in a drained fen peatland in southern Germany. We set up a factorial design on both land use types, on each three treatments, warming, increased water table level and the combination of warming and increased water table level as well as a control site were established. Temperature was manipulated with open-top chambers (OTCs) and water level manipulation was performed using a pumping system and sheet pile walls. The intensive grassland was cut three times in the year, the extensive grassland once in autumn 2011. Cattle slurry and mineral fertilizer (CAN) were deployed on the intensive grassland. Fluxes of CH4 and N2O were measured biweekly from December 2010 to January 2012 using opaque static closed chambers. The annual mean groundwater level (GWL) of the sites without water level manipulation was -41.5 cm b. g. and -30 cm b. g. at the water level manipulated sites on the intensive grassland. On the extensive grassland the GWL of the sites without water level manipulation was -32 cm b. g. and -21.5 cm b. g. at the water level manipulated sites. Air temperature in 0.2 m was increased in 2011 by 0.7 ° C at the treatments with OTCs on the intensive grassland and by 1.0 ° C at the treatments with OTCs on the extensive grassland respectively. The annual cumulative CH4 exchange ranged from 8.1 ± 3.8 kg C ha-1 yr-1 to 36.3 ± 8.6 kg C ha-1 yr-1on the extensive grassland and from -0.1 ± 0.3 kg C ha-1 yr-1 to 15.0 ± 1.9 kg C ha-1 yr-1 on the intensive grassland. The CH4 emissions of the treatments with increased water level on the intensive grassland were significantly higher compared to the control and warming sites. No significant differences could be observed between CH4 emissions of the treatments on the extensive grassland. However, we found a general significant relationship between CH4 fluxes, groundwater level and temperature. All sites on the intensive grassland show higher annual emissions of N2O compared to the sites on the extensive grassland. The annual cumulative N2O exchange ranged from 3.1 ± 0.5 kg N ha-1 yr-1 to 6.1 ± 0.4 kg N ha-1 yr-1on the intensive grassland and from 0.7 ± 0.1 kg N ha-1 yr-1 to 1.3 ± 0.2 kg N ha-1 yr-1 on the extensive grassland. Significant treatment effects could not be observed for N2O exchange on both land use types.

The discovery of deep-water seagrass meadows in a pristine Indian Ocean wilderness revealed by tracking green turtles.

PubMed

Esteban, N; Unsworth, R K F; Gourlay, J B Q; Hays, G C

2018-03-21

Our understanding of global seagrass ecosystems comes largely from regions characterized by human impacts with limited data from habitats defined as notionally pristine. Seagrass assessments also largely focus on shallow-water coastal habitats with comparatively few studies on offshore deep-water seagrasses. We satellite tracked green turtles (Chelonia mydas), which are known to forage on seagrasses, to a remote, pristine deep-water environment in the Western Indian Ocean, the Great Chagos Bank, which lies in the heart of one of the world's largest marine protected areas (MPAs). Subsequently we used in-situ SCUBA and baited video surveys to survey the day-time sites occupied by turtles and discovered extensive monospecific seagrass meadows of Thalassodendron ciliatum. At three sites that extended over 128 km, mean seagrass cover was 74% (mean range 67-88% across the 3 sites at depths to 29 m. The mean species richness of fish in seagrass meadows was 11 species per site (mean range 8-14 across the 3 sites). High fish abundance (e.g. Siganus sutor: mean MaxN.site -1  = 38.0, SD = 53.7, n = 5) and large predatory shark (Carcharhinus amblyrhynchos) (mean MaxN.site -1  = 1.5, SD = 0.4, n = 5) were recorded at all sites. Such observations of seagrass meadows with large top predators, are limited in the literature. Given that the Great Chagos Bank extends over approximately 12,500 km 2 and many other large deep submerged banks exist across the world's oceans, our results suggest that deep-water seagrass may be far more abundant than previously suspected. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

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...

Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.

PubMed

Zubieta, Chloe; Joseph, Rosanne; Krishna, S Sri; McMullan, Daniel; Kapoor, Mili; Axelrod, Herbert L; Miller, Mitchell D; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Carlton, Dennis; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C; Duan, Lian; Elias, Ylva; Elsliger, Marc-André; Feuerhelm, Julie; Grzechnik, Slawomir K; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Klock, Heath E; Knuth, Mark W; Kozbial, Piotr; Kumar, Abhinav; Marciano, David; Morse, Andrew T; Murphy, Kevin D; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Reyes, Ron; Rife, Christopher L; Schimmel, Paul; Trout, Christina V; van den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Hodgson, Keith O; Wooley, John; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A

2007-11-01

TyrA is a member of the dye-decolorizing peroxidase (DyP) family, a new family of heme-dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 A. TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold. Both domains contribute to the heme-binding site. Co-crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases. (c) 2007 Wiley-Liss, Inc.

Geophysical characterization of fractured bedrock at Site 8, former Pease Air Force Base, Newington, New Hampshire

USGS Publications Warehouse

Mack, Thomas J.; Degnan, James R.

2003-01-01

Borehole-geophysical logs collected from eight wells and direct-current resistivity data from three survey lines were analyzed to characterize the fractured bedrock and identify transmissive fractures beneath the former Pease Air Force Base, Newington, N.H. The following logs were used: caliper, fluid temperature and conductivity, natural gamma radiation, electromagnetic conductivity, optical and acoustic televiewer, and heat-pulse flowmeter. The logs indicate several foliation and fracture trends in the bedrock. Two fracture-correlated lineaments trending 28? and 29?, identified with low-altitude aerial photography, are coincident with the dominant structural trend. The eight boreholes logged at Site 8 generally have few fractures and have yields ranging from 0 to 40 gallons per minute. The fractures that probably resulted in high well yields (20?40 gallons per minute) strike northeast-southwest or by the right hand rule, have an orientation of 215?, 47?, and 51?. Two-dimensional direct-current resistivity methods were used to collect detailed subsurface information about the overburden, bedrock-fracture zone depths, and apparent-dip directions. Analysis of data inversions from data collected with dipole-dipole and Schlumberger arrays indicated electrically conductive zones in the bedrock that are probably caused by fractured rock. These zones are coincident with extensions of fracture-correlated lineaments. The fracture-correlated lineaments and geophysical-survey results indicate a possible northeast-southwest anisotropy to the fractured rock.

Molecular genetic analysis of volatile-anesthetic action.

PubMed Central

Keil, R L; Wolfe, D; Reiner, T; Peterson, C J; Riley, J L

1996-01-01

The mechanism(s) and site(s) of action of volatile inhaled anesthetics are unknown in spite of the clinical use of these agents for more than 150 years. In the present study, the model eukaryote Saccharomyces cerevisiae was used to investigate the action of anesthetic agents because of its powerful molecular genetics. It was found that growth of yeast cells is inhibited by the five common volatile anesthetics tested (isoflurane, halothane, enflurane, sevoflurane, and methoxyflurane). Growth inhibition by the agents is relatively rapid and reversible. The potency of these compounds as yeast growth inhibitors directly correlates with their lipophilicity as is predicted by the Meyer-Overton relationship, which directly correlates anesthetic potency of agents and their lipophilicity. The effects of isoflurane on yeast cells were characterized in the most detail. Yeast cells survive at least 48 h in a concentration of isoflurane that inhibits colony formation. Mutants resistant to the growth-inhibitory effects of isoflurane are readily selected. The gene identified by one of these mutations, zzz4-1, has been cloned and characterized. The predicted ZZZ4 gene product has extensive homology to phospholipase A2-activating protein, a GO effector protein of mice. Both zzz4-1 and a deletion of ZZZ4 confer resistance to all five of the agents tested, suggesting that signal transduction may be involved in the response of these cells to volatile anesthetics. PMID:8668160

Probing the chemistry, structure, and dynamics of the water-silica interface

NASA Astrophysics Data System (ADS)

Lockwood, Glenn K.

Despite its natural abundance and wide-ranging technological relevance, much remains unknown or unclear about water-silica interfaces. Computer simulation stands to bridge the gaps of knowledge left by experiment, and a recently developed Dissociative Water Potential has enabled the simulation of large amorphous silica surfaces in contact with water without having to impose a model of surface chemistry a priori. Earlier work with this model has revealed the existence of several protonated surface sites such as SiOH2 + and Si-(OH+)-Si that have yet to be extensively characterized. However, both experiment and quantum mechanical simulation have provided an increasing body of evidence that suggests these sites exist, and these sites may play key roles in some of the unexplained phenomena observed in water-silica systems. To this end, this Dissociative Water Potential has been applied to develop a comprehensive picture of the chemistry, structure, and dynamics of the water-silica interface that is unbiased by any expectation of what sites should form. The bridging OH site, Si-(OH+)-Si, does form and is characterized as a highly acidic site that occurs predominantly on strained Si-O-Si bridges near the interface. Similarly, the transient formation of SiOH2 + is observed, and this site is found to be more acidic than Si-(OH +)-Si. In addition to H3O+ that forms near the interface, all of these sites readily deprotonate and are expected to play a role in the enhanced proton conductivity experimentally observed in hydrated mesoporous silica. The reactions between water and silica are particularly relevant to the engineering of nuclear waste forms, and the role of water-silica interactions are also explored within the context of the degradation of silica-based waste forms exposed to radiation. Despite the significant simulation effort employed in glassy waste form research, no molecular models of radiation damage in silica include the effects of moisture. This deficiency is addressed, and water is found to play a significant role in accelerating the degradation of amorphous silica under irradiation. Water inhibits healing of the network and promotes the formation of voids into which more water can penetrate, giving way to new damage accumulation mechanisms not seen in any past simulations.

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.

Discrete persistent-chain model for protein binding on DNA.

PubMed

Lam, Pui-Man; Zhen, Yi

2011-04-01

We describe and solve a discrete persistent-chain model of protein binding on DNA, involving an extra σ(i) at a site i of the DNA. This variable takes the value 1 or 0, depending on whether or not the site is occupied by a protein. In addition, if the site is occupied by a protein, there is an extra energy cost ɛ. For a small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA. For higher forces, the model can be solved numerically to obtain force-extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force-extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of nonspecific binding. ©2011 American Physical Society

24 CFR 941.103 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... maximum project cost, as described in § 941.306: (1) Demolition of, or remediation of environmental... utility systems, and replacement of off-site underground utility systems, extensive rock and/or soil... preparation), administration, site acquisition, relocation, demolition of, and site remediation of...

Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

PubMed Central

Yoder, Anne D.; Chan, Lauren M.; dos Reis, Mario; Larsen, Peter A.; Campbell, C. Ryan; Rasoloarison, Rodin; Barrett, Meredith; Roos, Christian; Kappeler, Peter; Bielawski, Joseph; Yang, Ziheng

2014-01-01

Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available. PMID:24398377

77 FR 49021 - Notice of Proposed Withdrawal Extension and Opportunity for Public Meeting; AK

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-15

... resource integrity of the Paleoindian site known as Mesa Site. This notice gives an opportunity for the... laws, but not from leasing under the mineral leasing laws, to protect a Paleoindian site known as Mesa... protect the Federal interest in the Mesa Site. There are no suitable alternative sites available that...

Genesis and continuity of quaternary sand and gravel in glacigenic sediment at a proposed low-level radioactive waste disposal site in east-central Illinois

USGS Publications Warehouse

Troost, K.G.; Curry, B. Brandon

1991-01-01

The Illinois Department of Nuclear Safety has characterized the Martinsville Alternative Site (MAS) for a proposed low-level radioactive waste disposal facility. The MAS is located in east-central Illinois approximately 1.6 km (1 mi) north of the city of Martinsville. Geologic investigation of the 5.5-km2 (1380-acre) site revealed a sequence of chiefly Illinoian glacigenic sediments from 6 to 60 m (20-200 ft) thick overlying two major bedrock valleys carved in Pennsylvanian strata. Relatively permeable buried units include basal, preglacial alluvium; a complex of intraglacial and subglacial sediment; englacial deposits; and supraglacial fluvial deposits. Postglacial alluvium underlies stream valleys on and adjacent to the site. In most areas, the buried sand units are confined by low-permeability till, lacustrine sediment, colluvium, and loess. The distribution and thickness of the most extensive and continuous buried sand units have been modified considerably by subglacial erosion, and their distributions have been influenced by the buried bedrock valleys. The most continuous of the various sand units were deposited as preglacial and postglacial alluvium and are the uppermost and lowermost stratigraphic units at the alternative site. Sand units that were deposited in englacial or ice-marginal environments are less continuous. Aquifer pumping tests, potentiometric head data, and groundwater geochemistry analyses indicate minimal interaction of groundwater across localized interconnections of the permeable units. ?? 1991 Springer-Verlag New York Inc.

Structure of the human gene encoding the protein repair L-isoaspartyl (D-aspartyl) O-methyltransferase.

PubMed

DeVry, C G; Tsai, W; Clarke, S

1996-11-15

The protein L-isoaspartyl/D-aspartyl O-methyltransferase (EC 2.1.1.77) catalyzes the first step in the repair of proteins damaged in the aging process by isomerization or racemization reactions at aspartyl and asparaginyl residues. A single gene has been localized to human chromosome 6 and multiple transcripts arising through alternative splicing have been identified. Restriction enzyme mapping, subcloning, and DNA sequence analysis of three overlapping clones from a human genomic library in bacteriophage P1 indicate that the gene spans approximately 60 kb and is composed of 8 exons interrupted by 7 introns. Analysis of intron/exon splice junctions reveals that all of the donor and acceptor splice sites are in agreement with the mammalian consensus splicing sequence. Determination of transcription initiation sites by primer extension analysis of poly(A)+ mRNA from human brain identifies multiple start sites, with a major site 159 nucleotides upstream from the ATG start codon. Sequence analysis of the 5'-untranslated region demonstrates several potential cis-acting DNA elements including SP1, ETF, AP1, AP2, ARE, XRE, CREB, MED-1, and half-palindromic ERE motifs. The promoter of this methyltransferase gene lacks an identifiable TATA box but is characterized by a CpG island which begins approximately 723 nucleotides upstream of the major transcriptional start site and extends through exon 1 and into the first intron. These features are characteristic of housekeeping genes and are consistent with the wide tissue distribution observed for this methyltransferase activity.

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...

77 FR 76474 - Extension of Public Review and Comment Period for the Draft Programmatic Environmental Assessment...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-28

... Nuclear Security Administration (NNSA) Web site at: http://www.nnsa.energy.gov/nepa . Comments on the... DEPARTMENT OF ENERGY Extension of Public Review and Comment Period for the Draft Programmatic...: Department of Energy. ACTION: Extension of public review and comment period. SUMMARY: On December 12, 2012...

75 FR 443 - Public Land Order No. 7738; Extension of Public Land Order No. 6760, Nevada

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-05

... extension is necessary to continue protection of the Federal investment in the U.S. Forest Service Austin... made requires this extension to continue protection of the Federal investment in the Austin... leasing laws, to protect the Federal investment in the Austin Administrative Site, is hereby extended for...

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.

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

Organic carbon isotopes through the mid-Miocene: lack of a global signal

NASA Astrophysics Data System (ADS)

Gröcke, D. R.; Diester-Haaß, L.; Billups, K.

2006-12-01

The mid-Miocene Monterey Event is characterized by a period of extreme warmth and heaviest benthic and planktic δ13C values of the Cenozoic, followed by rapid cooling and associated extension of Antarctic ice sheets and decreasing δ13C values since ca. 14 Ma. We present bulk organic-carbon results from three ODP sites located in the Atlantic Ocean (Sites 608, 925, and 1265). What is initially apparent in the δ13Corg records from these sites is the lack of a positive δ13C excursion that is recorded in foraminifera. In a concurrent study, benthic foraminiferal accumulation rate derived productivity increases at all three sites between 17.5 13.5 Ma, paralleling the general trend of increasing foraminiferal δ13C records. However, an inverse relationship between δ13Corg and foraminiferal- derived productivity rates suggest that productivity is driven by cyclic changes in upwelling of oxidized, nutrient-rich bottom waters. During this period also there is no change in delta-delta between carbonate and organic matter, which indicates that there were no changes in pCO2 during the mid-Miocene. Also, δ13Corg values are typical of C3 photosynthesis in Site 608 and 1265 however the equatorial site (925) shows considerable variation suggestive of the presence of C3 input back to at least 16 Ma. Further work on δ13Corg and productivity proxies through the Miocene is critical in order to understand the global carbon cycle in the oceanic and atmospheric realms.

Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

PubMed

Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

Genome-wide activity of unliganded estrogen receptor-α in breast cancer cells

PubMed Central

Caizzi, Livia; Ferrero, Giulio; Cutrupi, Santina; Cordero, Francesca; Ballaré, Cecilia; Miano, Valentina; Reineri, Stefania; Ricci, Laura; Friard, Olivier; Testori, Alessandro; Corà, Davide; Caselle, Michele; Di Croce, Luciano; De Bortoli, Michele

2014-01-01

Estrogen receptor-α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions that are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in the absence of ligands and its functions on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ERα binds to more than 4,000 chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ERα binding is specifically linked to genes with developmental functions, compared with estrogen-induced binding. Moreover, we found that siRNA-mediated down-regulation of ERα in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Down-regulated mRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ERα down-regulation using shRNA, which caused cell growth arrest, was accompanied by increased H3K27me3 at ERα binding sites. Finally, we found that FOXA1 and AP2γ binding to several sites is decreased upon ERα silencing, suggesting that unliganded ERα participates, together with other factors, in the maintenance of the luminal-specific cistrome in breast cancer cells. PMID:24639548

Post-release monitoring of Antillean manatees: an assessment of the Brazilian rehabilitation and release programme

USGS Publications Warehouse

Normande, Iran C.; Malhado, Ana C. M.; Reid, James P.; Viana Junior, P.C.; Savaget, P. V. S.; Correia, R. A.; Luna, F. O.; R. J. Ladle,

2016-01-01

Mammalian reintroduction programmes frequently aim to reconnect isolated sub-populations and restore population viability. However, these long-term objectives are rarely evaluated due to the inadequacy of post-release monitoring. Here, we report the results of a unique long term telemetry-based monitoring programme for rehabilitated Antillean manatees (Trichechus manatus manatus) reintroduced into selected sites in northeast Brazil with the aim of reconnecting isolated relict populations. Twenty-one satellite-tagged rehabilitated manatees, 13 males and 8 females, were released into the wild from two sites between November 2008 and June 2013. Individual accumulation curves were plotted and home ranges were calculated through the fixed kernel method using 95% of the utilization distribution. The number and size of the Centres of Activity (COAs) were calculated using 50% of the utilization distribution. Manatees displayed a dichotomous pattern of movement, with individuals either characterized by sedentary habits or by much more extensive movements. Moreover, home range size was not significantly influenced by gender, age at release or release site. COAs were strongly associated with sheltered conditions within reefs and estuaries, and also by the presence of freshwater and feeding sites. Our data confirm that manatee reintroductions in Brazil have the potential to reconnect distant sub-populations. However, pre-release identification of potential long-distance migrants is currently unfeasible, and further analysis would be required to confirm genetic mixing of distant sub-populations.

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing.

PubMed

Massana, Ramon; Gobet, Angélique; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Chambouvet, Aurélie; Christen, Richard; Claverie, Jean-Michel; Decelle, Johan; Dolan, John R; Dunthorn, Micah; Edvardsen, Bente; Forn, Irene; Forster, Dominik; Guillou, Laure; Jaillon, Olivier; Kooistra, Wiebe H C F; Logares, Ramiro; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C; Probert, Ian; Romac, Sarah; Richards, Thomas; Santini, Sébastien; Shalchian-Tabrizi, Kamran; Siano, Raffaele; Simon, Nathalie; Stoeck, Thorsten; Vaulot, Daniel; Zingone, Adriana; de Vargas, Colomban

2015-10-01

Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

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...

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.

Cultured allogenic keratinocytes for extensive burns: a retrospective study over 15 years.

PubMed

Auxenfans, Celine; Shipkov, Hristo; Bach, Christine; Catherine, Zulma; Lacroix, Pierre; Bertin-Maghit, Marc; Damour, Odile; Braye, Fabienne

2014-02-01

The aim was to review the use and indications of cultured allogenic keratinocytes (CAlloK) in extensive burns and their efficiency. This retrospective study comprised 15 years (1997-2012). all patients who received CAlloK. patients who died before complete healing. Evaluation criteria were clinical. Time and success of wound healing after CAlloK use were evaluated. The CAlloK were used for 2 indications - STSG donor sites and deep 2nd degree burns in extensively burned patients. A total of 70 patients were included with severity Baux score of 99.2 (from 51 to 144) and mean percentage of TBSA of 63.49% (from 21 to 96%). Fifty nine patients received CAlloK for STSG donor sites with a mean number of applications of 4 and mean surface of 3800 cm(2) per patient. Treated donor sites were re-harvested 2.5 times. The mean time of complete epithelialization was 7 days. In 11 patients, CAlloK were used for deep 2nd degree burns. The mean percentage of burned surface was 73.7%. The mean surface of CAlloK per patient was 2545 cm(2). Complete healing was achieved in 6.4 days. The CAlloK allow rapid healing of STSG donor-sites and deep 2nd second degree burns in extensively burned patients. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

Cadmium cycling in the water column of the Kuroshio-Oyashio Extension region: Insights from dissolved and particulate isotopic composition

NASA Astrophysics Data System (ADS)

Yang, Shun-Chung; Zhang, Jing; Sohrin, Yoshiki; Ho, Tung-Yuan

2018-07-01

We measured dissolved and particulate Cd isotopic composition in the water column of a meridional transect across the Kuroshio-Oyashio Extension region in a Japanese GEOTRACES cruise to investigate the relative influence of physical and biogeochemical processes on Cd cycling in the Northwestern Pacific Ocean. Located at 30-50°N along 165°E, the transect across the extension region possesses dramatic hydrographic contrast. Cold surface water and a relatively narrow and shallow thermocline characterizes the Oyashio Extension region in contrast to a relatively warm and highly stratified surface water and thermocline in the Kuroshio Extension region. The contrasting hydrographic distinction at the study site provides us with an ideal platform to investigate the spatial variations of Cd isotope fractionation systems in the ocean. Particulate samples demonstrated biologically preferential uptake of light Cd isotopes, and the fractionation effect varied dramatically in the surface water of the two regions, with relatively large fractionation factors in the Oyashio region. Based on the relationship of dissolved Cd concentrations and isotopic composition, we found that a closed system fractionation model can reasonably explain the relationship in the Kuroshio region. However, using dissolved Cd isotopic data, either a closed system or steady-state open system fractionation model may explain the relationship in the surface water of the Oyashio region. Particulate δ114/110Cd data further supports that the surface water of the Oyashio region matches a steady-state open system model more closely. Contrary to the surface water, the distribution of potential density exhibits comparable patterns with Cd elemental and isotopic composition in the thermocline and deep water in the two extension regions, showing that physical processes are the dominant forcing controlling Cd cycling in the deep waters. The results demonstrate that Cd isotope fractionation can match either a closed or open system Rayleigh fractionation model, depending on the relative contribution of physical and biogeochemical processes on its cycling.

Goethite surface reactivity: a macroscopic investigation unifying proton, chromate, carbonate, and lead(II) adsorption.

PubMed

Villalobos, Mario; Pérez-Gallegos, Ayax

2008-10-15

The goethite surface structure has been extensively studied, but no convincing quantitative description of its highly variable surface reactivity as inversely related to its specific surface area (SSA) has been found. The present study adds experimental evidence and provides a unified macroscopic explanation to this anomalous behavior from differences in average adsorption capacities, and not in average adsorption affinities. We investigated the chromate anion and lead(II) cation adsorption behavior onto three different goethites with SSA varying from 50 to 94 m(2)/g, and analyzed an extensive set of published anion adsorption and proton charging data for variable SSA goethites. Maximum chromate adsorption was found to occupy on average from 3.1 to 9.7 sites/nm(2), inversely related to SSA. Congruency of oxyanion and Pb(II) adsorption behavior based on fractional site occupancy using these values, and a site density analysis suggest that: (i) ion binding occurs to singly and doubly coordinated sites, (ii) proton binding occurs to singly and triply coordinated sites (ranging from 6.2 to 8 total sites/nm(2), in most cases), and (iii) a predominance of (210) and/or (010) faces explains the high reactivity of low SSA goethites. The results imply that the macroscopic goethite adsorption behavior may be predicted without a need to investigate extensive structural details of each specific goethite of interest.

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...

Characterization of the human UDP-galactose:ceramide galactosyltransferase gene promoter.

PubMed

Tencomnao, T; Yu, R K; Kapitonov, D

2001-02-16

UDP-galactose:ceramide galactosyltransferase (CGT, EC 2.4.1.45) is a key enzyme in the biosynthesis of galactocerebroside, the most abundant glycosphingolipid in the myelin sheath. An 8 kb fragment upstream from the transcription initiation site of CGT gene was isolated from a human genomic DNA library. Primer extension analysis revealed a single transcription initiation site 329 bp upstream from the ATG start codon. Neither a consensus TATA nor a CCAAT box was identified in the proximity to the transcription start site; however, this region contains a high GC content and multiple putative regulatory elements. To investigate the transcriptional regulation of CGT, a series of 5' deletion constructs of the 5'-flanking region were generated and cloned upstream from the luciferase reporter gene. By comparing promoter activity in the human oligodendroglioma (HOG) and human neuroblastoma (LAN-5) cell lines, we found that the CGT promoter functions in a cell type-specific manner. Three positive cis-acting regulatory regions were identified, including a proximal region at -292/-256 which contains the potential binding sites for known transcription factors (TFs) such as Ets and SP1 (GC box), a distal region at -747/-688 comprising a number of binding sites such as the ERE half-site, NF1-like, TGGCA-BP, and CRE, and a third positive cis-acting region distally localized at -1325/-1083 consisting of binding sites for TFs such as nitrogen regulatory, TCF-1, TGGCA-BP, NF-IL6, CF1, bHLH, NF1-like, GATA, and gamma-IRE. A negative cis-acting domain localized in a far distal region at -1594/-1326 was also identified. Our results suggest the presence of both positive and negative cis-regulatory regions essential for the cell-specific expression in the TATA-less promoter of the human CGT gene.

COSTS TO REMEDIATE MTBE-CONTAMINATED SITES

EPA Science Inventory

The extensive contamination of methyl tert-butyl ether (MTBE) in ground water has introduced concerns about the increased cost of remediation of MTBE releases compared to sites with BTEX only contamination. In an attempt to evaluate these costs, cost information for 311 sites wa...

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...

Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440

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

Elmore, Joshua R.; Furches, Anna; Wolff, Gara N.

Pseudomonas putida strains are highly robust bacteria known for their ability to efficiently utilize a variety of carbon sources, including aliphatic and aromatic hydrocarbons. Recently, P. putida has been engineered to valorize the lignin stream of a lignocellulosic biomass pretreatment process. Nonetheless, when compared to platform organisms such as Escherichia coli, the toolkit for engineering P. putida is underdeveloped. Heterologous gene expression in particular is problematic. Plasmid instability and copy number variance provide challenges for replicative plasmids, while use of homologous recombination for insertion of DNA into the chromosome is slow and laborious. Furthermore, heterologous expression efforts to date typicallymore » rely on overexpression of exogenous pathways using a handful of poorly characterized promoters. In order to improve the P. putida toolkit, we developed a rapid genome integration system using the site-specific recombinase from bacteriophage Bxb1 to enable rapid, high efficiency integration of DNA into the P. putida chromosome. We also developed a library of synthetic promoters with various UP elements, -35 sequences, and -10 sequences, as well as different ribosomal binding sites. We tested these promoters using a fluorescent reporter gene, mNeonGreen, to characterize the strength of each promoter, and identified UP-element-promoter-ribosomal binding sites combinations capable of driving a ~150-fold range of protein expression levels. One additional integrating vector was developed that confers more robust kanamycin resistance when integrated at single copy into the chromosome. This genome integration and reporter systems are extensible for testing other genetic parts, such as examining terminator strength, and will allow rapid integration of heterologous pathways for metabolic engineering.« less

Isolation and characterization of the hemichrome-stabilized membrane protein aggregates from sickle erythrocytes. Major site of autologous antibody binding.

PubMed

Kannan, R; Labotka, R; Low, P S

1988-09-25

Because the interaction of denatured hemoglobins (i.e. hemichromes) with the red cell membrane has been associated with several abnormalities commonly observed in hemichrome-containing erythrocytes, we have undertaken to isolate and characterize the hemichrome-rich membrane protein aggregates from sickle cells. The aggregates were isolated by two procedures: one at low ionic strength by centrifugation of detergent-solubilized spectrin-depleted inside-out vesicles, and the other at physiological ionic strength by detergent solubilization of whole cells followed by cytoskeletal disruption and centrifugation. The extensively washed aggregates obtained by both methods yielded similar results. These insoluble complexes were found to be highly cross-linked by predominantly intermolecular disulfide bonds; however, other nonreducible covalent linkages were also observed. Both in the presence and absence of reducing agents, the aggregate disintegrated when the hemichromes were removed by high ionic strength, suggesting that the aggregate depended heavily on the cohesive properties of the hemichromes for stability. Protein assays demonstrated that the aggregates comprised approximately 1.3% of the total membrane protein, roughly two-thirds of which appeared to be globin chains. Other major components identified in the aggregate were band 3, ankyrin, bands 4.1, 4.9, and 5, glycophorins A and B, and autologous IgG. Quantitative analysis of the IgG content demonstrated that three-fourths of the surface-bound IgG on washed sickle cells was clustered at these aggregate sites, representing an enrichment of approximately 250-fold over nonaggregated regions of the membrane. Since clustered cell surface IgG is thought to trigger removal of erythrocytes from circulation, the hemichrome-induced membrane reorganization at these aggregate sites may be an important cause of the greatly shortened life span of sickle cells.

Chemical climatology of the southeastern United States, 1999-2013

NASA Astrophysics Data System (ADS)

Hidy, G. M.; Blanchard, C. L.; Baumann, K.; Edgerton, E.; Tanenbaum, S.; Shaw, S.; Knipping, E.; Tombach, I.; Jansen, J.; Walters, J.

2014-06-01

A series of experiments (the Southern Oxidant and Aerosol Study-SOAS) took place in central Alabama in June-July 2013 as part of the broader Southern Atmosphere Study (SAS). These projects were aimed at studying oxidant photochemistry and formation and impacts of aerosols at a detailed process level in a location where high biogenic organic vapor emissions interact with anthropogenic emissions, and the atmospheric chemistry occurs in a subtropical climate in North America. The majority of the ground-based experiments were located at the Southeastern Aerosol Research and Characterization (SEARCH) Centreville (CTR) site near Brent, Alabama, where extensive, unique aerometric measurements of meteorology, trace gases and particles have been made from the early 1990s through 2013. The SEARCH network data permits a characterization of temporal and spatial context of the SOAS findings. The long-term measurements show that the SOAS experiments took place during the second wettest and coolest year in the 2000-2013 period, with lower than average solar radiation. The pollution levels at CTR and other SEARCH sites were the lowest since full measurements began in 1999. This dataset provides a perspective for the SOAS program in terms of long-term average chemistry (chemical climatology) and short-term comparisons of summer average spatial variability across the Southeast at high temporal (hourly) resolution. Changes in anthropogenic gas and particle emissions between 1999 and 2013, account for the decline in pollutant concentrations at the monitoring sites in the region. The long-term and short-term data provide an opportunity to contrast SOAS results with temporally and spatially variable conditions in support for the development of tests for the robustness of SOAS findings.

Water quality following extensive beetle-induced tree mortality: Interplay of aromatic carbon loading, disinfection byproducts, and hydrologic drivers.

PubMed

Brouillard, Brent M; Dickenson, Eric R V; Mikkelson, Kristin M; Sharp, Jonathan O

2016-12-01

The recent bark beetle epidemic across western North America may impact water quality as a result of elevated organic carbon release and hydrologic shifts associated with extensive tree dieback. Analysis of quarterly municipal monitoring data from 2004 to 2014 with discretization of six water treatment facilities in the Rocky Mountains by extent of beetle impact revealed a significant increasing trend in total organic carbon (TOC) and total trihalomethane (TTHM) production within high (≳50% areal infestation) beetle-impacted watersheds while no or insignificant trends were found in watersheds with lower impact levels. Alarmingly, the TTHM concentration trend in the high impact sites exceeded regulatory maximum contaminant levels during the most recent two years of analysis (2013-14). To evaluate seasonal differences, explore the interplay of water quality and hydrologic processes, and eliminate variability associated with municipal reporting, these treatment facilities were targeted for more detailed surface water sampling and characterization. Surface water samples collected from high impact watersheds exhibited significantly higher TOC, aromatic signatures, and disinfection byproduct (DBP) formation potential than watersheds with lower infestation levels. Spectroscopic analyses of surface water samples indicated that these heightened DBP precursor levels are a function of both elevated TOC loading and increased aromatic character. This association was heightened during precipitation and runoff events in high impact sites, supporting the hypothesis that altered hydrologic flow paths resulting from tree mortality mobilize organic carbon and elevate DBP formation potential for several months after runoff ceases. The historical trends found here likely underestimate the full extent of TTHM shifts due to monitoring biases with the extended seasonal release of DBP precursors increasing the potential for human exposure. Collectively, our analysis suggests that while water quality impacts continue to rise nearly one decade after infestation, significant increases in TOC mobilization and DBP precursors are limited to watersheds that experience extensive tree mortality. Copyright © 2016 Elsevier B.V. All rights reserved.

Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain.

PubMed

Buczek, Pawel; Horvath, Martin P

2006-06-23

The Oxytricha nova telemere binding protein alpha subunit binds single strand DNA and participates in a nucleoprotein complex that protects the very ends of chromosomes. To understand how the N-terminal, DNA binding domain of alpha interacts with DNA we measured the stoichiometry, enthalpy (DeltaH), entropy (DeltaS), and dissociation constant (K(D-DNA)) for binding telomere DNA fragments at different temperatures and salt concentrations using native gel electrophoresis and isothermal titration calorimetry (ITC). About 85% of the total free energy of binding corresponded with non-electrostatic interactions for all DNAs. Telomere DNA fragments d(T(2)G(4)), d(T(4)G(4)), d(G(3)T(4)G(4)), and d(G(4)T(4)G(4)) each formed monovalent protein complexes. In the case of d(T(4)G(4)T(4)G(4)), which has two tandemly repeated d(TTTTTGGGG) telomere motifs, two binding sites were observed. The high-affinity "A site" has a dissociation constant, K(D-DNA(A)) = 13(+/-4) nM, while the low-affinity "B site" is characterized by K(D-DNA(B)) = 5600(+/-600) nM at 25 degrees C. Nucleotide substitution variants verified that the A site corresponds principally with the 3'-terminal portion of d(T(4)G(4)T(4)G(4)). The relative contributions of entropy (DeltaS) and enthalpy (DeltaH) for binding reactions were DNA length-dependent as was heat capacity (DeltaCp). These trends with respect to DNA length likely reflect structural transitions in the DNA molecule that are coupled with DNA-protein association. Results presented here are important for understanding early intermediates and subsequent stages in the assembly of the full telomere nucleoprotein complex and how binding events can prepare the telomere DNA for extension by telomerase, a critical event in telomere biology.

Statistics for stochastic modeling of volume reduction, hydrograph extension, and water-quality treatment by structural stormwater runoff best management practices (BMPs)

USGS Publications Warehouse

Granato, Gregory E.

2014-01-01

The U.S. Geological Survey (USGS) developed the Stochastic Empirical Loading and Dilution Model (SELDM) in cooperation with the Federal Highway Administration (FHWA) to indicate the risk for stormwater concentrations, flows, and loads to be above user-selected water-quality goals and the potential effectiveness of mitigation measures to reduce such risks. SELDM models the potential effect of mitigation measures by using Monte Carlo methods with statistics that approximate the net effects of structural and nonstructural best management practices (BMPs). In this report, structural BMPs are defined as the components of the drainage pathway between the source of runoff and a stormwater discharge location that affect the volume, timing, or quality of runoff. SELDM uses a simple stochastic statistical model of BMP performance to develop planning-level estimates of runoff-event characteristics. This statistical approach can be used to represent a single BMP or an assemblage of BMPs. The SELDM BMP-treatment module has provisions for stochastic modeling of three stormwater treatments: volume reduction, hydrograph extension, and water-quality treatment. In SELDM, these three treatment variables are modeled by using the trapezoidal distribution and the rank correlation with the associated highway-runoff variables. This report describes methods for calculating the trapezoidal-distribution statistics and rank correlation coefficients for stochastic modeling of volume reduction, hydrograph extension, and water-quality treatment by structural stormwater BMPs and provides the calculated values for these variables. This report also provides robust methods for estimating the minimum irreducible concentration (MIC), which is the lowest expected effluent concentration from a particular BMP site or a class of BMPs. These statistics are different from the statistics commonly used to characterize or compare BMPs. They are designed to provide a stochastic transfer function to approximate the quantity, duration, and quality of BMP effluent given the associated inflow values for a population of storm events. A database application and several spreadsheet tools are included in the digital media accompanying this report for further documentation of methods and for future use. In this study, analyses were done with data extracted from a modified copy of the January 2012 version of International Stormwater Best Management Practices Database, designated herein as the January 2012a version. Statistics for volume reduction, hydrograph extension, and water-quality treatment were developed with selected data. Sufficient data were available to estimate statistics for 5 to 10 BMP categories by using data from 40 to more than 165 monitoring sites. Water-quality treatment statistics were developed for 13 runoff-quality constituents commonly measured in highway and urban runoff studies including turbidity, sediment and solids; nutrients; total metals; organic carbon; and fecal coliforms. The medians of the best-fit statistics for each category were selected to construct generalized cumulative distribution functions for the three treatment variables. For volume reduction and hydrograph extension, interpretation of available data indicates that selection of a Spearman’s rho value that is the average of the median and maximum values for the BMP category may help generate realistic simulation results in SELDM. The median rho value may be selected to help generate realistic simulation results for water-quality treatment variables. MIC statistics were developed for 12 runoff-quality constituents commonly measured in highway and urban runoff studies by using data from 11 BMP categories and more than 167 monitoring sites. Four statistical techniques were applied for estimating MIC values with monitoring data from each site. These techniques produce a range of lower-bound estimates for each site. Four MIC estimators are proposed as alternatives for selecting a value from among the estimates from multiple sites. Correlation analysis indicates that the MIC estimates from multiple sites were weakly correlated with the geometric mean of inflow values, which indicates that there may be a qualitative or semiquantitative link between the inflow quality and the MIC. Correlations probably are weak because the MIC is influenced by the inflow water quality and the capability of each individual BMP site to reduce inflow concentrations.

First evidence of an extensive Acheulean large cutting tool accumulation in Europe from Porto Maior (Galicia, Spain).

PubMed

Méndez-Quintas, E; Santonja, M; Pérez-González, A; Duval, M; Demuro, M; Arnold, L J

2018-02-15

We describe a European Acheulean site characterised by an extensive accumulation of large cutting tools (LCT). This type of Lower Paleolithic assemblage, with dense LCT accumulations, has only been found on the African continent and in the Near East until now. The identification of a site with large accumulations of LCTs favours the hypothesis of an African origin for the Acheulean of Southwest Europe. The lithic tool-bearing deposits date back to 293-205 thousand years ago. Our chronological findings confirm temporal overlap between sites with clear "African" Acheulean affinities and Early Middle Paleolithic sites found elsewhere in the region. These complex technological patterns could be consistent with the potential coexistence of different human species in south-western Europe during the Middle Pleistocene.

A Needs Assessment of Aquaculture Extension Agents, Specialists, and Program Administrators in Extension Programming

ERIC Educational Resources Information Center

Schwarz, Michael H.; Gibson, Jerry

2010-01-01

The study reported here identified continuing education and training needs of aquaculture Extension agents, specialists, and program administrators in 10 competency areas relating to the need for continuing education or training. Fourteen resources on the AquaNIC Web site were also evaluated, as was the efficacy of the AQUA-EXT listserv. Data were…

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.

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.

A climatology of weather-driven mixing events in a dimictic Arctic lake

NASA Astrophysics Data System (ADS)

Cooke, Melanie; MacIntyre, Sally; Kushner, Paul

2014-05-01

For dimictic and polymictic Arctic lakes, mixing during the ice-free season is primarily controlled by the passage of cold fronts and their associated strong winds. At Toolik Lake, a Long Term Ecological Research site in Alaska, year-to-year variability in lake stability and mixing frequency has been considerable over the past 14 summers. Mixing is important for lake productivity, distributing dissolved gases and nutrients through the water column. Summertime Arctic warming might be expected to stabilize Arctic lakes such as Toolik, but the control of individual weather events on a season's mixing characteristics complicates the ability to predict trends in stability and mixing. With this motivation, this work aims to characterize weather systems that are conducive to mixing at Toolik. High resolution lake and meteorological data from the site were used to characterize mixing while atmospheric reanalysis data were used to describe the weather systems. Mixing events were first identified using an automated algorithm based on Lake Number and lake thermal structure. The algorithm identified mixing events that are separated by at least the timescale of weather systems, so that any given weather event should cause at most one mixing event. Because low Lake Number conditions typically highlight strong wind events, temperature profile data over time were used to identify thermocline deepening as a complementary indicator for mixing. Mixing events were found to be most often characterized by simultaneous occurrence of a low Lake Number condition and thermocline deepening. Once mixing events were identified, they were classified according to their corresponding atmospheric structures. Two primary weather system types with distinct characteristics were determined to be associated with mixing. The analysis suggests that changing the occurrence of these weather system types might change the summertime thermal structure of Toolik Lake, and by extension other lakes in the region.

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

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.

Comparative Geostatistical Analysis of Flowmeter and Direct-Push Hydraulic Conductivity Profiles at the MADE Site

NASA Astrophysics Data System (ADS)

Bohling, G.; Liu, G.; Knobbe, S. J.; Reboulet, E. C.; Hyndman, D. W.; Dietrich, P.; Butler, J. J.

2010-12-01

Spatial variations in hydraulic conductivity (K) are a critical control on subsurface solute transport. Characterization of such variations at the resolution (cm to dm) required for transport investigations, however, has proven to be a formidable challenge. A new generation of direct-push (DP) tools has now been developed for the characterization of vertical K variations at this resolution. These tools, which can be run in high- (0.015-m) and low- (0.4 m) resolution modes, were recently applied to the extensively studied and highly heterogeneous MADE site. Results from a geostatistical analysis of 64 DP K profiles compare favorably with the flowmeter K data that have served as the primary basis for previous MADE studies. The global statistics of the low-resolution DP and flowmeter K data are in excellent agreement. The correlation structures for the high-resolution DP data show excellent agreement with those computed from the flowmeter data. However, the geometric mean DP K value for high-resolution profiling is roughly one order of magnitude lower than the geometric mean flowmeter K value, possibly as a result of the biases inherent in each approach compounded with differences in the areal distribution of flowmeter and DP profile locations. A DP profile through the MADE aquifer to a depth of 12 m can be completed as rapidly as 1.5-2 hours, a small fraction of the time required to obtain a single flowmeter profile when well drilling, installation, and development are considered. The results of this study demonstrate that DP profiling is a practically feasible approach for characterization of spatial variations in K at the resolution required for transport investigations in highly heterogeneous systems.

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

On Goal-Oriented, Hydrogeological Site Investigation: A Holistic Approach (Henry Darcy Medal Lecture)

NASA Astrophysics Data System (ADS)

Rubin, Yoram

2016-04-01

UQ (for Uncertainty Quantification) is a critical element of groundwater management and by extension, of hydrological site investigation. While it is clear that UQ is an important goal, there is ambiguity as to what the target of the UQ should be, and how to make UQ relevant in the context of public policy. Planning for UQ (meaning what measurements to take, where, how many, what frequency, etc.), one could consider environmental performance parameters (EPMs, such as concentrations or travel time) as the targets of site investigation. But there is a need to go beyond EPMs, and to consider the uncertainty related to impacts such as enhanced cancer-risk due to groundwater contamination or, more generally, to decisions facing regulators. In any case, UQ requires site investigation, and decision-makers, who end up paying for it, are not really interested in EPMs: they care about making operational decisions that are defensible legally and justified from the perspective of public good. The key to UQ, whether considering EPMS or operational decisions concerning the public good, is defining a suitable strategy for site investigation. There is a body of published works on relating site investigations with EPMs, but much less is known on how to support operational decisions with strategies for site characterization. In this lecture, I will address this issue and I will outline a comprehensive approach for addressing it using a statistical formalism that couples hypothesis testing with Bayesian statistics. I refer to this approach as goal-oriented site investigation. I will show how site investigation strategies, with specifics such as which measurements to take and where, could be related to goals lined with operational decisions. This includes (1) defining the relevant goals; (2) formulating hypotheses; (3) defining alternative strategies for site investigation and (4) evaluating them in terms of probabilities for making errors in accepting or rejecting the hypotheses.

Vegetative communities, Davis and Lavender Canyons, Paradox Basin, Utah: ecosystem studies

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

Not Available

1983-04-01

The major vegetative communities of Davis and Lavender canyons located in southeastern Utah are characterized. The report identifies potential secondary impacts and appropriate mitigation options. The Davis Canyon and Lavender Canyon Study Area contains nine major vegetative communities: galleta-shadscale, juniper-blackbrush, juniper-shadscale-ephedra, shadscale-ephedra, grayia-shadscale, juniper, drywash, greasewood, and riparian. The natural recovery times of these communities are exceedingly long. Natural reinvasion of various species would take from 15 to 100 years. No threatened or endangered plant species were identified in the study area. Davis and Lavender canyons have been subject to off-road vehicle activity and extensive grazing. The plant communities maymore » be subject to additional impacts as a result of increased human activity and off-highway activities such as camping, hiking, and hunting could result in changes in cover, composition, and frequency of plant species. Mitigation options for potential impacts include shuttle-busing workers to the site from the highway and fencing site access roads to prevent vehicles from leaving the roads.« less

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.

Management of Chronic Hyperplastic Pulpitis in Mandibular Molars of Middle Aged Adults- A Multidisciplinary Approach

PubMed Central

Lingeswaran, Somiya; Ari, Geetha; Thyagarajan, Ramakrishnan; Logaranjani, Anitha

2016-01-01

The molar tooth of children and young adults is a common site for chronic hyperplastic pulpitis (pulp polyp). It rarely occurs in middle aged adults. This condition is usually characterized by extensive involvement of the pulp, dictating the extraction of involved tooth. Extraction of permanent molars can lead to transient or permanent malocclusion, aesthetic, phonetic and functional problems. Here we report a case of pulp polyp in mandibular first molar of a 33-year-old woman that grew into the carious cavity. The aim of this case report is to describe the diagnosis of a chronic hyperplastic pulpitis involving the permanent molar as well as to describe its management in order to preserve them as a functional unit of the dentition. PMID:26894192

Management of Chronic Hyperplastic Pulpitis in Mandibular Molars of Middle Aged Adults- A Multidisciplinary Approach.

PubMed

Anilkumar, Kanakamedala; Lingeswaran, Somiya; Ari, Geetha; Thyagarajan, Ramakrishnan; Logaranjani, Anitha

2016-01-01

The molar tooth of children and young adults is a common site for chronic hyperplastic pulpitis (pulp polyp). It rarely occurs in middle aged adults. This condition is usually characterized by extensive involvement of the pulp, dictating the extraction of involved tooth. Extraction of permanent molars can lead to transient or permanent malocclusion, aesthetic, phonetic and functional problems. Here we report a case of pulp polyp in mandibular first molar of a 33-year-old woman that grew into the carious cavity. The aim of this case report is to describe the diagnosis of a chronic hyperplastic pulpitis involving the permanent molar as well as to describe its management in order to preserve them as a functional unit of the dentition.

Characterization of the electrical output of flat-plate photovoltaic arrays

NASA Technical Reports Server (NTRS)

Gonzalez, C. C.; Hill, G. M.; Ross, R. G., Jr.

1982-01-01

The electric output of flat-plate photovoltaic arrays changes constantly, due primarily to changes in cell temperature and irradiance level. As a result, array loads such as direct-current to alternating-current power conditioners must be able to accommodate widely varying input levels, while maintaining operation at or near the array maximum power point.The results of an extensive computer simulation study that was used to define the parameters necessary for the systematic design of array/power-conditioner interfaces are presented as normalized ratios of power-conditioner parameters to array parameters, to make the results universally applicable to a wide variety of system sizes, sites, and operating modes. The advantages of maximum power tracking and a technique for computing average annual power-conditioner efficiency are discussed.

Multiple, Pan-Enteric Perforation Secondary to Intestinal Tuberculosis

PubMed Central

Masood, Irfan; Majid, Zain; Rafiq, Ali; Rind, Waqas; Zia, Aisha; Raza, Sajjad

2015-01-01

Free perforation is one of the most feared complications of the intestinal tuberculosis. The terminal ileum is the most common site of perforation, while the majority of (90%) perforations are solitary. Herein, we describe a case of a 25-year-old male who presented with generalized peritonitis requiring an emergency exploratory laparotomy, which revealed pan-enteric perforation characterized by multiple perforations of the small bowel extending 10–15 cm from the DJ flexure up to the terminal ileum. The perforations were primarily closed, while 6–8 cm of the diseased terminal ileum was resected and the two ends were brought out as double-barreled ostomy. To the best of our knowledge, such an extensive tuberculous perforation of the small bowel has not been previously reported in the literature before. PMID:26798540

Structural Characterization of an Alternative Mode of Tigecycline Binding to the Bacterial Ribosome

PubMed Central

Schedlbauer, Andreas; Kaminishi, Tatsuya; Ochoa-Lizarralde, Borja; Dhimole, Neha; Zhou, Shu; López-Alonso, Jorge P.

2015-01-01

Although both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of tRNA to the ribosomal A site, tigecycline shows increased efficacy in both in vitro and in vivo activity assays and escapes the most common resistance mechanisms associated with the tetracycline class of antibiotics. These differences in activities are attributed to the tert-butyl-glycylamido side chain found in tigecycline. Our structural analysis by X-ray crystallography shows that tigecycline binds the bacterial 30S ribosomal subunit with its tail in an extended conformation and makes extensive interactions with the 16S rRNA nucleotide C1054. These interactions restrict the mobility of C1054 and contribute to the antimicrobial activity of tigecycline, including its resistance to the ribosomal protection proteins. PMID:25753625

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

Biomolecular characterization of wild sicilian oregano: phytochemical screening of essential oils and extracts, and evaluation of their antioxidant activities.

PubMed

Tuttolomondo, Teresa; La Bella, Salvatore; Licata, Mario; Virga, Giuseppe; Leto, Claudio; Saija, Antonella; Trombetta, Domenico; Tomaino, Antonio; Speciale, Antonio; Napoli, Edoardo M; Siracusa, Laura; Pasquale, Andrea; Curcuruto, Giusy; Ruberto, Giuseppe

2013-03-01

An extensive survey of wild Sicilian oregano was made. A total of 57 samples were collected from various sites, followed by taxonomic characterization from an agronomic perspective. Based on morphological and production characteristics obtained from the 57 samples, cluster analysis was used to divide the samples into homogeneous groups, to identify the best biotypes. All samples were analyzed for their phytochemical content, applying a cascade-extraction protocol and hydrodistillation, to obtain the non volatile components and the essential oils, respectively. The extracts contained thirteen polyphenol derivatives, i.e., four flavanones, seven flavones, and two organic acids. Their qualitative and quantitative characterization was carried out by LC/MS analyses. The essential oils were characterized using a combination of GC-FID and GC/MS analyses; a total of 81 components were identified. The major components of the oils were thymol, p-cymene, and γ-terpinene. Cluster analysis was carried out on both phytochemical profiles and resulted in the division of the oregano samples into different chemical groups. The antioxidant activity of the essential oils and extracts was investigated by the Folin-Ciocalteau (FC) colorimetric assay, by UV radiation-induced peroxidation in liposomal membranes (UV-IP test), and by determining the O(2)(∙-)-scavenging activity. Copyright © 2013 Verlag Helvetica Chimica Acta AG, Zürich.

Interpretation of the Relationship between Benthic Fauna, Geologic Distributions, and Methane Seeps at Southern Hydrate Ridge, Oregon Continental Margin

NASA Astrophysics Data System (ADS)

Bigham, K.; Kelley, D. S.; Delaney, J. R.

2016-12-01

Deposits of methane sequestered along continental margins and their associated seeps are found worldwide. These seeps are of increasing interest and importance because of their potential as an energy source, their contribution to greenhouse gases, and the unique community of chemosynthetic microorganisms and fauna that they host. One of the best­studied methane seep sites is Southern Hydrate Ridge, which is at a water depth of 800 m. It is located 90 km west of Newport, Oregon. Despite extensive geophysical and biological research completed here, no studies have quantified the relationship of seep sites and seafloor geology to the spatial distribution and abundances of microbial and macrofaunal communities. High resolution, georeferenced photomosaics of the individual seeps and the associated biological communities at this site were collected in 2011, using the remotely operated vehicle ROPOS. Detailed analyses of these images has allowed for the quantification and characterization of the diversity and structure of the faunal community. Results show that both the distribution and abundances of seep organisms are highly variable. Further examination of these photomosaics may improve understanding of the relationships between faunal distributions and seep locations, with implications for the impacts that chemical gradients have on these ecosystems.

Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution

PubMed Central

Duan, Yuange; Dou, Shengqian; Zhang, Hong; Wu, Changcheng; Wu, Mingming

2018-01-01

Abstract The adenosine-to-inosine (A-to-I) RNA editomes have been systematically characterized in various metazoan species, and many editing sites were found in clusters. However, it remains unclear whether the clustered editing sites tend to be linked in the same RNA molecules or not. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. This present study also suggests that linkage of editing should be considered in elucidating the functional consequences of RNA editing. PMID:29048557

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

PubMed Central

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-01-01

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. PMID:25943545

Morphology and mixing of black carbon particles collected in central California during the CARES field study

DOE PAGES

Moffet, Ryan C.; O'Brien, Rachel E.; Alpert, Peter A.; ...

2016-11-23

Aerosol absorption is strongly dependent on the internal heterogeneity (mixing state) and morphology of individual particles containing black carbon (BC) and other non-absorbing species. Here, we examine an extensive microscopic data set collected in the California Central Valley during the CARES 2010 field campaign. During a period of high photochemical activity and pollution buildup, the particle mixing state and morphology were characterized using scanning transmission X-ray microscopy (STXM) at the carbon K-edge. Observations of compacted BC core morphologies and thick organic coatings at both urban and rural sites provide evidence of the aged nature of particles, highlighting the importance ofmore » highly aged particles at urban sites during periods of high photochemical activity. Based on the observation of thick coatings and more convex BC inclusion morphology, either the aging was rapid or the contribution of fresh BC emissions at the urban site was relatively small compared to background concentrations. Most particles were observed to have the BC inclusion close to the center of the host. However, host particles containing inorganic rich inclusions had the BC inclusion closer to the edge of the particle. Furthermore, these measurements of BC morphology and mixing state provide important constraints for the morphological effects on BC optical properties expected in aged urban plumes.« less

Morphology and mixing of black carbon particles collected in central California during the CARES field study

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

Moffet, Ryan C.; O'Brien, Rachel E.; Alpert, Peter A.

Aerosol absorption is strongly dependent on the internal heterogeneity (mixing state) and morphology of individual particles containing black carbon (BC) and other non-absorbing species. Here, we examine an extensive microscopic data set collected in the California Central Valley during the CARES 2010 field campaign. During a period of high photochemical activity and pollution buildup, the particle mixing state and morphology were characterized using scanning transmission X-ray microscopy (STXM) at the carbon K-edge. Observations of compacted BC core morphologies and thick organic coatings at both urban and rural sites provide evidence of the aged nature of particles, highlighting the importance ofmore » highly aged particles at urban sites during periods of high photochemical activity. Based on the observation of thick coatings and more convex BC inclusion morphology, either the aging was rapid or the contribution of fresh BC emissions at the urban site was relatively small compared to background concentrations. Most particles were observed to have the BC inclusion close to the center of the host. However, host particles containing inorganic rich inclusions had the BC inclusion closer to the edge of the particle. Furthermore, these measurements of BC morphology and mixing state provide important constraints for the morphological effects on BC optical properties expected in aged urban plumes.« less

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...

Wireless Channel Characterization in the 5 GHz Microwave Landing System Extension Band for Airport Surface Areas

NASA Technical Reports Server (NTRS)

Matolak, David W.

2007-01-01

In this project final report, entitled "Wireless Channel Characterization in the 5 GHz Microwave Landing System Extension Band for Airport Surface Areas," we provide a detailed description and model representation for the wireless channel in the airport surface environment in this band. In this executive summary, we review report contents, describe the achieved objectives and major findings, and highlight significant conclusions and recommendations.

Decadal and seasonal changes in temperature, salinity, nitrate, and chlorophyll in inshore and offshore waters along southeast Australia

NASA Astrophysics Data System (ADS)

Kelly, Paige; Clementson, Lesley; Lyne, Vincent

2015-06-01

Sixty years of oceanographic in situ data at Port Hacking (34°S) and Maria Island (42°S) and 15 years of satellite-derived chlorophyll a (chl a) in inshore and offshore waters of southeast Australia show changes in the seasonality and trend of water properties consistent with long-term intensification and southerly extensions of East Australian Current (EAC) water. Decadal analyses reveal that the EAC extension water at Maria Island increased gradually from the 1940s to 1980s, followed by a rapid increase since the 1990s. This acceleration coincided with enhanced winter nitrate, implying increased injections of subantarctic water at Maria Island. Satellite-derived chl a at six coastal sites and offshore companion sites in the western Tasman Sea showed significant inshore-offshore variations in seasonal cycle and long-term trend. After 2004-2005, the Maria Island seasonal cycle became increasingly similar to those of Bass Strait and St. Helens, suggesting that the EAC extension water was extending further southward. Comparative analyses of inshore-offshore sites showed that the presence of EAC extension water declined offshore. Seasonal cycles at Maria Island show a recent shift away from the traditional spring bloom, toward increased winter biomass, and enhanced primary productivity consistent with extensions of warm, energetic EAC extension water and more frequent injections of cooler, fresher nitrate-replete waters. Overall, we find complex temporal, latitudinal, and inshore-offshore changes in multiple water masses, particularly at Maria Island, and changes in primary productivity that will profoundly impact fisheries and ecosystems.

THE DNAPL REMEDIATION CHALLENGE: IS THERE A CASE FOR SOURCE DEPLETION?

EPA Science Inventory

Releases of Dense Non-Aqueous Phase Liquids (DNAPLs) at a large number of public and private sector sites in the United States pose significant challenges in site remediation and long-term site management. Extensive contamination of groundwater occurs as a result of significant ...

77 FR 63437 - Notice of Extension of Public Comment Period for Environmental Impact Statement for the San...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-16

... correspondence. FOR FURTHER INFORMATION CONTACT: Chief Engineer, Engineering Service (138), San Francisco...-4810, extension 2009. The SFVAMC LRDP and Draft EIS are available for viewing on the SFVAMC Web site...

Framework for Site Characterization for Monitored Natural Attenuation of Volatile Organic Compounds in Ground Water

EPA Science Inventory

Monitored Natural Attenuation (MNA) is unique among remedial technologies in relying entirely on natural processes to achieve site-specific objectives. Site characterization is essential to provide site-specific data and interpretations for the decision-making process (i.e., to ...

Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones

PubMed Central

Schwartz, Mathieu; Didierjean, Claude; Hecker, Arnaud; Girardet, Jean-Michel; Morel-Rouhier, Mélanie; Gelhaye, Eric; Favier, Frédérique

2016-01-01

Glutathionyl-hydroquinone reductases (GHRs) belong to the recently characterized Xi-class of glutathione transferases (GSTXs) according to unique structural properties and are present in all but animal kingdoms. The GHR ScECM4 from the yeast Saccharomyces cerevisiae has been studied since 1997 when it was found to be potentially involved in cell-wall biosynthesis. Up to now and in spite of biological studies made on this enzyme, its physiological role remains challenging. The work here reports its crystallographic study. In addition to exhibiting the general GSTX structural features, ScECM4 shows extensions including a huge loop which contributes to the quaternary assembly. These structural extensions are probably specific to Saccharomycetaceae. Soaking of ScECM4 crystals with GS-menadione results in a structure where glutathione forms a mixed disulfide bond with the cysteine 46. Solution studies confirm that ScECM4 has reductase activity for GS-menadione in presence of glutathione. Moreover, the high resolution structures allowed us to propose new roles of conserved residues of the active site to assist the cysteine 46 during the catalytic act. PMID:27736955

Medical Humanitarianism Under Atmospheric Violence: Health Professionals in the 2013 Gezi Protests in Turkey.

PubMed

Aciksoz, Salih Can

2016-06-01

During the 2013 Gezi protests in Turkey, volunteering health professionals provided on-site medical assistance to protesters faced with police violence characterized by the extensive use of riot control agents. This led to a government crackdown on the medical community and the criminalization of "unauthorized" first aid amidst international criticisms over violations of medical neutrality. Drawing from ethnographic observations, in-depth interviews with health care professionals, and archival research, this article ethnographically analyzes the polarized encounter between the Turkish government and medical professionals aligned with social protest. I demonstrate how the context of "atmospheric violence"-the extensive use of riot control agents like tear gas-brings about new politico-ethical spaces and dilemmas for healthcare professionals. I then analyze how Turkish health professionals framed their provision of health services to protestors in the language of medical humanitarianism, and how the state dismissed their claims to humanitarian neutrality by criminalizing emergency care. Exploring the vexed role that health workers and medical organizations played in the Gezi protests and the consequent political contestations over doctors' ethical, professional, and political responsibilities, this article examines challenges to medical humanitarianism and neutrality at times of social protest in and beyond the Middle East.

A shift in the spatial pattern of Iberian droughts during the 17th century

NASA Astrophysics Data System (ADS)

Domínguez-Castro, F.; García-Herrera, R.; Ribera, P.; Barriendos, M.

2010-06-01

In this paper, series of drought occurrence and drought extension in the Iberian Peninsula are constructed for the 1600-1750 period from seven rogation series. These rogation ceremony records come from Bilbao, Catalonia, Zamora, Zaragoza, Toledo, Murcia and Seville. They are distributed across the Peninsula and include the areas with the most characteristic Iberian climate types, influenced by the Atlantic and the Mediterranean conditions, described from modern data. A seasonal division of the series shows that spring is a critical season for rogation series in most of Iberia, being Bilbao the only site were the highest number of rogations is detected for a different season. The annual analysis of the series shows a dramatic difference between the period 1600-1652, when droughts are characterized by its local character; and the period 1653-1749, when they affect to broader regions or even to the whole Peninsula. The analysis of spring series confirms the existence of the two periods detected in the annual analysis. Finally, secondary documentary sources are used to further characterise the two most extended droughts in the period, 1664 and 1680, and to verify the extension of the areas affected by droughts recorded through rogation series.

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants.

PubMed

Mustafa, Ghada A; Abd-Elgawad, Amr; Ouf, Amged; Siam, Rania

2016-07-01

The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported "Egyptian Red Sea Coastal Microbiome," sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identifying Internet Sites to Coordinate with National Science Education Standards

ERIC Educational Resources Information Center

Fehrenbach, Carolyn R.; Morris, Maxine G.

2004-01-01

Identifying Internet sites to coordinate with National Science Education Standards can be challenging for teachers and students. By identifying quality free Internet sites in science, teachers and students can use the extensive resources of the Internet to enhance learning and instruction while meeting National Science Education Content Standards…

10 CFR 960.3-4 - Environmental impacts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REPOSITORY Implementation Guidelines § 960.3-4 Environmental impacts. Environmental impacts shall be considered by the DOE throughout the site characterization, site selection, and repository development..., during site characterization and repository construction, operation, closure, and decommissioning. ...

Effects of the Extended Water Retention Curve on Coupled Heat and Water Transport in the Vadose Zone

NASA Astrophysics Data System (ADS)

Yang, Z.; Mohanty, B.

2017-12-01

Understanding and simulating coupled heat and water transfer appropriately in the shallow subsurface is of vital significance for accurate prediction of soil evaporation that would improve the coupling between land surface and atmosphere. The theory of Philip and de Vries (1957) and its extensions (de Vries, 1958; Milly, 1982), although physically incomplete, are still adopted successfully to describe the coupled heat and water movement in field soils. However, the adsorptive water retention, which was ignored in Philip and de Vries theory and its extensions for characterizing soil hydraulic parameters, was shown to be non-negligible for soil moisture and evaporation flux calculation in dry field soils based on a recent synthetic analysis (Mohanty and Yang, 2013). In this study, we attempt to comprehensively investigate the effects of full range water retention curve on coupled heat and water transport simulation with a focus on soil moisture content, temperature and soil evaporative flux, based on two synthetic (sand and loam) and two field sites (Riverside, California and Audubon, Arizona) analysis. The results of synthetic sand and loam numerical modeling showed that when neglecting the adsorptive water retention, the resulting simulated soil water content would be larger, and the evaporative flux would be lower, respectively, compared to that obtained by the full range water retention curve mode. The simulated temperature did not show significant difference with or without accounting for adsorptive water retention. The evaporation underestimation when neglecting the adsorptive water retention is mainly caused by isothermal hydraulic conductivity underprediction. These synthetic findings were further corroborated by the Audubon, Arizona field site experimental results. The results from Riverside, California field experimental site showed that the soil surface can reach very dry status, although the soil profile below the drying front is not dry, which also to some extent justifies the necessity of employing full range water retention function in such generally not quite dry scenarios.

SUMMARY OF TECHNIQUES AND UNIQUE USES FOR DIRECT PUSH METHODS IN SITE CHARACTERIZATION ON CONTAMINATED FIELD SITES

EPA Science Inventory

Site characterization of subsurface contaminant transport is often hampered by a lack of knowledge of site heterogeneity and temporal variations in hydrogeochemistry. Two case studies are reviewed to illustrate the utility of macro-scale mapping information along with spatially-...

Weather Conditions During the 2013 SAS/SOAS Field Campaign: Providing Meteorological Context to the Extensive Project Measurements

NASA Astrophysics Data System (ADS)

Moore, J.; Farkas, C. M.

2013-12-01

The Southeast Atmosphere Study (SAS)/Southern Oxidant and Aerosol Study (SOAS) (url: http://www.eol.ucar.edu/projects/sas/) was a joint project supported by the National Science Foundation, the Environmental Protection Agency, Electric Power Research Institute and 30 US and International Research Institutions, and was the largest U.S. air quality study in decades. This collaborative project addressed various components of air quality, chemical and aerosol constituent evolution over the SE US. An international team of investigators brought an unprecedented suite of chemical species filter sampling equipment and in-situ sensors to characterize the atmosphere and the chemical processes occurring within it with specific emphasis on the characterization of the content, form and evolution of chemical and aerosol species in the humid Southeast US from 1 June-15 July during summer. The main ';super site' brought ~100 participants and ~50 specialized samplers and analyzers to the EPRI sponsored SouthEastern Aerosol and Atmospheric Characterization (SEARCH) Network site near Brent, Alabama. The purpose of this presentation is to provide the meteorological context to the observations that were made at the central Alabama ';super site' described above. The long-term climatology of the region suggested that the weather would be relatively quiet during the period with the occasional air mass change (frontal passage) and a few days of showers and/or windy conditions. What actually happened during the 45-day campaign was generally a much more unsettled period that included several frontal passages, a large number of rainy days and cooler than normal temperatures. Table 1 provides a preliminary summary of conditions during the campaign. The number of quiet or stagnant periods that might allow the buildup of various chemical constituents important to the study were infrequent and did not last for extended periods. Contact will be made with the Alabama State Climatologist to improve our perspective about the weather conditions that transpired during the 45-day project period. The wetter than normal conditions did result in several rainfall records in the region. We will also contact colleagues at the other ground sites (Look Rock, TN and Raleigh, NC) to compare and contrast their weather conditions during the SOAS deployment.Table 1. Preliminary summary of general weather conditions during the 45 day SOAS campaign during June-July, 2013

Use of ultra-lightweight geofoam to reduce stresses in highway culvert extensions.

DOT National Transportation Integrated Search

2005-10-01

Culvert extension under highway embankment construction is a regular and important practice when roadway widening occurs. At some existing sites, concrete thickness and reinforcing steel of culvert tops and walls were stepped-down in sections of the ...

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

PubMed Central

Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

2016-01-01

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent. PMID:26779141

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

PubMed

Ambroset, Chloé; Coluzzi, Charles; Guédon, Gérard; Devignes, Marie-Dominique; Loux, Valentin; Lacroix, Thomas; Payot, Sophie; Leblond-Bourget, Nathalie

2015-01-01

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.

Towards a mechanistic and physiological understanding of a ferredoxin disulfide reductase from the domains Archaea and Bacteria.

PubMed

Prakash, Divya; Walters, Karim A; Martinie, Ryan J; McCarver, Addison C; Kumar, Adepu K; Lessner, Daniel J; Krebs, Carsten; Golbeck, John H; Ferry, James G

2018-05-02

Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster.  UV-Vis, EPR and Mӧssbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active-site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR advancing the physiological understanding of FDRs role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show FDR homologs are widespread in diverse microbes from the domain Bacteria. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Estrogen receptor-independent catechol estrogen binding activity: protein binding studies in wild-type, Estrogen receptor-alpha KO, and aromatase KO mice tissues.

PubMed

Philips, Brian J; Ansell, Pete J; Newton, Leslie G; Harada, Nobuhiro; Honda, Shin-Ichiro; Ganjam, Venkataseshu K; Rottinghaus, George E; Welshons, Wade V; Lubahn, Dennis B

2004-06-01

Primary evidence for novel estrogen signaling pathways is based upon well-documented estrogenic responses not inhibited by estrogen receptor antagonists. In addition to 17beta-E2, the catechol estrogen 4-hydroxyestradiol (4OHE2) has been shown to elicit biological responses independent of classical estrogen receptors in estrogen receptor-alpha knockout (ERalphaKO) mice. Consequently, our research was designed to biochemically characterize the protein(s) that could be mediating the biological effects of catechol estrogens using enzymatically synthesized, radiolabeled 4-hydroxyestrone (4OHE1) and 4OHE2. Scatchard analyses identified a single class of high-affinity (K(d) approximately 1.6 nM), saturable cytosolic binding sites in several ERalphaKO estrogen-responsive tissues. Specific catechol estrogen binding was competitively inhibited by unlabeled catechol estrogens, but not by 17beta-E2 or the estrogen receptor antagonist ICI 182,780. Tissue distribution studies indicated significant binding differences both within and among various tissues in wild-type, ERalphaKO, and aromatase knockout female mice. Ligand metabolism experiments revealed extensive metabolism of labeled catechol estrogen, suggesting that catechol estrogen metabolites were responsible for the specific binding. Collectively, our data provide compelling evidence for the interaction of catechol estrogen metabolites with a novel binding protein that exhibits high affinity, specificity, and selective tissue distribution. The extensive biochemical characterization of this binding protein indicates that this protein may be a receptor, and thus may mediate ERalpha/beta-independent effects of catechol estrogens and their metabolites.

Little cigars, big cigars: omissions and commissions of harm and harm reduction information on the Internet.

PubMed

Dollar, Katherine M; Mix, Jacqueline M; Kozlowski, Lynn T

2008-05-01

We conducted a comparative analysis of "harm," "harm reduction," and "little cigar" information about cigars on 10 major English-language health Web sites. The sites were from governmental and nongovernmental organizations based in seven different countries and included "harm" and "harm reduction" information, discussions of little cigars, quantitative estimates of health risks, and qualifying behavioral characteristics (inhalation, number per day). Of the 10 Web sites, 7 offered statements explicitly indicating that cigars may be safer than cigarettes. None of the Web sites reviewed described that little cigars are likely as dangerous as cigarettes. Some Web sites provided quantitative estimates of health risks and extensive discussions of qualifying factors. Reading grade levels were higher than desirable. Extensive and complex information on the reduced risks of cigars compared with cigarettes is available on Web sites affiliated with prominent health organizations. Yet these sites fail to warn consumers that popular cigarette-like little cigars and cigarillos are likely to be just as dangerous as cigarettes, even for those who have never smoked cigarettes. Improvement of these Web sites is urgently needed to provide the public with high-quality health information.

Snow Depth Calibrations for Electromagnetic Induction Investigations at a Former Munitions Waste Disposal Site in Alaska

NASA Astrophysics Data System (ADS)

Glaser, D. R., II; Wagner, A. M.; Gelvin, A.; Saari, S.; Staples, A.; Larsen, G.

2017-12-01

A US Army legacy munitions waste site was identified adjacent to a river near a small arms range in Alaska. As part of remediation efforts, geophysical studies were conducted to characterize the extent of buried metal debris at the site. Time-domain electromagnetic surveys were completed over the site to meet the regulatory guidance for site cleanup. Time-domain and frequency-domain electromagnetic induction, magnetic gradiometry, and ground penetrating radar subsurface geophysical studies were deployed over soil, water, and snow surface conditions throughout the impacted area. The time-domain electromagnetic induction results acquired during summer months, presented clear indications of trenches located directly perpendicular to and adjacent to the river. However, in the follow up investigation where the snow-pack was greater than one meter, the response amplitude of the metallic debris was dampened and possible targets were missed. This was confirmed by the subsequent magnetic gradiometry survey which identified a suspected extension of one of the trenches through the river on to the seasonal sand bar island. The region is subject to extremely cold temperatures as well as significant snow pack and permafrost soil conditions. The snow presented a negative impact to the accurate assessment of the site by changing the effective investigation depth. To address this we developed an approach using ground penetrating radar data calibrated with physical snow depth measurements to generate continuous estimates of snow depth and spatially correct the electromagnetic induction data to the corresponding regulatory amplitude limit as if the snow were not present. Limitations of the approach as related to the signal floor of the electromagnetic induction response were also assessed.

Boulder Distributions at Legacy Landing Sites: Assessing Regolith Production Rates and Landing Site Hazards

NASA Technical Reports Server (NTRS)

Watkins, R. N.; Jolliff, B. L.; Lawrence, S. J.; Hayne, P. O.; Ghent, R. R.

2017-01-01

Understanding how the distribution of boulders on the lunar surface changes over time is key to understanding small-scale erosion processes and the rate at which rocks become regolith. Boulders degrade over time, primarily as a result of micrometeorite bombardment so their residence time at the surface can inform the rate at which rocks become regolith or become buried within regolith. Because of the gradual degradation of exposed boulders, we expect that the boulder population around an impact crater will decrease as crater age increases. Boulder distributions around craters of varying ages are needed to understand regolith production rates, and Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images provide one of the best tools for conducting these studies. Using NAC images to assess how the distribution of boulders varies as a function of crater age provides key constraints for boulder erosion processes. Boulders also represent a potential hazard that must be addressed in the planning of future lunar landings. A boulder under a landing leg can contribute to deck tilt, and boulders can damage spacecraft during landing. Using orbital data to characterize boulder populations at locations where landers have safely touched down (Apollo, Luna, Surveyor, Chang'e-3) provides validation for landed mission hazard avoidance planning. Additionally, counting boulders at legacy landing sites is useful because: 1) LROC has extensive coverage of these sites at high resolutions (approximately 0.5 meters per pixel). 2) Returned samples from craters at these sites have been radiometrically dated, allowing assessment of how boulder distributions vary as a function of crater age. 3) Surface photos at these sites can be used to correlate with remote sensing measurements.

A groundwater management plan for Stuttgart.

PubMed

Vasin, Sandra; Carle, Achim; Lang, Ulrich; Kirchholtes, Hermann Josef

2016-09-01

In general, groundwater in urban areas is exposed to anthropogenic influence and suffers from concentrations of contaminants. Stuttgart, as a highly industrialized city, has more than 5000 contaminated sites which might influence the Stuttgart's mineral water quality. Despite tremendous efforts and intensive single site orientated remediation since 1984 in downtown, the mineral springs were still affected with chlorinated hydrocarbons at low concentrations. Therefore, the applied practices of environmental management and measures for mitigation of pollution sources were not sufficient and had to be adjusted. The main goal of this study is to define an integral remediation plan (a groundwater management plan), focusing on the key sources of chlorinated solvents which are relevant for the mineral springs. For the large-scale investigated area of 26.6km(2) and eight aquifers, an extensive investigation and characterization methods were used in order to delineate the contamination plumes. By means of a 3D numerical model, the prioritization of the contaminated sites could be performed. Five contaminated sites with high remediation priority and need for optimized or additional remediation efforts were determined. For those five contaminated sites feasibility studies were performed which resulted in recommendation of remediation measures with total costs of more than 12.5 million euros. The proposed strategy and approach are suitable for multiple sources of contamination. Only in this way, the contributions of single contaminated sites to the total groundwater contamination can be identified and local remediation measures with their spatial impact simulated. Due to very complex geological conditions, technically there is no alternative to this strategy in order to achieve the contamination reduction in groundwater. Copyright © 2015 Elsevier B.V. All rights reserved.

Characterization of the human gene (TBXAS1) encoding thromboxane synthase.

PubMed

Miyata, A; Yokoyama, C; Ihara, H; Bandoh, S; Takeda, O; Takahashi, E; Tanabe, T

1994-09-01

The gene encoding human thromboxane synthase (TBXAS1) was isolated from a human EMBL3 genomic library using human platelet thromboxane synthase cDNA as a probe. Nucleotide sequencing revealed that the human thromboxane synthase gene spans more than 75 kb and consists of 13 exons and 12 introns, of which the splice donor and acceptor sites conform to the GT/AG rule. The exon-intron boundaries of the thromboxane synthase gene were similar to those of the human cytochrome P450 nifedipine oxidase gene (CYP3A4) except for introns 9 and 10, although the primary sequences of these enzymes exhibited 35.8% identity each other. The 1.2-kb of the 5'-flanking region sequence contained potential binding sites for several transcription factors (AP-1, AP-2, GATA-1, CCAAT box, xenobiotic-response element, PEA-3, LF-A1, myb, basic transcription element and cAMP-response element). Primer-extension analysis indicated the multiple transcription-start sites, and the major start site was identified as an adenine residue located 142 bases upstream of the translation-initiation site. However, neither a typical TATA box nor a typical CAAT box is found within the 100-b upstream of the translation-initiation site. Southern-blot analysis revealed the presence of one copy of the thromboxane synthase gene per haploid genome. Furthermore, a fluorescence in situ hybridization study revealed that the human gene for thromboxane synthase is localized to band q33-q34 of the long arm of chromosome 7. A tissue-distribution study demonstrated that thromboxane synthase mRNA is widely expressed in human tissues and is particularly abundant in peripheral blood leukocyte, spleen, lung and liver. The low but significant levels of mRNA were observed in kidney, placenta and thymus.

Evidence from the northwestern Venezuelan Andes for extraterrestrial impact: The black mat enigma

NASA Astrophysics Data System (ADS)

Mahaney, W. C.; Kalm, V.; Krinsley, D. H.; Tricart, P.; Schwartz, S.; Dohm, J.; Kim, K. J.; Kapran, B.; Milner, M. W.; Beukens, R.; Boccia, S.; Hancock, R. G. V.; Hart, K. M.; Kelleher, B.

2010-03-01

A carbon-rich black layer encrusted on a sandy pebbly bed of outwash in the northern Venezuelan Andes, previously considered the result of an alpine grass fire, is now recognized as a 'black mat' candidate correlative with Clovis Age sites in North America, falling within the range of 'black mat' dated sites (~ 12.9 ka cal BP). As such, the bed at site MUM7B, which dates to < 11.8 ka 14C years BP (raw dates) and appears to be contemporaneous with the Younger Dryas (YD) cooling event, marks a possibly much more extensive occurrence than previously identified. No fossils (megafauna) or tool assemblages were observed at this newly identified candidate site (3800 a.m.s.l.), as in the case of the North American sites. Here, evidence is presented for an extraterrestrial impact event at ~ 12.9 ka. The impact-related Andean bed, located ~ 20 cm above 13.7-13.3 ka cal BP alluvial and glaciolacustrine deposits, falls within the sediment characteristics and age range of 'black mat' dated sites (~ 12.9 ka cal BP) in North America. Site sediment characteristics include: carbon, glassy spherules, magnetic microspherules, carbon mat 'welded' onto coarse granular material, occasional presence of platinum group metals (Rh and Ru), planar deformation features (pdfs) in fine silt-size fragmental grains of quartz, as well as orthoclase, and monazite (with an abundance of Rare Earth Elements—REEs). If the candidate site is 'black mat', correlative with the 'black mat' sites of North America, such an extensive occurrence may support the hypothesized airburst/impact over the Laurentide Glacier, which led to a reversal of Allerød warming and the onset of YD cooling and readvance of glaciers. While this finding does not confirm such, it merits further investigation, which includes the reconnaissance for additional sites in South America. Furthermore, if confirmed, such an extensive occurrence may corroborate an impact origin.

A survey of selected Internet pharmacies in the United States.

PubMed

Peterson, A M

2001-01-01

To determine whether differences in the provision of pharmacy services exist among different types of Internet pharmacies. Survey of selected pharmacies with a presence on the Internet. Data were abstracted onto a data collection form for further analysis. Data collection was limited to 3 weeks. U.S.-based Internet pharmacies that allow patients to purchase prescription medications online. Pharmacies were identified using a metasearch engine with the search terms "Internet pharmacy" and "Internet pharmacist." Survey. Comparisons of availability of 10 commonly used products representing a variety of product categories, prescription verification methods, and privacy issues; and determinations of site navigability, drug information and provider access, and payment methods. Sites were categorized as "chain pharmacy extensions," "mail order pharmacies," "independent pharmacy extensions," and "online pharmacies." Thirty-three sites were reviewed. There was significant variation among the four types of pharmacies selling prescriptions over the Internet. Most pharmacies provided all of the drugs in the survey. Patients were required to provide their own prescription at 88% of the sites, and 75% of sites used mail or fax to verify prescription integrity. More than 50% of sites had privacy policies posted, and 64% used cookies. Chain pharmacy extensions required completion of an average of 10.2 pages to order drugs versus 2.4 to 4 pages for all other site types. Drug information was written at an eighth-grade reading level at 36% of the sites. More than two-thirds of the sites provided a toll-free telephone for a health care professional. Nearly 80% of the sites accepted health insurance, and 95% accepted credit cards; however, only 40% used a secure transmission mechanism for patient or payment information. Internet pharmacies provide varying levels of service. Policies regarding the use of the Internet for obtaining medications should focus on improving the privacy of consumer information and ensuring the secure transmission of financial information.

Integrated Earth Science Research in Deep Underground Science and Engineering Laboratories

NASA Astrophysics Data System (ADS)

Wang, J. S.; Hazen, T. C.; Conrad, M. E.; Johnson, L. R.; Salve, R.

2004-12-01

There are three types of sites being considered for deep-underground earth science and physics experiments: (1) abandoned mines (e.g., the Homestake Gold Mine, South Dakota; the Soudan Iron Mine, Minnesota), (2) active mines/facilities (e.g., the Henderson Molybdenum Mine, Colorado; the Kimballton Limestone Mine, Virginia; the Waste Isolation Pilot Plant [in salt], New Mexico), and (3) new tunnels (e.g., Icicle Creek in the Cascades, Washington; Mt. San Jacinto, California). Additional sites have been considered in the geologically unique region of southeastern California and southwestern Nevada, which has both very high mountain peaks and the lowest point in the United States (Death Valley). Telescope Peak (along the western border of Death Valley), Boundary Peak (along the California-Nevada border), Mt. Charleston (outside Las Vegas), and Mt. Tom (along the Pine Creek Valley) all have favorable characteristics for consideration. Telescope Peak can site the deepest laboratory in the United States. The Mt. Charleston tunnel can be a highway extension connecting Las Vegas to Pahrump. The Pine Creek Mine next to Mt. Tom is an abandoned tungsten mine. The lowest levels of the mine are accessible by nearly horizontal tunnels from portals in the mining base camp. Drainage (most noticeable in the springs resulting from snow melt) flows (from the mountain top through upper tunnel complex) out of the access tunnel without the need for pumping. While the underground drifts at Yucca Mountain, Nevada, have not yet been considered (since they are relatively shallow for physics experiments), they have undergone extensive earth science research for nearly 10 years, as the site for future storage of nation's spent nuclear fuels. All these underground sites could accommodate different earth science and physics experiments. Most underground physics experiments require depth to reduce the cosmic-ray-induced muon flux from atmospheric sources. Earth science experiments can be spatially extensive, from sub-room-size scale to ten-kilometer scale. The DUSEL sites with vertical depth and lateral extent can accommodate many different experiments. Hydrologic studies can characterize the in-flow along drifts, ramps, and shafts. Geophysical and rock mechanics studies can have seismic and electromagnetic sensors stationed on site, for both local monitoring of excavations and long-term stability, and mine-scale network of sensors to form a large aperture for tomography imaging. The geo-biochemical studies can include the ecological evaluation of the effects of introduced materials and the search for the origin of life in isolated fluid pockets at depth. The muon flux can be measured underground to detect empty space (or lack of it) above detectors, as demonstrated at the Chephren pyramid, Egypt, in the 1970s and currently at the Pyramid of the Sun, Mexico. Conventional geophysical tomography, with wave propagation through rock mass, can be extended to include particle rays, with high-energy muon flux as an example. Muons interacting with atoms have implications for both geochemical and biological processes. This type of research can further promote collaboration between earth scientists with physicists. A deep laboratory can accommodate a deep campus for suites of physics detectors, and several campuses at different depths within the same site for earth science experiments in rock mechanics, hydrology, geochemistry, ecology, geo-microbiology, coupled processes, and many other branches of earth and planetary sciences.

EPIC'S PRODUCTS AND SERVICES

EPA Science Inventory

EPIC completes approximately 150 site characterizations annually using current and historical aerial photographs. This work is done in support of EPA Regional and Program
offices. Site characterization provides detailed information about a site and its history, often going ba...

Remedial Action Plan and site design for stabilization of the inactive uranium mill tailings site at Durango, Colorado: Attachment 3, Groundwater hydrology report. Revised final report

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

Not Available

1991-12-01

The US Environmental Protection Agency (EPA) has established health and environmental protection regulations to correct and prevent groundwater contamination resulting from processing activities at inactive uranium milling sites. According to the Uranium Mill Tailings Radiation Control Act of 1978, (UMTRCA) the US Department of Energy (DOE) is responsible for assessing the inactive uranium processing sites. The DOE has determined this assessment shall include information on hydrogeologic site characterization. The water resources protection strategy that describes how the proposed action will comply with the EPA groundwater protection standards is presented in Attachment 4. Site characterization activities discussed in this section include:more » Characterization of the hydrogeologic environment; characterization of existing groundwater quality; definition of physical and chemical characteristics of the potential contaminant source; and description of local water resources.« less

Remediation System Evaluation, Mattiace Petrochemical Superfund Site

EPA Pesticide Factsheets

The Mattiace Petrochemical Superfund Site, located in an industrial area near the harbor of Glen Cove, isapproximately 1.9 acres and has extensive soil and groundwater contamination of volatile organiccompounds stemming from the operations of...

Improving energy efficiency of facilities.

DOT National Transportation Integrated Search

2016-10-01

The Indiana Department of Transportation (INDOT) has entered into an agreement with the Purdue University Manufacturing Extension Partnership (MEP) to perform energy assessments on six sites. The six sites were selected to represent a variety of type...

Hard clam walking: Active horizontal locomotion of adult Mercenaria mercenaria at the sediment surface and behavioral suppression after extensive sampling

PubMed Central

Europe, James R.; Tettelbach, Christian R. H.; Havelin, Jason; Rodgers, Brooke S.; Furman, Bradley T.; Velasquez, Marissa

2017-01-01

Locomotion of infaunal bivalve mollusks primarily consists of vertical movements related to burrowing; horizontal movements have only been reported for a few species. Here, we characterize hard clam walking: active horizontal locomotion of adults (up to 118 mm shell length, SL) of the commercially important species, Mercenaria mercenaria, at the sediment surface—a behavior only briefly noted in the literature. We opportunistically observed walking over a 10-yr period, at 9 different sites in the Peconic Bays, New York, USA, and tested several hypotheses for the underlying cause of this behavior through quantitative field sampling and reproductive analyses. Hard clam walking was exhibited by males and females at equal frequency, predominantly during June/July and October, when clams were in peak spawning condition. Extensive walking behavior appears to be cued by a minimum population density; we suggest it may be mediated by unidentified pheromone(s), infaunal pressure waves and/or other unidentified factors. There was no directionality exhibited by walking clams, but individuals in an area of extensive walking were highly aggregated and walking clams were significantly more likely to move toward a member of the opposite sex. Thus, we conclude that hard clam walking serves to aggregate mature individuals prior to spawning, thereby facilitating greater fertilization success. In the process of investigating this behavior, however, we apparently oversampled one population and reduced clam densities below the estimated minimum threshold density and, in so doing, suppressed extensive walking for a period of >3 years running. This not only reinforces the importance of detailed field investigations of species biology and ecology, even for those that are considered to be well studied, but also highlights the need for greater awareness of the potential for research activities to affect focal species behavior. PMID:28278288

Environmental Baseline Studies of St. Marys River Near Neebish Island, Michigan, Prior to Proposed Extension of Navigation Season, 1981. Great Lakes- St. Lawrence Seaway, Navigation Season Extension Program

DTIC Science & Technology

1983-06-01

fall offshore readings indicated acidic conditions. A range of 4.8 - 9.2 S.U. occurred, which was larger than that reported in 1980 studies. The...submersed plants, as well as for emergent and terrestrial species. However, the increase in biomass is most obvious in those plants that abscise photo...while fall offshore pH values at all sites ranged towards more acidic conditions. No major differences between sites occurred. Winter Sedimentation

No evidence for depletion of carbohydrate pools in Scots pine (Pinus sylvestris L.) under drought stress

PubMed Central

Gruber, A.; Pirkebner, D.; Florian, C.; Oberhuber, W.

2012-01-01

The physiological mechanisms leading to Scots pine (Pinus sylvestris L.) decline in the dry inner Alpine valleys are still unknown. Testing the carbon starvation hypothesis, we analysed the seasonal course of mobile carbohydrate pools (NSC) of Scots pine growing at a xeric and a dry-mesic site within an inner Alpine dry valley (750 m a.s.l., Tyrol, Austria) during the year 2009, which was characterized by exceptional soil dryness. Although, soil moisture content dropped to c. 10% at both sites during the growing season, NSC concentrations were rising in all tissues (branch, stem, root) till end of July, except in needles where maxima were reached around bud break. NSC concentrations were not significantly different in the analysed tissues at the xeric and the dry-mesic site. At the dry-mesic site NSC concentrations in the above ground tree biomass were significantly higher during the period of radial growth. An accumulation of NSC in roots at the end of July indicates a change in carbon allocation after an early cessation in above ground growth, possibly due to elevated below ground carbon demand. In conclusion our results revealed that extensive soil dryness during the growing season did not lead to carbon depletion. However, even though C-reserves were not exhausted, a sequestration of carbohydrate pools during drought periods might lead to deficits in carbon supply that weaken tree vigour and drive tree mortality. PMID:21974742

42 CFR 485.703 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

.... Public health agency. An official agency established by a State or local government, the primary function... the primary site. The extension location is part of the rehabilitation agency. The extension location... function or activity and that— (1) Includes initial direction and periodic observation of the actual...

42 CFR 485.703 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

.... Public health agency. An official agency established by a State or local government, the primary function... the primary site. The extension location is part of the rehabilitation agency. The extension location... function or activity and that— (1) Includes initial direction and periodic observation of the actual...

42 CFR 485.703 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

.... Public health agency. An official agency established by a State or local government, the primary function... the primary site. The extension location is part of the rehabilitation agency. The extension location... function or activity and that— (1) Includes initial direction and periodic observation of the actual...

42 CFR 485.703 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

.... Public health agency. An official agency established by a State or local government, the primary function... the primary site. The extension location is part of the rehabilitation agency. The extension location... function or activity and that— (1) Includes initial direction and periodic observation of the actual...

42 CFR 485.703 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... Public health agency. An official agency established by a State or local government, the primary function... the primary site. The extension location is part of the rehabilitation agency. The extension location... function or activity and that— (1) Includes initial direction and periodic observation of the actual...

10 CFR 960.3-2-2-4 - The environmental assessment.

Code of Federal Regulations, 2011 CFR

2011-01-01

... the site-characterization activities at the site on public health and safety and the environment; a discussion of alternative activities related to site characterization that may be taken to avoid such impact; and an assessment of the regional and local impacts of locating a repository at the site. The draft...

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

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Recommendation of sites for characterization. 960.3-2-3 Section 960.3-2-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites...

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

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Recommendation of sites for characterization. 960.3-2-3 Section 960.3-2-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites...

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

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Recommendation of sites for characterization. 960.3-2-3 Section 960.3-2-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites...

SUMMARY OF TECNIQUES AND UNIQUE USES FOR DIRECT PUSH METHODS IN SITE CHARACTERIZATION ON CONTAMINATED FIELD SITES

EPA Science Inventory

At many of the sites where we have been asked to assist in site characterization, we have discovered severe discrepancies that new technologies may be able to prevent. This presentation is designed to illustrate these new technologies or unique uses of existing technology and the...

Massive GGAAs in genomic repetitive sequences serve as a nuclear reservoir of NF-κB.

PubMed

Wu, Jian; Wang, Qiao; Dai, Wei; Wang, Wei; Yue, Ming; Wang, Jinke

2018-04-13

Nuclear factor κB (NF-κB) is a DNA-binding transcription factor. Characterizing its genomic binding sites is crucial for understanding its gene regulatory function and mechanism in cells. This study characterized the binding sites of NF-κB RelA/p65 in the tumor neurosis factor-α (TNFα) stimulated HeLa cells by a precise chromatin immunoprecipitation-sequencing (ChIP-seq). The results revealed that NF-κB binds nontraditional motifs (nt-motifs) containing conserved GGAA quadruplet. Moreover, nt-motifs mainly distribute in the peaks nearby centromeres that contain a larger number of repetitive elements such as satellite, simple repeats and short interspersed nuclear elements (SINEs). This intracellular binding pattern was then confirmed by the in vitro detection, indicating that NF-κB dimers can bind the nontraditional κB (nt-κB) sites with low affinity. However, this binding hardly activates transcription. This study thus deduced that NF-κB binding nt-motifs may realize functions other than gene regulation as NF-κB binding traditional motifs (t-motifs). To testify the deduction, many ChIP-seq data of other cell lines were then analyzed. The results indicate that NF-κB binding nt-motifs is also widely present in other cells. The ChIP-seq data analysis also revealed that nt-motifs more widely distribute in the peaks with low-fold enrichment. Importantly, it was also found that NF-κB binding nt-motifs is mainly present in the resting cells, whereas NF-κB binding t-motifs is mainly present in the stimulated cells. Astonishingly, no known function was enriched by the gene annotation of nt-motif peaks. Based on these results, this study proposed that the nt-κB sites that extensively distribute in larger numbers of repeat elements function as a nuclear reservoir of NF-κB. The nuclear NF-κB proteins stored at nt-κB sites in the resting cells may be recruited to the t-κB sites for regulating its target genes upon stimulation. Copyright © 2018 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Global biodiversity monitoring: from data sources to essential biodiversity variables

USGS Publications Warehouse

Proenca, Vania; Martin, Laura J.; Pereira, Henrique M.; Fernandez, Miguel; McRae, Louise; Belnap, Jayne; Böhm, Monika; Brummitt, Neil; Garcia-Moreno, Jaime; Gregory, Richard D.; Honrado, Joao P; Jürgens, Norbert; Opige, Michael; Schmeller, Dirk S.; Tiago, Patricia; van Sway, Chris A

2016-01-01

Essential Biodiversity Variables (EBVs) consolidate information from varied biodiversity observation sources. Here we demonstrate the links between data sources, EBVs and indicators and discuss how different sources of biodiversity observations can be harnessed to inform EBVs. We classify sources of primary observations into four types: extensive and intensive monitoring schemes, ecological field studies and satellite remote sensing. We characterize their geographic, taxonomic and temporal coverage. Ecological field studies and intensive monitoring schemes inform a wide range of EBVs, but the former tend to deliver short-term data, while the geographic coverage of the latter is limited. In contrast, extensive monitoring schemes mostly inform the population abundance EBV, but deliver long-term data across an extensive network of sites. Satellite remote sensing is particularly suited to providing information on ecosystem function and structure EBVs. Biases behind data sources may affect the representativeness of global biodiversity datasets. To improve them, researchers must assess data sources and then develop strategies to compensate for identified gaps. We draw on the population abundance dataset informing the Living Planet Index (LPI) to illustrate the effects of data sources on EBV representativeness. We find that long-term monitoring schemes informing the LPI are still scarce outside of Europe and North America and that ecological field studies play a key role in covering that gap. Achieving representative EBV datasets will depend both on the ability to integrate available data, through data harmonization and modeling efforts, and on the establishment of new monitoring programs to address critical data gaps.

Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase.

PubMed

Schwans, Jason P; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-11-05

Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active-site energetics. The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects.

Uncovering the Determinants of a Highly Perturbed Tyrosine pKa in the Active Site of Ketosteroid Isomerase†

PubMed Central

Schwans, Jason P.; Sunden, Fanny; Gonzalez, Ana; Tsai, Yingssu; Herschlag, Daniel

2013-01-01

Within the idiosyncratic enzyme active site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near to charged groups or within hydrophobic pockets, Tyr57 of a P. putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semi-synthesis, 13C NMR spectroscopy, absorbance spectroscopy, and x-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from introduction of nearby anionic groups arise from accompanying active site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen bond donors, two Tyr side chains and a water molecule, positioned by other side chains and by a water-mediated hydrogen bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions, rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active site energetics. The extensive dataset provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects. PMID:24151972

SINGLE HEATER TEST FINAL REPORT

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

J.B. Cho

The Single Heater Test is the first of the in-situ thermal tests conducted by the U.S. Department of Energy as part of its program of characterizing Yucca Mountain in Nevada as the potential site for a proposed deep geologic repository for the disposal of spent nuclear fuel and high-level nuclear waste. The Site Characterization Plan (DOE 1988) contained an extensive plan of in-situ thermal tests aimed at understanding specific aspects of the response of the local rock-mass around the potential repository to the heat from the radioactive decay of the emplaced waste. With the refocusing of the Site Characterization Planmore » by the ''Civilian Radioactive Waste Management Program Plan'' (DOE 1994), a consolidated thermal testing program emerged by 1995 as documented in the reports ''In-Situ Thermal Testing Program Strategy'' (DOE 1995) and ''Updated In-Situ Thermal Testing Program Strategy'' (CRWMS M&O 1997a). The concept of the Single Heater Test took shape in the summer of 1995 and detailed planning and design of the test started with the beginning fiscal year 1996. The overall objective of the Single Heater Test was to gain an understanding of the coupled thermal, mechanical, hydrological, and chemical processes that are anticipated to occur in the local rock-mass in the potential repository as a result of heat from radioactive decay of the emplaced waste. This included making a priori predictions of the test results using existing models and subsequently refining or modifying the models, on the basis of comparative and interpretive analyses of the measurements and predictions. A second, no less important, objective was to try out, in a full-scale field setting, the various instruments and equipment to be employed in the future on a much larger, more complex, thermal test of longer duration, such as the Drift Scale Test. This ''shake down'' or trial aspect of the Single Heater Test applied not just to the hardware, but also to the teamwork and cooperation between multiple organizations performing their part in the test.« less

Integrated investigations of environmental effects of historical mining in the Basin and Boulder Mining Districts, Boulder River watershed, Jefferson County, Montana

USGS Publications Warehouse

Nimick, David A.; Church, Stan E.; Finger, Susan E.

2004-01-01

The Boulder River watershed is one of many watersheds in the western United States where historical mining has left a legacy of acid mine drainage and elevated concentrations of potentially toxic trace elements. Abandoned mine lands commonly are located on or affect Federal land. Cleaning up these Federal lands will require substantial investment of resources. As part of a cooperative effort with Federal land-management agencies, the U.S. Geological Survey implemented an Abandoned Mine Lands Initiative in 1997. The goal of the initiative was to use the watershed approach to develop a strategy for gathering and communicating the scientific information needed to formulate effective and cost-efficient remediation of affected lands in a watershed. The watershed approach is based on the premise that contaminated sites that have the most profound effect on water and ecosystem quality within an entire watershed should be identified, characterized, and ranked for remediation.The watershed approach provides an effective means to evaluate the overall status of affected resources and helps to focus remediation at sites where the most benefit will be gained in the watershed. Such a large-scale approach can result in the collection of extensive information on the geology and geochemistry of rocks and sediment, the hydrology and water chemistry of streams and ground water, and the diversity and health of aquatic and terrestrial organisms. During the assessment of the Boulder River watershed, we inventoried historical mines, defined geological conditions, assessed fish habitat, collected and chemically analyzed hundreds of water and sediment samples, conducted toxicity tests, analyzed fish tissue and indicators of physiological malfunction, examined invertebrates and biofilm, and defined hydrological regimes. Land- and resource-management agencies are faced with evaluating risks associated with thousands of potentially harmful mine sites, and this level of effort is not always feasible for every affected watershed. The detailed work described in this report can help Federal land-management agencies decide which characterization efforts would be most useful in characterization of other affected watersheds.

Identification of high-permeability subsurface structures with multiple point geostatistics and normal score ensemble Kalman filter

NASA Astrophysics Data System (ADS)

Zovi, Francesco; Camporese, Matteo; Hendricks Franssen, Harrie-Jan; Huisman, Johan Alexander; Salandin, Paolo

2017-05-01

Alluvial aquifers are often characterized by the presence of braided high-permeable paleo-riverbeds, which constitute an interconnected preferential flow network whose localization is of fundamental importance to predict flow and transport dynamics. Classic geostatistical approaches based on two-point correlation (i.e., the variogram) cannot describe such particular shapes. In contrast, multiple point geostatistics can describe almost any kind of shape using the empirical probability distribution derived from a training image. However, even with a correct training image the exact positions of the channels are uncertain. State information like groundwater levels can constrain the channel positions using inverse modeling or data assimilation, but the method should be able to handle non-Gaussianity of the parameter distribution. Here the normal score ensemble Kalman filter (NS-EnKF) was chosen as the inverse conditioning algorithm to tackle this issue. Multiple point geostatistics and NS-EnKF have already been tested in synthetic examples, but in this study they are used for the first time in a real-world case study. The test site is an alluvial unconfined aquifer in northeastern Italy with an extension of approximately 3 km2. A satellite training image showing the braid shapes of the nearby river and electrical resistivity tomography (ERT) images were used as conditioning data to provide information on channel shape, size, and position. Measured groundwater levels were assimilated with the NS-EnKF to update the spatially distributed groundwater parameters (hydraulic conductivity and storage coefficients). Results from the study show that the inversion based on multiple point geostatistics does not outperform the one with a multiGaussian model and that the information from the ERT images did not improve site characterization. These results were further evaluated with a synthetic study that mimics the experimental site. The synthetic results showed that only for a much larger number of conditioning piezometric heads, multiple point geostatistics and ERT could improve aquifer characterization. This shows that state of the art stochastic methods need to be supported by abundant and high-quality subsurface data.

U.S. Department of Energy's site screening, site selection, and initial characterization for storage of CO2 in deep geological formations

USGS Publications Warehouse

Rodosta, T.D.; Litynski, J.T.; Plasynski, S.I.; Hickman, S.; Frailey, S.; Myer, L.

2011-01-01

The U.S. Department of Energy (DOE) is the lead Federal agency for the development and deployment of carbon sequestration technologies. As part of its mission to facilitate technology transfer and develop guidelines from lessons learned, DOE is developing a series of best practice manuals (BPMs) for carbon capture and storage (CCS). The "Site Screening, Site Selection, and Initial Characterization for Storage of CO2 in Deep Geological Formations" BPM is a compilation of best practices and includes flowchart diagrams illustrating the general decision making process for Site Screening, Site Selection, and Initial Characterization. The BPM integrates the knowledge gained from various programmatic efforts, with particular emphasis on the Characterization Phase through pilot-scale CO2 injection testing of the Validation Phase of the Regional Carbon Sequestration Partnership (RCSP) Initiative. Key geologic and surface elements that suitable candidate storage sites should possess are identified, along with example Site Screening, Site Selection, and Initial Characterization protocols for large-scale geologic storage projects located across diverse geologic and regional settings. This manual has been written as a working document, establishing a framework and methodology for proper site selection for CO2 geologic storage. This will be useful for future CO2 emitters, transporters, and storage providers. It will also be of use in informing local, regional, state, and national governmental agencies of best practices in proper sequestration site selection. Furthermore, it will educate the inquisitive general public on options and processes for geologic CO2 storage. In addition to providing best practices, the manual presents a geologic storage resource and capacity classification system. The system provides a "standard" to communicate storage and capacity estimates, uncertainty and project development risk, data guidelines and analyses for adequate site characterization, and guidelines for reporting estimates within the classification based on each project's status. 

78 FR 40820 - 60-Day Notice of Proposed Information Collection: Exchange Programs Alumni Web Site Registration

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-08

...: Exchange Programs Alumni Web Site Registration ACTION: Notice of request for public comment. SUMMARY: The... following methods: Web: Persons with access to the Internet may use the Federal Docket Management System... Programs Alumni Web site Registration OMB Control Number: 1405-0192 Type of Request: Extension of an...

Expert Panel Reviews of Research Centers: The Site Visit Process

ERIC Educational Resources Information Center

Lawrenz, Frances; Thao, Mao; Johnson, Kelli

2012-01-01

Site visits are used extensively in a variety of settings within the evaluation community. They are especially common in making summative value decisions about the quality and worth of research programs/centers. However, there has been little empirical research and guidance about how to appropriately conduct evaluative site visits of research…

Raw material variability of an active pharmaceutical ingredient and its relevance for processability in secondary continuous pharmaceutical manufacturing.

PubMed

Stauffer, F; Vanhoorne, V; Pilcer, G; Chavez, P-F; Rome, S; Schubert, M A; Aerts, L; De Beer, T

2018-06-01

Active Pharmaceutical Ingredients (API) raw material variability is not always thoroughly considered during pharmaceutical process development, mainly due to low quantities of drug substance available. However, synthesis, crystallization routes and production sites evolve during product development and product life cycle leading to changes in physical material attributes which can potentially affect their processability. Recent literature highlights the need for a global approach to understand the link between material synthesis, material variability, process and product quality. The study described in this article aims at explaining the raw material variability of an API using extensive material characterization on a restricted number of representative batches using multivariate data analysis. It is part of a larger investigation trying to link the API drug substance manufacturing process, the resulting physical API raw material attributes and the drug product continuous manufacturing process. Eight API batches produced using different synthetic routes, crystallization, drying, delumping processes and processing equipment were characterized, extensively. Seventeen properties from seven characterization techniques were retained for further analysis using Principal Component Analysis (PCA). Three principal components (PCs) were sufficient to explain 92.9% of the API raw material variability. The first PC was related to crystal length, agglomerate size and fraction, flowability and electrostatic charging. The second PC was driven by the span of the particle size distribution and the agglomerates strength. The third PC was related to surface energy. Additionally, the PCA allowed to summarize the API batch-to-batch variability in only three PCs which can be used in future drug product development studies to quantitatively evaluate the impact of the API raw material variability upon the drug product process. The approach described in this article could be applied to any other compound which is prone to batch-to-batch variability. Copyright © 2018 Elsevier B.V. All rights reserved.

Impacts of intensive forestry on early rotation trends in site carbon pools in the southeastern US

Treesearch

Raija Laiho; Felipe Sanchez; Allan Tiarks; Phillip M. Dougherty; Carl C. Trettin

2003-01-01

The effects of different silvicultural practices on site, especially soil, carbon (C) pools are still poorly known. We studied changes in site C pools during the first 5 years following harvesting and conversion of two extensively managed pine-hardwood stands to intensively managed loblolly pine plantations. One study site was located on the lower Atlantic Coastal...

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

Blasting for abandoned-mine land reclamation (closure of individual subsidence features and erratic, undocumented underground coal-mine workings). Final report

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

Workman, J.L.; Thompson, J.

1991-01-01

The study has examined the feasibility of blasting for mitigating various abandoned mine land features on AML sites. The investigation included extensive field trial blasts at sites in North Dakota and Montana. A blasting technique was used that was based on spherical cratering concepts. At the Beulah, North Dakota site thirteen individual vertical openings (sinkholes) were blasted with the intent to fill the voids. The blasts were designed to displace material laterally into the void. Good success was had in filling the sinkholes. At the White site in Montana erratic underground rooms with no available documentation were collapsed. An aditmore » leading into the mine was also blasted. Both individual room blasting and area pattern blasting were studied. A total of eight blasts were fired on the one acre area. Exploration requirements and costs were found to be extensive.« less

Stennis Space Center Verification & Validation Capabilities

NASA Technical Reports Server (NTRS)

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

2005-01-01

Scientists within NASA s 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 and moderate 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 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, atmospheric monitoring equipment, and thermal calibration ponds to characterize remote sensing data products. 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.

Involvement of the C-terminal extension of the alpha polypeptide and of the PucC protein in LH2 complex biosynthesis in Rubrivivax gelatinosus.

PubMed

Steunou, Anne-Soisig; Ouchane, Soufian; Reiss-Husson, Françoise; Astier, Chantal

2004-05-01

The facultative phototrophic nonsulfur bacterium Rubrivivax gelatinosus exhibits several differences from other species of purple bacteria in the organization of its photosynthetic genes. In particular, the puc operon contains only the pucB and pucA genes encoding the beta and alpha polypeptides of the light-harvesting 2 (LH2) complex. Downstream of the pucBA operon is the pucC gene in the opposite transcriptional orientation. The transcription of pucBA and pucC has been studied. No pucC transcript was detected either by Northern blotting or by reverse transcription-PCR analysis. The initiation site of pucBA transcription was determined by primer extension, and Northern blot analysis revealed the presence of two transcripts of 0.8 and 0.65 kb. The half-lives of both transcripts are longer in cells grown semiaerobically than in photosynthetically grown cells, and the small transcript is the less stable. It was reported that the alpha polypeptide, encoded by the pucA gene, presents a C-terminal extension which is not essential for LH2 function in vitro. The biological role of this alanine- and proline-rich C-terminal extension in vivo has been investigated. Two mutants with C-terminal deletions of 13 and 18 residues have been constructed. Both present the two pucBA transcripts, while their phenotypes are, respectively, LH2+ and LH2-, suggesting that a minimal length of the C-terminal extension is required for LH2 biogenesis. Another important factor involved in the LH2 biogenesis is the PucC protein. To gain insight into the function of this protein in R. gelatinosus, we constructed and characterized a PucC mutant. The mutant is devoid of LH2 complex under semiaerobiosis but still produces a small amount of these antennae under photosynthetic growth conditions. This conditional phenotype suggests the involvement of another factor in LH2 biogenesis.

Active Site Detection by Spatial Conformity and Electrostatic Analysis—Unravelling a Proteolytic Function in Shrimp Alkaline Phosphatase

PubMed Central

Chakraborty, Sandeep; Minda, Renu; Salaye, Lipika; Bhattacharjee, Swapan K.; Rao, Basuthkar J.

2011-01-01

Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - C ata L ytic A ctive S ite P rediction (CLASP). In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD) between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP), one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP), where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in vitro. PMID:22174814

Glycyl radical activating enzymes: Structure, mechanism, and substrate interactions☆

PubMed Central

Shisler, Krista A.; Broderick, Joan B.

2014-01-01

The glycyl radical enzyme activating enzymes (GRE–AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe–4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE–AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE–AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE–AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes. PMID:24486374

Hess Tower field study: sonic measurements at a former building-integrated wind farm site

NASA Astrophysics Data System (ADS)

Araya, Daniel

2017-11-01

Built in 2010, Hess Tower is a 29-story office building located in the heart of downtown Houston, TX. Unique to the building is a roof structure that was specifically engineered to house ten vertical-axis wind turbines (VAWTs) to partially offset the energy demands of the building. Despite extensive atmospheric boundary layer (ABL) wind tunnel tests to predict the flow conditions on the roof before the building was constructed, the Hess VAWTs were eventually removed after allegedly one of the turbines failed and fell to the ground. This talk presents in-situ sonic anemometry measurements taken on the roof of Hess Tower at the former turbine locations. We compare this wind field characterization to the ABL wind tunnel data to draw conclusions about building-integrated wind farm performance and prediction capability.

Thermal power systems small power systems applications project. Volume 2: Detailed report

NASA Technical Reports Server (NTRS)

Marriott, A. T.

1979-01-01

Small power system technology as applied to power plants up to 10 MW in size was considered. Markets for small power systems were characterized and cost goals were established for the project. Candidate power plant system design concepts were selected for evaluation and preliminary performance and cost assessments were made. Breakeven capital costs were determined for leading contenders among the candidate systems. The potential use of small power systems in providing part of the demand for pumping power by the extensive aqueduct system of California, was studied. Criteria and methodologies were developed for the ranking of candidate power plant system design concepts. Experimental power plant concepts of 1 MW rating were studied to define a power plant configuration for subsequent detail design construction, testing and evaluation. Site selection criteria and ground rules were developed.

Electron Microscopy Analysis of the Nucleolus of Trypanosoma cruzi

NASA Astrophysics Data System (ADS)

López-Velázquez, Gabriel; Hernández, Roberto; López-Villaseñor, Imelda; Reyes-Vivas, Horacio; Segura-Valdez, María De L.; Jiménez-García, Luis F.

2005-08-01

The nucleolus is the main site for synthesis and processing of ribosomal RNA in eukaryotes. In mammals, plants, and yeast the nucleolus has been extensively characterized by electron microscopy, but in the majority of the unicellular eukaryotes no such studies have been performed. Here we used ultrastructural cytochemical and immunocytochemical techniques as well as three-dimensional reconstruction to analyze the nucleolus of Trypanosoma cruzi, which is an early divergent eukaryote of medical importance. In T. cruzi epimastigotes the nucleolus is a spherical intranuclear ribonucleoprotein organelle localized in a relatively central position within the nucleus. Dense fibrillar and granular components but not fibrillar centers were observed. In addition, nuclear bodies resembling Cajal bodies were observed associated to the nucleolus in the surrounding nucleoplasm. Our results provide additional morphological data to better understand the synthesis and processing of the ribosomal RNA in kinetoplastids.

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

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 4 2013-01-01 2013-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

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

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

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

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

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

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Site recommendation for characterization. 960.3-1-4-3 Section 960.3-1-4-3 Energy DEPARTMENT OF ENERGY GENERAL GUIDELINES FOR THE PRELIMINARY SCREENING OF POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-1-4-3 Site recommendation...

Reactor-pumped laser facility at DOE's Nevada Test Site

NASA Astrophysics Data System (ADS)

Lipinski, Ronald J.

1994-05-01

The Nevada Test Site (NTS) is one excellent possibility for a laser power beaming site. It is in the low latitudes of the U.S., is in an exceptionally cloud-free area of the southwest, is already an area of restricted access (which enhances safety considerations), and possesses a highly skilled technical team with extensive engineering and research capabilities from underground testing of our nation's nuclear deterrence. The average availability of cloud-free clear line of site to a given point in space is about 84%. With a beaming angle of +/- 60 degree(s) from the zenith, about 52 geostationary-orbit (GEO) satellites could be accessed continuously from NTS. In addition, the site would provide an average view factor of about 10% for orbital transfer from low earth orbit to GEO. One of the major candidates for a long-duration, high- power laser is a reactor-pumped laser being developed by DOE. The extensive nuclear expertise at NTS makes this site a prime candidate for utilizing the capabilities of a rector pumped laser for power beaming. The site then could be used for many dual-use roles such as industrial material processing research, defense testing, and removing space debris.

Rapid and Minimally Traumatic Replacement of Stimulator Extension Cables: Technical Note on a Novel Use for Sternal Wire.

PubMed

Henderson, Fraser; Takacs, Istvan

2017-01-01

Troubleshooting of deep brain stimulators (DBSs, Activa SC/PC/RC Medtronic PLC, Minneapolis, Minnesota, USA) sometimes results in a decision to replace a tunneled stretch-coil extension cable. We present a simple technique to accomplish this atraumatically without a tunneling tool. In the treatment of patients with a DBS, complication avoidance and efficiency of operative time are paramount. We sought to find the safest, most effective, and fastest method of performing the conceptually simple yet technically nuanced act of replacing lead extension cables. We connected #6 (8.0 metric) surgical steel 18″ (45-cm) monofilament (Ethicon US, LLC, Somerville, New Jersey, USA), also known as #6 sternal wire, in line with DBS extension cables (Medtronic DBS Extension 37086-60) in novel fashion to overcome intraprocedural hurdles encountered during the past decade in a busy functional neurosurgery service. Patients tolerate the procedure well and return home shortly after recovery with no complications. A less expensive and faster technique for passing pulse generator extension cables may be the use of a sternal wire. Using the described technique, pulse generators may be quickly and safely adjusted from side to side and site to site as the clinical situation dictates. Copyright © 2016 Elsevier Inc. All rights reserved.

Measurement of the end-to-end distances between the femoral and tibial insertion sites of the anterior cruciate ligament during knee flexion and with rotational torque.

PubMed

Wang, Joon Ho; Kato, Yuki; Ingham, Sheila J M; Maeyama, Akira; Linde-Rosen, Monica; Smolinski, Patrick; Fu, Freddie H

2012-10-01

The aim of this study was to determine the end-to-end distance changes in anterior cruciate ligament (ACL) fibers during flexion/extension and internal/external rotation of the knee. The positional relation between the femur and tibia of 10 knees was digitized on a robotic system during flexion/extension and with an internal/external rotational torque (5 Nm). The ACL insertion site data, acquired by 3-dimensional scanning, were superimposed on the positional data. The end-to-end distances of 5 representative points on the femoral and tibial insertion sites of the ACL were calculated. The end-to-end distances of all representative points except the most anterior points were longest at full extension and shortest at 90°. The distances of the anteromedial (AM) and posterolateral (PL) bundles were 37.2 ± 2.1 mm and 27.5 ± 2.8 mm, respectively, at full extension and 34.7 ± 2.4 mm and 20.7 ± 2.3 mm, respectively, at 90°. Only 4 knees had an isometric point, which was 1 of the 3 anterior points. Under an internal torque, both bundles became longer with statistical meaning at all flexion angles (P = .005). The end-to-end distances of all points became longest with internal torque at full extension and shortest with an external torque at 90°. Only 4 of 10 specimens had an isometric point at a variable anterior point. The end-to-end distances of the AM and PL bundles were longer in extension and shorter in flexion. The nonisometric tendency of the ACL and the end-to-end distance change during knee flexion/extension and internal/external rotation should be considered during ACL reconstruction to avoid overconstraint of the graft. Copyright © 2012 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

MX Siting Investigation. Prime Characterization Sites Central High Plains Candidate Siting Province.

DTIC Science & Technology

1979-02-15

information obtained from these studies , in combination with data obtained in the Screen- ing studies , has been used for geotechnical ranking (FN-TR-25). I...Plains Candi- date Siting Province (CSP), one of six provinces included in the geotechnical Characterization studies . The location of the sites within...remaining after Intermediate Screening were divided into CSPs based on similar geotechnical characteristics. Intermediate Screening studies (FN-TR-17

Robotic Telecytology for Remote Cytologic Evaluation without an On-site Cytotechnologist or Cytopathologist: A Tale of Implementation and Review of Constraints

PubMed Central

Sirintrapun, Sahussapont Joseph; Rudomina, Dorota; Mazzella, Allix; Feratovic, Rusmir; Alago, William; Siegelbaum, Robert; Lin, Oscar

2017-01-01

Background: The first satellite center to offer interventional radiology procedures at Memorial Sloan Kettering Cancer Center opened in October 2014. Two of the procedures offered, fine needle aspirations and core biopsies, required rapid on-site cytologic evaluation of smears and biopsy touch imprints for cellular content and adequacy. The volume and frequency of such evaluations did not justify hiring on-site cytotechnologists, and therefore, a dynamic robotic telecytology (TC) solution was created. In this technical article, we present a detailed description of our implementation of robotic TC. Methods: Pathology devised the remote robotic TC solution after acknowledging that it would not be cost effective to staff cytotechnologists on-site at the satellite location. Sakura VisionTek was selected as our robotic TC solution. In addition to configuration of the dynamic robotic TC solution, pathology realized integrating the technology solution into operations would require a multidisciplinary effort and reevaluation of existing staffing and workflows. Results: Extensively described are the architectural framework and multidisciplinary process re-design, created to navigate the constraints of our technical, cultural, and organizational environment. Also reviewed are the benefits and challenges associated with available desktop sharing solutions, particularly accounting for information security concerns. Conclusions: Dynamic robotic TC is effective for immediate evaluations performed without on-site cytotechnology staff. Our goal is providing an extensive perspective of the implementation process, particularly technical, cultural, and operational constraints. Through this perspective, our template can serve as an extensible blueprint for other centers interested in implementing robotic TC without on-site cytotechnologists. PMID:28966832

Robotic Telecytology for Remote Cytologic Evaluation without an On-site Cytotechnologist or Cytopathologist: A Tale of Implementation and Review of Constraints.

PubMed

Sirintrapun, Sahussapont Joseph; Rudomina, Dorota; Mazzella, Allix; Feratovic, Rusmir; Alago, William; Siegelbaum, Robert; Lin, Oscar

2017-01-01

The first satellite center to offer interventional radiology procedures at Memorial Sloan Kettering Cancer Center opened in October 2014. Two of the procedures offered, fine needle aspirations and core biopsies, required rapid on-site cytologic evaluation of smears and biopsy touch imprints for cellular content and adequacy. The volume and frequency of such evaluations did not justify hiring on-site cytotechnologists, and therefore, a dynamic robotic telecytology (TC) solution was created. In this technical article, we present a detailed description of our implementation of robotic TC. Pathology devised the remote robotic TC solution after acknowledging that it would not be cost effective to staff cytotechnologists on-site at the satellite location. Sakura VisionTek was selected as our robotic TC solution. In addition to configuration of the dynamic robotic TC solution, pathology realized integrating the technology solution into operations would require a multidisciplinary effort and reevaluation of existing staffing and workflows. Extensively described are the architectural framework and multidisciplinary process re-design, created to navigate the constraints of our technical, cultural, and organizational environment. Also reviewed are the benefits and challenges associated with available desktop sharing solutions, particularly accounting for information security concerns. Dynamic robotic TC is effective for immediate evaluations performed without on-site cytotechnology staff. Our goal is providing an extensive perspective of the implementation process, particularly technical, cultural, and operational constraints. Through this perspective, our template can serve as an extensible blueprint for other centers interested in implementing robotic TC without on-site cytotechnologists.

The environmental implications of intensified land use in developing countries

PubMed Central

Tinker, P. B.

1997-01-01

The major agricultural intensifications in the developed world over the last half century have produced a range of important environmental problems. These include pollution, damage to wildlife and landscape and other issues, both on- and off-site. These are largely being controlled by scientific investigation and Government regulation. As developing countries increase agricultural production over the next 30 years, this may also cause even more serious environmental damage.
The paper distinguishes between production-related on-site damage, and off-site and more extensive effects. Both may involve soil and water effects, such as soil erosion, salinization, siltation, eutrophication and loss of water quality. The use of more agrochemicals can damage water quality, health, wildlife and biodiversity. Loss of habitat from the extension of farming is particularly damaging to biodiversity. A developing off-site problem is the production of greenhouse gases by farming systems, including the conversion of forests to farmland. In the future the introduction of genetically engineered species of plants, animals or microbes will need secure control.
Work, probably on a catchment basis, is necessary to understand and control these problems. The three main requirements are much better environmental information from the developing world; the selection of environmental indicators to be monitored; and the support of local farmers in protecting the environment. There are encouraging indications of farmer concern and action over obvious on-site damage, but this may not extend to extensive off-site issues. The main danger is that developing food scarcity would cause the environmental issues to be ignored in a race for production.

Integrated monitoring of hydrogeomorphic, vegetative, and edaphic conditions in riparian ecosystems of Great Basin National Park, Nevada

USGS Publications Warehouse

Beever, Erik A.; Pyke, D.A.

2004-01-01

In contrast to the more incised riparian channels of central Nevada, we observed knickzones, downcutting, and incision only rarely and usually with limited extent in the walking surveys. Downcutting occurred most frequently and extensively in Strawberry and Snake creeks, due in part to their more erodible soils. According to a hydrogeomorphologist with extensive experience in Great Basin riparian systems, the sediment-delivery and hydrologic systems appeared relatively undisturbed in most reaches, with respect to grazing animals and other types of anthropogenic alteration. Site elevation of the 31 transects ranged from 1,950-2,987 m, and stream slope (i.e., gradient) was relatively steep (mean = 9.3%, range 3-16%). Strawberry Creek averaged the lowest maximum water depth, and correspondingly had greatest width/depth ratios. Baker Creek sites averaged the smallest amount of tree-canopy gaps, whereas Snake Creek sites on average had the largest proportion of gaps in understory vegetation. Sites in terrace-bound valley types averaged the lowest slope in the channel as well as the least cover of trees, litter, and vegetation overall, whereas alluviated, boulder-bed canyon sites averaged the greatest widths of the active channel. Sites in Lehman Creek averaged nearly twice as much coarse woody debris as sites from any other creek, whereas Baker Creek sites averaged greatest tree cover (mean = 67%, range 40 – 96%) and species richness (mean = 17.3 species). Multivariate ordinations suggested that sites in leveed outwash valleys and alluvial-fan-influenced valleys had the greatest inter-site heterogeneity in plant composition, whereas sites in incised moraine-filled valleys appeared most homogeneous. Differences among homogeneity of sites within vegetation types were less pronounced, but sites dominated by either aspen and Woodsʼ rose or narrow-leaved cottonwood had the most similar plant communities among sites of the same vegetation type. A number of species were faithful indicators of various valley and vegetation types, using either set of plant-frequency data. We estimate that all 31 sites could be subsequently re-sampled in 14-18 field days by individuals possessing familiarity of the riparian flora of the southern Snake Range. As with any research, monitoring-focused investigations must balance the concerns for number of ecosystem attributes measured, extensiveness in time and space of sampling periods and locations, and the time and cost of sampling.

A Task-oriented Approach for Hydrogeological Site Characterization

NASA Astrophysics Data System (ADS)

Rubin, Y.; Nowak, W.; de Barros, F.

2010-12-01

Hydrogeological site characterization is a challenging task from several reasons: (1) the large spatial variability and scarcity of prior information render the outcome of any planned sampling campaign uncertain; (2) there are no simple tools for comparing between the many alternative measurement techniques and data acquisition strategies, and (3) physical and budgetary constraints associated with data acquisition. This paper presents several ideas on how to plan sampling campaigns in a rational manner while addressing these challenges. The first idea is to recognize that different sites and different problems require different characterization strategies. Hence the idea is to plan data acquisition according to its capability for meeting site-specific goals. For example, the characterization needs at a “research problem” site (e.g., a site intended to investigate the transport of uranium in the subsurface such as in Hanford) are different from those of a “problem” site (e.g., contaminated site associated with a health risk to human such as Camp Lejeune, or determining the safe yield of an aquifer). This distinction requires planners to define the characterization goal(s) in a quantitative manner. The second idea is to define metrics that could link specific data types and data acquisition strategies with the site-specific goals in a way that would allow planners to compare between strongly different, alternatives strategies at the design stage (even prior to data acquisition) and to modify the strategies as more data become available. To meet this goal, we developed the concept of the (comparative) information yield curve. Finally, we propose to look at site characterization from the perspective of statistical hypothesis testing, whereby data acquisition strategies could be evaluated in terms of their ability to support or refute various hypotheses made with regard to the characterization goals, and the strategies could be modified once the test is completed. Accept/reject regions for hypothesis testing can be determined based on goals determined by regulations or by agreement between the stakeholders. Hypothesis-driven design could help in minimizing the chances of making wrong decision (false positives or false negatives) with regard to the site-specific goals.

HIV genetic information and clonal growth

Cancer.gov

Based on an analysis of blood cells from five HIV-infected individuals, NCI researchers have identified more than 2,400 HIV DNA insertion sites. Analysis of these sites showed that there is extensive clonal expansion (growth) of HIV infected cells.

Elastic extension of a local analysis facility on external clouds for the LHC experiments

NASA Astrophysics Data System (ADS)

Ciaschini, V.; Codispoti, G.; Rinaldi, L.; Aiftimiei, D. C.; Bonacorsi, D.; Calligola, P.; Dal Pra, S.; De Girolamo, D.; Di Maria, R.; Grandi, C.; Michelotto, D.; Panella, M.; Taneja, S.; Semeria, F.

2017-10-01

The computing infrastructures serving the LHC experiments have been designed to cope at most with the average amount of data recorded. The usage peaks, as already observed in Run-I, may however originate large backlogs, thus delaying the completion of the data reconstruction and ultimately the data availability for physics analysis. In order to cope with the production peaks, the LHC experiments are exploring the opportunity to access Cloud resources provided by external partners or commercial providers. In this work we present the proof of concept of the elastic extension of a local analysis facility, specifically the Bologna Tier-3 Grid site, for the LHC experiments hosted at the site, on an external OpenStack infrastructure. We focus on the Cloud Bursting of the Grid site using DynFarm, a newly designed tool that allows the dynamic registration of new worker nodes to LSF. In this approach, the dynamically added worker nodes instantiated on an OpenStack infrastructure are transparently accessed by the LHC Grid tools and at the same time they serve as an extension of the farm for the local usage.

76 FR 3838 - Approval and Promulgation of One-Year Extension for Attaining the 1997 8-Hour Ozone Standard for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-21

... accordance with requirements for a 1-year extension, the Philadelphia Area's 4th highest daily 8-hour...) The maximum 4th highest daily 8-hour monitored value at any monitoring site in the Philadelphia area...

Topographic models for predicting malaria vector breeding habitats: potential tools for vector control managers.

PubMed

Nmor, Jephtha C; Sunahara, Toshihiko; Goto, Kensuke; Futami, Kyoko; Sonye, George; Akweywa, Peter; Dida, Gabriel; Minakawa, Noboru

2013-01-16

Identification of malaria vector breeding sites can enhance control activities. Although associations between malaria vector breeding sites and topography are well recognized, practical models that predict breeding sites from topographic information are lacking. We used topographic variables derived from remotely sensed Digital Elevation Models (DEMs) to model the breeding sites of malaria vectors. We further compared the predictive strength of two different DEMs and evaluated the predictability of various habitat types inhabited by Anopheles larvae. Using GIS techniques, topographic variables were extracted from two DEMs: 1) Shuttle Radar Topography Mission 3 (SRTM3, 90-m resolution) and 2) the Advanced Spaceborne Thermal Emission Reflection Radiometer Global DEM (ASTER, 30-m resolution). We used data on breeding sites from an extensive field survey conducted on an island in western Kenya in 2006. Topographic variables were extracted for 826 breeding sites and for 4520 negative points that were randomly assigned. Logistic regression modelling was applied to characterize topographic features of the malaria vector breeding sites and predict their locations. Model accuracy was evaluated using the area under the receiver operating characteristics curve (AUC). All topographic variables derived from both DEMs were significantly correlated with breeding habitats except for the aspect of SRTM. The magnitude and direction of correlation for each variable were similar in the two DEMs. Multivariate models for SRTM and ASTER showed similar levels of fit indicated by Akaike information criterion (3959.3 and 3972.7, respectively), though the former was slightly better than the latter. The accuracy of prediction indicated by AUC was also similar in SRTM (0.758) and ASTER (0.755) in the training site. In the testing site, both SRTM and ASTER models showed higher AUC in the testing sites than in the training site (0.829 and 0.799, respectively). The predictability of habitat types varied. Drains, foot-prints, puddles and swamp habitat types were most predictable. Both SRTM and ASTER models had similar predictive potentials, which were sufficiently accurate to predict vector habitats. The free availability of these DEMs suggests that topographic predictive models could be widely used by vector control managers in Africa to complement malaria control strategies.

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.

Site Characterization and Monitoring Technical Support Center FY16 Report

EPA Science Inventory

SCMTSC’s primary goal is to provide technical assistance to regional programs on complex hazardous waste site characterization issues. This annual report illustrates the range and extent of projects that SCMTSC supported in FY 2016. Our principal audiences are site project manage...

Baseline Ecological Risk Assessment for the Upland at the LCP Chemical Site, Brunswick, Georgia - Site Investigation/Analysis and Risk Characterization (Final)

EPA Pesticide Factsheets

Site Investigation/Analysis and Risk Characterization (Final) Prepared for Honeywell International Inc. Prepared by CDR Environmental Specialists, Inc. August 2010 Region ID: 04 DocID: 10746263, DocDate: 08-01-2010

Reading, Learning and Enacting: Interpretation at Visitor Sites in the Wet Tropics Rainforest of Australia

ERIC Educational Resources Information Center

McNamara, Karen Elizabeth; Prideaux, Bruce

2010-01-01

The northern Wet Tropics rainforest of Australia was declared a world heritage site in 1988 and now supports an extensive tourism industry that attracts an estimated 2.5 million local and international visits annually. As part of the visitor experience, many sites include both environmental and cultural interpretation experiences, which range from…

75 FR 13268 - Extension of the Public Comment Period for the Draft Tank Closure and Waste Management...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-19

... Management Environmental Impact Statement for the Hanford Site, Richland, WA AGENCY: Department of Energy... Statement for the Hanford Site, Richland, Washington (Draft EIS, DOE/EIS-00391), made available for public... Draft EIS is also available through the Hanford Web site at: http://www.hanford.gov/orp . Issued in...

75 FR 53999 - Notice of Request for the Extension of Currently Approved Information Collection

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-02

... identified by the docket number by only one of the following methods: 1. Web site: www.regulations.gov . Follow the instructions for submitting comments on the U.S. Government electronic docket site. (Note: The... comments.) All electronic submissions must be made to the U.S. Government electronic docket site at http...

Effects of Low Flying Aircraft on Archaeological Structures

DTIC Science & Technology

1988-09-26

obtained from direct observation of aircraft overflights at one particular site, Ixng House, near Kayenta . Arizona. 2. THE SITE The Long House site is...located approximately 20 km southwest of Kayenta , Arizona, as shown in Figure 1. The Long House ruins were part of an extensive Anasazi agricultural...community that was (Received for Publication 22 September 1988) 1 UTAH COLORADO ARIZONANEW MEXICO LONG HOUSE I FARMINGTON SITE KAYENTA I CHACO CANYON

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.

Ka-Band Atmospheric Phase Stability Measurements in Goldstone, CA; White Sands, NM; and Guam

NASA Technical Reports Server (NTRS)

Zemba, Michael J.; Morse, Jacquelynne Rose; Nessel, James A.

2014-01-01

As spacecraft communication links are driven to higher frequencies (e.g. Ka-band) both by spectrum congestion and the appeal of higher data rates, the propagation phenomena at these frequencies must be well characterized for effective system design. In particular, the phase stability of a site at a given frequency will govern whether or not the site is a practical location for an antenna array, particularly if uplink capabilities are desired. Propagation studies to characterize such phenomena must be done on a site-by-site basis due to the wide variety of climates and weather conditions at each ground terminal. Accordingly, in order to statistically characterize the atmospheric effects on Ka-Band links, site test interferometers (STIs) have been deployed at three of NASA's operational sites to directly measure each site's tropospheric phase stability. Using three years of results from these experiments, this paper will statistically characterize the simultaneous atmospheric phase noise measurements recorded by the STIs deployed at the following ground station sites: the Goldstone Deep Space Communications Complex near Barstow, CA; the White Sands Ground Terminal near Las Cruces, NM; and the Guam Remote Ground Terminal on the island of Guam.

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

Meckel, Timothy; Trevino, Ramon

This project characterized the Miocene-age sub-seafloor stratigraphy in the near-offshore portion of the Gulf of Mexico adjacent to the Texas coast. The large number of industrial sources of carbon dioxide (CO₂) in coastal counties and the high density of onshore urbanization and environmentally sensitive areas make this offshore region extremely attractive for long-term storage of carbon dioxide emissions from industrial sources (CCS). The study leverages dense existing geologic data from decades of hydrocarbon exploration in and around the study area to characterize the regional geology for suitability and storage capacity. Primary products of the study include: regional static storage capacitymore » estimates, sequestration “leads” and prospects with associated dynamic capacity estimates, experimental studies of CO₂-brine-rock interaction, best practices for site characterization, a large-format ‘Atlas’ of sequestration for the study area, and characterization of potential fluid migration pathways for reducing storage risks utilizing novel high-resolution 3D (HR3D) seismic surveys. In addition, three subcontracted studies address source-to-sink matching optimization, offshore well bore management and environmental aspects. The various geologic data and interpretations are integrated and summarized in a series of cross-sections and maps, which represent a primary resource for any near-term commercial deployment of CCS in the area. The regional study characterized and mapped important geologic features (e.g., Clemente-Tomas fault zone, the regionally extensive Marginulina A and Amphistegina B confining systems, etc.) that provided an important context for regional static capacity estimates and specific sequestration prospects of the study. A static capacity estimate of the majority of the Study area (14,467 mi 2) was estimated at 86 metric Gigatonnes. While local capacity estimates are likely to be lower due to reservoir-scale characteristics, the offshore Miocene interval is a storage resource of National interest for providing CO₂ storage as an atmospheric emissions abatement strategy. The natural petroleum system was used as an analog to infer seal quality and predict possible migration pathways of fluids in an engineered system of anthropogenic CO₂ injection and storage. The regional structural features (e.g., Clemente-Tomas fault zone) that exert primary control on the trapping and distribution of Miocene hydrocarbons are expected to perform similarly for CCS. Industrial-scale CCS will require storage capacity utilizing well-documented Miocene hydrocarbon (dominantly depleted gas) fields and their larger structural closures, as well as barren (unproductive, brine-filled) closures. No assessment was made of potential for CO₂ utilization for enhanced oil and gas recovery. The use of 3D numerical fluid flow simulations have been used in the study to greatly assist in characterizing the potential storage capacity of a specific reservoir. Due to the complexity of geologic systems (stratigraphic heterogeneity) and inherent limitations on producing a 3D geologic model, these simulations are typically simplified scenarios that explore the influence of model property variability (sensitivity study). A specific site offshore San Luis Pass (southern Galveston Island) was undertaken successfully, indicating stacked storage potential. Downscaling regional capacity estimates to the local scale (and the inverse) has proven challenging, and remains an outstanding gap in capacity assessments. In order to characterize regional seal performance and identify potential brine and CO₂ leakage pathways, results from three high-resolution 3D (HR3D) seismic datasets acquired by the study using novel HR3D (P-Cable) acquisition system showed steady and significant improvements in data quality because of improved acquisition and processing technique. Finely detailed faults and stratigraphy in the shallowest 1000 milliseconds (~800 m) of data allowed for the identification and mapping of unconformable surfaces including what is probably a surface associated with the last Pleistocene glacial lowstand. The identification of a previously unrecognized (in commercial seismic data) gas chimney that was clearly defined in the 2013 HR3D survey, indicates that HR3D surveys may be useful as both a characterization tool for the overburden of a potential carbon sequestration site and as an additional monitoring tool for future engineered injection sites. Geochemical modeling indicated that injection of CO₂ would result in minor dissolution of calcite, K-feldspar and albite. In addition, modeling of typical brines in Miocene age rocks indicate that approximately 5% of injection capacity would result from CO₂ dissolution into the brine. After extensive searches, no rock samples of the Marginulina A and Amphistegina B seals (“caprocks”) were obtained, but analyses of available core samples of other Miocene age mudrocks (seals or caprocks) indicate that they have sealing ability sufficient for potential CO 2 storage in underlying sandstone units.« less

Environmental waste site characterization utilizing aerial photographs and satellite imagery: Three sites in New Mexico, USA

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

Van Eeckhout, E.; Pope, P.; Becker, N.

1996-04-01

The proper handling and characterization of past hazardous waste sites is becoming more and more important as world population extends into areas previously deemed undesirable. Historical photographs, past records, current aerial satellite imagery can play an important role in characterizing these sites. These data provide clear insight into defining problem areas which can be surface samples for further detail. Three such areas are discussed in this paper: (1) nuclear wastes buried in trenches at Los Alamos National Laboratory, (2) surface dumping at one site at Los Alamos National Laboratory, and (3) the historical development of a municipal landfill near Lasmore » Cruces, New Mexico.« less

CO{sub 2} Sequestration Capacity and Associated Aspects of the Most Promising Geologic Formations in the Rocky Mountain Region: Local-Scale Analyses

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

Laes, Denise; Eisinger, Chris; Morgan, Craig

2013-07-30

The purpose of this report is to provide a summary of individual local-­scale CCS site characterization studies conducted in Colorado, New Mexico and Utah. These site-­ specific characterization analyses were performed as part of the “Characterization of Most Promising Sequestration Formations in the Rocky Mountain Region” (RMCCS) project. The primary objective of these local-­scale analyses is to provide a basis for regional-­scale characterization efforts within each state. Specifically, limits on time and funding will typically inhibit CCS projects from conducting high-­ resolution characterization of a state-­sized region, but smaller (< 10,000 km{sup 2}) site analyses are usually possible, and suchmore » can provide insight regarding limiting factors for the regional-­scale geology. For the RMCCS project, the outcomes of these local-­scale studies provide a starting point for future local-­scale site characterization efforts in the Rocky Mountain region.« less

Variability of aerosol vertical distribution in the Sahel

NASA Astrophysics Data System (ADS)

Cavalieri, O.; Cairo, F.; Fierli, F.; di Donfrancesco, G.; Snels, M.; Viterbini, M.; Cardillo, F.; Chatenet, B.; Formenti, P.; Marticorena, B.; Rajot, J. L.

2010-12-01

In this work, we have studied the seasonal and inter-annual variability of the aerosol vertical distribution over Sahelian Africa for the years 2006, 2007 and 2008, characterizing the different kind of aerosols present in the atmosphere in terms of their optical properties observed by ground-based and satellite instruments, and their sources searched for by using trajectory analysis. This study combines data acquired by three ground-based micro lidar systems located in Banizoumbou (Niger), Cinzana (Mali) and M'Bour (Senegal) in the framework of the African Monsoon Multidisciplinary Analysis (AMMA), by the AEROsol RObotic NETwork (AERONET) sun-photometers and by the space-based Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) onboard the CALIPSO satellite (Cloud-Aerosol Lidar and Infrared Pathfinder Observations). During winter, the lower levels air masses arriving in the Sahelian region come mainly from North, North-West and from the Atlantic area, while in the upper troposphere air flow generally originates from West Africa, crossing a region characterized by the presence of large biomass burning sources. The sites of Cinzana, Banizoumbou and M'Bour, along a transect of aerosol transport from East to West, are in fact under the influence of tropical biomass burning aerosol emission during the dry season, as revealed by the seasonal pattern of the aerosol optical properties, and by back-trajectory studies. Aerosol produced by biomass burning are observed mainly during the dry season and are confined in the upper layers of the atmosphere. This is particularly evident for 2006, which was characterized by a large presence of biomass burning aerosols in all the three sites. Biomass burning aerosol is also observed during spring when air masses originating from North and East Africa pass over sparse biomass burning sources, and during summer when biomass burning aerosol is transported from the southern part of the continent by the monsoon flow. During summer months, the entire Sahelian region is under the influence of Saharan dust aerosols: the air masses in low levels arrive from West Africa crossing the Sahara desert or from the Southern Hemisphere crossing the Guinea Gulf while in the upper layers air masses still originate from North, North-East. The maximum of the desert dust activity is observed in this period which is characterized by large AOD (above 0.2) and backscattering values. It also corresponds to a maximum in the extension of the aerosol vertical distribution (up to 6 km of altitude). In correspondence, a progressive cleaning up of the lowermost layers of the atmosphere is occurring, especially evident in the Banizoumbou and Cinzana sites. Summer is in fact characterized by extensive and fast convective phenomena. Lidar profiles show at times large dust events loading the atmosphere with aerosol from the ground up to 6 km of altitude. These events are characterized by large total attenuated backscattering values, and alternate with very clear profiles, sometimes separated by only a few hours, indicative of fast removal processes occurring, likely due to intense convective and rain activity. The inter-annual variability in the three year monitoring period is not very significant. An analysis of the aerosol transport pathways, aiming at detecting the main source regions, revealed that air originated from the Saharan desert is present all year long and it is observed in the lower levels of the atmosphere at the beginning and at the end of the year. In the central part of the year it extends upward and the lower levels are less affected by air masses from Saharan desert when the monsoon flow carries air from the Guinea Gulf and the Southern Hemisphere inland.

Multiscale Structure of UXO Site Characterization: Spatial Estimation and Uncertainty Quantification

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

Ostrouchov, George; Doll, William E.; Beard, Les P.

2009-01-01

Unexploded ordnance (UXO) site characterization must consider both how the contamination is generated and how we observe that contamination. Within the generation and observation processes, dependence structures can be exploited at multiple scales. We describe a conceptual site characterization process, the dependence structures available at several scales, and consider their statistical estimation aspects. It is evident that most of the statistical methods that are needed to address the estimation problems are known but their application-specific implementation may not be available. We demonstrate estimation at one scale and propose a representation for site contamination intensity that takes full account of uncertainty,more » is flexible enough to answer regulatory requirements, and is a practical tool for managing detailed spatial site characterization and remediation. The representation is based on point process spatial estimation methods that require modern computational resources for practical application. These methods have provisions for including prior and covariate information.« less

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).

Devil's Slide: An evolving feature of California's coastal landscape

NASA Astrophysics Data System (ADS)

Thomas, M.; Loague, K.

2013-12-01

Coastal landslides in the United States remain a persistent threat to human life and urban development. The focus of this study is a landslide-prone section of the central California coastline, approximately 20 km south of San Francisco, known as Devil's Slide. This investigation employs an extensive aerial image inventory, digital elevation models (DEMs), and a water balance / limit-equilibrium approach to better understand the spatial and temporal characteristics of deep-seated bedrock slides at the site. Photographic surveys of the area reveal nearly three kilometers of headscarp and a complex network of slope failures that respond to hydrologic, seismic, and anthropogenic perturbations. DEM analysis suggests that, for a 145-year period (1866 to 2010), the study area experienced an average coastal retreat rate of 0.14 m yr-1 and an average volumetric loss of 11,216 m3 yr-1. At least 38% of the landscape evolution in the steep coastal terrain has been driven by slope failure events. A loosely coupled water balance / limit-equilibrium analysis quantitatively illustrates the precarious nature of the active landslide zone at the site. The slope is shown to be unstable for a large suite of equally-likely scenarios. The analyses presented herein suggest that future work should include a rigorous characterization of pore-water pressure development, driven by comprehensive simulations of subsurface hydrologic response, to improve our understanding of slope failure initiation at the Devil's Slide site.

Active site mutant transgene confers tolerance to human β-glucuronidase without affecting the phenotype of MPS VII mice

PubMed Central

Sly, William S.; Vogler, Carole; Grubb, Jeffrey H.; Zhou, Mi; Jiang, Jinxing; Zhou, Xiao Yan; Tomatsu, Shunji; Bi, Yanhua; Snella, Elizabeth M.

2001-01-01

Mucopolysaccharidosis type VII (MPS VII; Sly syndrome) is an autosomal recessive lysosomal storage disorder due to an inherited deficiency of β-glucuronidase. A naturally occurring mouse model for this disease was discovered at The Jackson Laboratory and shown to be due to homozygosity for a 1-bp deletion in exon 10 of the gus gene. The murine model MPS VII (gusmps/mps) has been very well characterized and used extensively to evaluate experimental strategies for lysosomal storage diseases, including bone marrow transplantation, enzyme replacement therapy, and gene therapy. To enhance the value of this model for enzyme and gene therapy, we produced a transgenic mouse expressing the human β-glucuronidase cDNA with an amino acid substitution at the active site nucleophile (E540A) and bred it onto the MPS VII (gusmps/mps) background. We demonstrate here that the mutant mice bearing the active site mutant human transgene retain the clinical, morphological, biochemical, and histopathological characteristics of the original MPS VII (gusmps/mps) mouse. However, they are now tolerant to immune challenge with human β-glucuronidase. This “tolerant MPS VII mouse model” should be useful for preclinical trials evaluating the effectiveness of enzyme and/or gene therapy with the human gene products likely to be administered to human patients with MPS VII. PMID:11226217

Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution.

PubMed

Duan, Yuange; Dou, Shengqian; Zhang, Hong; Wu, Changcheng; Wu, Mingming; Lu, Jian

2018-01-01

The adenosine-to-inosine (A-to-I) RNA editomes have been systematically characterized in various metazoan species, and many editing sites were found in clusters. However, it remains unclear whether the clustered editing sites tend to be linked in the same RNA molecules or not. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. This present study also suggests that linkage of editing should be considered in elucidating the functional consequences of RNA editing. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

53BP1 is a reader of the DNA damage-induced H2A Lys15 ubiquitin mark

PubMed Central

Fradet-Turcotte, Amélie; Canny, Marella D.; Escribano-Díaz, Cristina; Orthwein, Alexandre; Leung, Charles C.Y.; Huang, Hao; Landry, Marie-Claude; Kitevski-LeBlanc, Julianne; Noordermeer, Sylvie M.; Sicheri, Frank; Durocher, Daniel

2014-01-01

53BP1 (TP53BP1) is a chromatin-associated factor that promotes immunoglobulin class switching and DNA double-strand break (DSB) repair by non-homologous end joining. To accomplish its function in DNA repair, 53BP1 accumulates at DSB sites downstream of the RNF168 ubiquitin ligase. How ubiquitin recruits 53BP1 to break sites remains enigmatic since its relocalization involves recognition of H4 Lys20 (H4K20) methylation by its Tudor domain. Here we elucidate how 53BP1 is recruited to the chromatin that flanks DSB sites. We show that 53BP1 recognizes mono-nucleosomes containing dimethylated H4K20 (H4K20me2) and H2A ubiquitylated on Lys15 (H2AK15ub), the latter being a product of RNF168 action on chromatin. 53BP1 binds to nucleosomes minimally as a dimer using its previously characterized methyl-lysine-binding Tudor domain and a C-terminal extension, termed the ubiquitylation-dependent recruitment (UDR) motif, which interacts with the epitope formed by H2AK15ub and its surrounding residues on the H2A tail. 53BP1 is therefore a bivalent histone modification reader that recognizes a histone “code” produced by DSB signaling. PMID:23760478

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.

PubMed

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-07-01

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Single-molecule localization microscopy reveals molecular transactions during RAD51 filament assembly at cellular DNA damage sites

PubMed Central

Haas, Kalina T; Lee, MiYoung; Esposito, Alessandro; Venkitaraman, Ashok R

2018-01-01

Abstract RAD51 recombinase assembles on single-stranded (ss)DNA substrates exposed by DNA end-resection to initiate homologous recombination (HR), a process fundamental to genome integrity. RAD51 assembly has been characterized using purified proteins, but its ultrastructural topography in the cell nucleus is unexplored. Here, we combine cell genetics with single-molecule localization microscopy and a palette of bespoke analytical tools, to visualize molecular transactions during RAD51 assembly in the cellular milieu at resolutions approaching 30–40 nm. In several human cell types, RAD51 focalizes in clusters that progressively extend into long filaments, which abut—but do not overlap—with globular bundles of replication protein A (RPA). Extended filaments alter topographically over time, suggestive of succeeding steps in HR. In cells depleted of the tumor suppressor protein BRCA2, or overexpressing its RAD51-binding BRC repeats, RAD51 fails to assemble at damage sites, although RPA accumulates unhindered. By contrast, in cells lacking a BRCA2 carboxyl (C)-terminal region targeted by cancer-causing mutations, damage-induced RAD51 assemblies initiate but do not extend into filaments. We suggest a model wherein RAD51 assembly proceeds concurrently with end-resection at adjacent sites, via an initiation step dependent on the BRC repeats, followed by filament extension through the C-terminal region of BRCA2. PMID:29309696

Monitoring interseismic activity on the Ilan Plain (NE Taiwan) using Small Baseline PS-InSAR, GPS and leveling measurements: partitioning from arc-continent collision and backarc extension

NASA Astrophysics Data System (ADS)

Su, Zhe; Hu, Jyr-Ching; Wang, Erchie; Li, Yongsheng; Yang, Yinghui; Wang, Pei-Ling

2018-01-01

The Ilan Plain, located in Northeast Taiwan, represents a transition zone between oblique collision (between the Luzon Arc and the Eurasian Plate) and backarc extension (the Okinawa Trough). The mechanism for this abrupt transition from arc-continent collision to backarc extension remains uncertain. We used Global Positioning System (GPS), leveling and multi-interferogram Small Baseline Persistent Scatterer Interferometry (SBAS-PSI) data to monitor the interseismic activity in the basin. A common reference site was selected for the data sets. The horizontal component of GPS and the vertical measurements of the leveling data were converted to line-of-sight (LOS) data and compared with the SBAS-PSI data. The comparison shows that the entire Ilan Plain is undergoing rapid subsidence at a maximum rate of -11 ± 2 mm yr-1 in the LOS direction. We speculate that vertical deformation and anthropogenic activity may play important roles in this deformation. We also performed a joint inversion modeling that combined both the DInSAR and strong motion data to constrain the source model of the 2005 Ilan earthquake. The best-fitting model predicts that the Sansing fault caused the 2005 Ilan earthquake. The observed transtensional deformation is dominated by the normal faulting with a minor left-lateral strike-slip motion. We compared our SBAS-PSI results with the short-term (2005-2009) groundwater level changes. The results indicate that although pumping-induced surface subsidence cannot be excluded, tectonic deformation, including rapid southward movement of the Ryukyu arc and backarc extension of the Okinawa Trough, characterizes the opening of the Ilan Plain. Furthermore, a series of normal and left-lateral strike-slip transtensional faults, including the Choshui and Sansing faults, form a bookshelf-like structure that accommodates the extension of the plain. Although situated in a region of complex structural interactions, the Ilan Plain is primarily controlled by extension rather than by shortening. As the massive, pre-existing Philippines-Ryukyu island arc was pierced by the Philippine Sea Plate, the Ilan Plain formed as a remnant backarc basin on the northeastern corner of Taiwan.

Extensive forearm deep venous thrombosis following a severe infliximab infusion reaction.

PubMed

Ryan, Barbara M; Romberg, Marielle; Wolters, Frank; Stockbrugger, Reinhold W

2004-09-01

Here we describe a patient with Crohn's disease who developed a severe infliximab infusion reaction (IIR), complicated 1 day later by severe swelling of the forearm and hand ipsilateral to the site of infliximab infusion. This proved to be extensive forearm deep venous thrombosis. The site of thrombosis and the chronological relationship with the IIR implicates a hypersensitivity to infliximab in the causation of the venous thrombosis in this case. With an increasing trend towards re-treating patients with known IIRs, clinicians should be aware of this potentially serious and previously unreported complication.

FATE AND TRANSPORT MODELING OF CONTAMINANTS OF CONCERN FROM A CAFO IN AN AGRICULTURAL WATERSHED

EPA Science Inventory

The groundwater flow and transport modeling effort will require hydrogeological site characterization and the development of a conceptual flow model for the site. Site characterization will involve an assessment of both the surface and subsurface and be accomplished through joint...

Structure and Biochemical Properties of the Alkene Producing Cytochrome P450 OleTJE (CYP152L1) from the Jeotgalicoccus sp. 8456 Bacterium*

PubMed Central

Belcher, James; McLean, Kirsty J.; Matthews, Sarah; Woodward, Laura S.; Fisher, Karl; Rigby, Stephen E. J.; Nelson, David R.; Potts, Donna; Baynham, Michael T.; Parker, David A.; Leys, David; Munro, Andrew W.

2014-01-01

The production of hydrocarbons in nature has been documented for only a limited set of organisms, with many of the molecular components underpinning these processes only recently identified. There is an obvious scope for application of these catalysts and engineered variants thereof in the future production of biofuels. Here we present biochemical characterization and crystal structures of a cytochrome P450 fatty acid peroxygenase: the terminal alkene forming OleTJE (CYP152L1) from Jeotgalicoccus sp. 8456. OleTJE is stabilized at high ionic strength, but aggregation and precipitation of OleTJE in low salt buffer can be turned to advantage for purification, because resolubilized OleTJE is fully active and extensively dissociated from lipids. OleTJE binds avidly to a range of long chain fatty acids, and structures of both ligand-free and arachidic acid-bound OleTJE reveal that the P450 active site is preformed for fatty acid binding. OleTJE heme iron has an unusually positive redox potential (−103 mV versus normal hydrogen electrode), which is not significantly affected by substrate binding, despite extensive conversion of the heme iron to a high spin ferric state. Terminal alkenes are produced from a range of saturated fatty acids (C12–C20), and stopped-flow spectroscopy indicates a rapid reaction between peroxide and fatty acid-bound OleTJE (167 s−1 at 200 μm H2O2). Surprisingly, the active site is highly similar in structure to the related P450BSβ, which catalyzes hydroxylation of fatty acids as opposed to decarboxylation. Our data provide new insights into structural and mechanistic properties of a robust P450 with potential industrial applications. PMID:24443585

Draft environmental assessment: Davis Canyon site, Utah. Nuclear Waste Policy Act (Section 112). [Contains glossary

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

Not Available

1984-12-01

In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for Nuclear Waste Repositories. These evaluations are reported in this draft environmental assessment (EA), which is being issued for public review and comment. The DOE findings and determinations that are based on these evaluationsmore » are preliminary and subject to public review and comment. A final EA will be prepared after considering the comments received. On the basis of the evaluations reported in this draft EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. The site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site - the Lavender Canyon site. Although the Lavender Canyon site appears to be suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. Furthermore, the DOE finds that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is proposing to nominate the Davis Canyon site as one of five sites suitable for characterization. Having compared the Davis Canyon site with the other four sites proposed for nomination, the DOE has determined that the Davis Canyon site is not one of the three preferred sites for recommendation to the President as candidates for characterization.« less

Airborne and Ground-Based Optical Characterization of Legacy Underground Nuclear Test Sites

NASA Astrophysics Data System (ADS)

Vigil, S.; Craven, J.; Anderson, D.; Dzur, R.; Schultz-Fellenz, E. S.; Sussman, A. J.

2015-12-01

Detecting, locating, and characterizing suspected underground nuclear test sites is a U.S. security priority. Currently, global underground nuclear explosion monitoring relies on seismic and infrasound sensor networks to provide rapid initial detection of potential underground nuclear tests. While seismic and infrasound might be able to generally locate potential underground nuclear tests, additional sensing methods might be required to further pinpoint test site locations. Optical remote sensing is a robust approach for site location and characterization due to the ability it provides to search large areas relatively quickly, resolve surface features in fine detail, and perform these tasks non-intrusively. Optical remote sensing provides both cultural and surface geological information about a site, for example, operational infrastructure, surface fractures. Surface geological information, when combined with known or estimated subsurface geologic information, could provide clues concerning test parameters. We have characterized two legacy nuclear test sites on the Nevada National Security Site (NNSS), U20ak and U20az using helicopter-, ground- and unmanned aerial system-based RGB imagery and light detection and ranging (lidar) systems. The multi-faceted information garnered from these different sensing modalities has allowed us to build a knowledge base of how a nuclear test site might look when sensed remotely, and the standoff distances required to resolve important site characteristics.

77 FR 35464 - Modifications to the Disability Determination Procedures; Extension of Testing of Some Disability...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-13

...-772-1213 or TTY 1-800-325-0778, or visit our Internet site, Social Security Online, at http://www... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2012-0029] Modifications to the Disability Determination Procedures; Extension of Testing of Some Disability Redesign Features AGENCY: Social Security...

78 FR 45010 - Modifications to the Disability Determination Procedures; Extension of Testing of Some Disability...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-25

...-772-1213 or TTY 1-800-325-0778, or visit our Internet site, Social Security Online, at http://www... SOCIAL SECURITY ADMINISTRATION [Docket No. SSA-2013-0030] Modifications to the Disability Determination Procedures; Extension of Testing of Some Disability Redesign Features AGENCY: Social Security...

76 FR 39887 - Extension of Agency Information Collection Activity Under OMB Review: Highway Corporate Security...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-07

... Information Collection Activity Under OMB Review: Highway Corporate Security Review AGENCY: Transportation... industry by way of its Highway Corporate Security Review (CSR) Program, which encompasses site visits and... Title: Highway Corporate Security Review. Type of Request: Extension of a currently approved collection...

The Implications of Well-Formedness on Web-Based Educational Resources.

ERIC Educational Resources Information Center

Mohler, James L.

Within all institutions, Web developers are beginning to utilize technologies that make sites more than static information resources. Databases such as XML (Extensible Markup Language) and XSL (Extensible Stylesheet Language) are key technologies that promise to extend the Web beyond the "information storehouse" paradigm and provide…

Measurement Sets and Sites Commonly Used for High Spatial Resolution Image Product Characterization

NASA Technical Reports Server (NTRS)

Pagnutti, Mary

2006-01-01

Scientists within NASA's 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 has enabled the in-flight characterization of satellite high spatial resolution remote sensing system products form Space Imaging IKONOS, Digital Globe QuickBird, and ORBIMAGE OrbView, as well as advanced multispectral airborne digital camera products. SSC utilizes engineered geodetic targets, edge targets, radiometric tarps, atmospheric monitoring equipment and their Instrument Validation Laboratory to characterize high spatial resolution remote sensing data products. This presentation describes the SSC characterization capabilities and techniques in the visible through near infrared spectrum and examples of calibration results.

Site Characterization for a Deep Borehole Field Test

NASA Astrophysics Data System (ADS)

Kuhlman, K. L.; Hardin, E. L.; Freeze, G. A.; Sassani, D.; Brady, P. V.

2015-12-01

The US Department of Energy Office of Nuclear Energy is at the beginning of 5-year Deep Borehole Field Test (DBFT) to investigate the feasibility of constructing and characterizing two boreholes in crystalline basement rock to a depth of 5 km (16,400 ft). The concept of deep borehole disposal for radioactive waste has some advantages over mined repositories, including incremental construction and loading, the enhanced natural barriers provided by deep continental crystalline basement, and reduced site characterization. Site characterization efforts need to determine an eligible site that does not have the following disqualifying characteristics: greater than 2 km to crystalline basement, upward vertical fluid potential gradients, presence of economically exploitable natural resources, presence of high permeability connection to the shallow subsurface, and significant probability of future seismic or volcanic activity. Site characterization activities for the DBFT will include geomechanical (i.e., rock in situ stress state, and fluid pressure), geological (i.e., rock and fracture infill lithology), hydrological (i.e., quantity of fluid, fluid convection properties, and solute transport mechanisms), and geochemical (i.e., rock-water interaction and natural tracers) aspects. Both direct (i.e., sampling and in situ testing) and indirect (i.e., borehole geophysical) methods are planned for efficient and effective characterization of these site aspects and physical processes. Borehole-based characterization will be used to determine the variability of system state (i.e., stress, pressure, temperature, and chemistry) with depth, and interpretation of material and system parameters relevant to numerical site simulation. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135

PubMed Central

Stoops, Emily H.; Hull, Michael; Olesen, Christina; Mistry, Kavita; Harder, Jennifer L.; Rivera-Molina, Felix; Toomre, Derek

2015-01-01

In polarized epithelial cells, newly synthesized cell surface proteins travel in carrier vesicles from the trans Golgi network to the apical or basolateral plasma membrane. Despite extensive research on polarized trafficking, the sites of protein delivery are not fully characterized. Here we use the SNAP tag system to examine the site of delivery of the apical glycoprotein gp135. We show that a cohort of gp135 is delivered to a ring surrounding the base of the primary cilium, followed by microtubule-dependent radial movement away from the cilium. Delivery to the periciliary ring was specific to newly synthesized and not recycling protein. A subset of this newly delivered protein traverses the basolateral membrane en route to the apical membrane. Crumbs3a, another apical protein, was not delivered to the periciliary region, instead making its initial apical appearance in a pattern that resembled its steady-state distribution. Our results demonstrate a surprising “hot spot” for gp135 protein delivery at the base of the primary cilium and suggest the existence of a novel microtubule-based directed movement of a subset of apical surface proteins. PMID:26504168

Understanding the adsorptive and photoactivity properties of Ag-graphene oxide nanocomposites.

PubMed

Martínez-Orozco, R D; Rosu, H C; Lee, Soo-Wohn; Rodríguez-González, V

2013-12-15

Nanocomposites of graphene oxide (GO) and silver nanoparticles (AgNPs) were synthetized using a practical photochemical silver functionalization. Their photocatalytic activities were evaluated with two dyes, Rhodamine B and Indigo Carmine, under visible-light irradiation. The prepared nanocomposites were characterized by HRTEM, FESEM, XRD, Raman, FTIR and UV-vis absorption spectroscopy. These nanocomposites present new defect domains of sp(3) type in combination with several graphitic functional groups that act as nucleation sites for anchoring AgNPs, while the sp(2)-sp(3) edge defects domains of GO generate the photoactivity. Furthermore, their photocatalytic performances are governed by their large adsorption capacity, and strong interaction with dye chromophores. A comprehensive photocatalytic way underlying the importance of adsorption is suggested to explain the low visible-light responsive photoactivity of the AgNPs-GO nanocomposites and the possible binding-site saturation. Then, the usage of H2SO4 allows the production of ionic species and helps to confirm the strong adsorption of both dyes. The ability to synthesize AgNPs-GO nanocomposites with extensive adsorptive capacity is certainly of interest for the efficient removal of hazardous materials. Copyright © 2013 Elsevier B.V. All rights reserved.

Central Sensitization-Based Classification for Temporomandibular Disorders: A Pathogenetic Hypothesis

PubMed Central

Cattaneo, Ruggero; Marci, Maria Chiara; Pietropaoli, Davide; Ortu, Eleonora

2017-01-01

Dysregulation of Autonomic Nervous System (ANS) and central pain pathways in temporomandibular disorders (TMD) is a growing evidence. Authors include some forms of TMD among central sensitization syndromes (CSS), a group of pathologies characterized by central morphofunctional alterations. Central Sensitization Inventory (CSI) is useful for clinical diagnosis. Clinical examination and CSI cannot identify the central site(s) affected in these diseases. Ultralow frequency transcutaneous electrical nerve stimulation (ULFTENS) is extensively used in TMD and in dental clinical practice, because of its effects on descending pain modulation pathways. The Diagnostic Criteria for TMD (DC/TMD) are the most accurate tool for diagnosis and classification of TMD. However, it includes CSI to investigate central aspects of TMD. Preliminary data on sensory ULFTENS show it is a reliable tool for the study of central and autonomic pathways in TMD. An alternative classification based on the presence of Central Sensitization and on individual response to sensory ULFTENS is proposed. TMD may be classified into 4 groups: (a) TMD with Central Sensitization ULFTENS Responders; (b) TMD with Central Sensitization ULFTENS Nonresponders; (c) TMD without Central Sensitization ULFTENS Responders; (d) TMD without Central Sensitization ULFTENS Nonresponders. This pathogenic classification of TMD may help to differentiate therapy and aetiology. PMID:28932132

Intracranial meningeal hemangiopericytoma: Recurrences at the initial and distant intracranial sites and extraneural metastases to multiple organs

PubMed Central

WEI, GUANGQUAN; KANG, XIAOWEI; LIU, XIANPING; TANG, XING; LI, QINLONG; HAN, JUNTAO; YIN, HONG

2015-01-01

Regardless of the controversial pathogenesis, intracranial meningeal hemangiopericytoma (M-HPC) is a rare, highly cellular and vascularized mesenchymal tumor that is characterized by a high tendency for recurrence and extraneural metastasis, despite radical excision and postoperative radiotherapy. M-HPC shares similar clinical manifestations and radiological findings with meningioma, which causes difficulty in differentiation of this entity from those prognostically favorable mimics prior to surgery. Treatment of M-HPC, particularly in metastatic settings, remains a challenge. A case is described of primary M-HPC with recurrence at the initial and distant intracranial sites and extraneural multiple-organ metastases in a 36-year-old female. The metastasis of M-HPC was extremely extensive, and to the best of our knowledge this is the first case of M-HPC with delayed metastasis to the bilateral kidneys. The data suggests that preoperative computed tomography and magnetic resonance imaging could provide certain diagnostic clues and useful information for more optimal treatment planning. The results may imply that novel drugs, such as temozolomide and bevacizumab, as a component of multimodality therapy of M-HPC may deserve further investigation. PMID:26171177

Population genetics of the wild yeast Saccharomyces paradoxus.

PubMed Central

Johnson, Louise J; Koufopanou, Vassiliki; Goddard, Matthew R; Hetherington, Richard; Schäfer, Stefanie M; Burt, Austin

2004-01-01

Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species. PMID:15020405

Atmospheric stability analysis over statically and dynamically rough surfaces

NASA Astrophysics Data System (ADS)

Maric, Emina; Metzger, Meredith; Singha, Arindam; Sadr, Reza

2011-11-01

The ratio of buoyancy flux to turbulent kinetic energy production in the atmospheric surface layer is investigated experimentally for air flow over two types of surfaces characterized by static and dynamic roughness. In this study, ``static'' refers to the time-invariant nature of naturally-occurring roughness over a mud/salt playa; while, ``dynamic'' refers to the behavior of water waves along an air-water interface. In both cases, time-resolved measurements of the momentum and heat fluxes were acquired from synchronized 3D sonic anemometers mounted on a vertical tower. Field campaigns were conducted at two sites, representing the ``statically'' and ``dynamically'' rough surfaces, respectively: (1) the SLTEST facility in Utah's western desert, and (2) the new Doha airport in Qatar under construction along the coast of the Persian Gulf. Note, at site 2, anemometers were located directly above the water by extension from a tower secured to the end of a 1 km-long pier. Comparisons of the Monin-Obukhov length, flux Richardson number, and gradient Richardson number are presented, and discussed in the context of the observed evolution of the turbulent spectra in response to diurnal variations of atmospheric stability. Supported by the Qatar National Research Fund.

The placenta harbors a unique microbiome.

PubMed

Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, James

2014-05-21

Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA-based and whole-genome shotgun (WGS) metagenomic studies. Identified taxa and their gene carriage patterns were compared to other human body site niches, including the oral, skin, airway (nasal), vaginal, and gut microbiomes from nonpregnant controls. We characterized a unique placental microbiome niche, composed of nonpathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. In aggregate, the placental microbiome profiles were most akin (Bray-Curtis dissimilarity <0.3) to the human oral microbiome. 16S-based operational taxonomic unit analyses revealed associations of the placental microbiome with a remote history of antenatal infection (permutational multivariate analysis of variance, P = 0.006), such as urinary tract infection in the first trimester, as well as with preterm birth <37 weeks (P = 0.001). Copyright © 2014, American Association for the Advancement of Science.

Assessment of snow modeling decisions in the extra-tropical Andes Cordillera

NASA Astrophysics Data System (ADS)

Mendoza, P. A.; Musselman, K. N.; Raleigh, M. S.; Clark, M. P.; McPhee, J. P.

2017-12-01

Improving model realism is an ongoing challenge for the cryosphere research community, not only to advance process understanding, but also to quantify and reduce uncertainty under global warming conditions. This work attempts to characterize the interplay and impact of user decisions about snow model structure and parameter specification on model uncertainty. Snow simulations were conducted in the extra-tropical Andes - a mountainous region that acts as a natural reservoir for Central Chile and Western Argentina. To address this topic, we apply the Structure for Unifying Multiple Modeling Alternatives (SUMMA) to simulate seasonal snowpack dynamics at three sites with different hydroclimatic regimes (semi-arid, Mediterranean, and temperate humid). Results are verified against extensive ground-based observations. Site elevations decrease from north to south, whereas precipitation amounts increase with latitude. Results highlight the impact of different windflow and snow transport decisions on model skill during the accumulation period, and different parameterizations (e.g., albedo decay) on spring simulations. We anticipate that the outcomes from this study will have important implications on current and future research, in particular on the configuration of snow models used to quantify the availability of water resources in this region.

The 100-C-7 Remediation Project. An Overview of One of DOE's Largest Remediation Projects - 13260

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

Post, Thomas C.; Strom, Dean; Beulow, Laura

The U.S. Department of Energy Richland Operations Office (RL), U.S. Environmental Protection Agency (EPA) and Washington Closure Hanford LLC (WCH) completed remediation of one of the largest waste sites in the U.S. Department of Energy complex. The waste site, 100-C-7, covers approximately 15 football fields and was excavated to a depth of 85 feet (groundwater). The project team removed a total of 2.3 million tons of clean and contaminated soil, concrete debris, and scrap metal. 100-C-7 lies in Hanford's 100 B/C Area, home to historic B and C Reactors. The waste site was excavated in two parts as 100-C-7 andmore » 100-C-7:1. The pair of excavations appear like pit mines. Mining engineers were hired to design their tiered sides, with safety benches every 17 feet and service ramps which allowed equipment access to the bottom of the excavations. The overall cleanup project was conducted over a span of almost 10 years. A variety of site characterization, excavation, load-out and sampling methodologies were employed at various stages of remediation. Alternative technologies were screened and evaluated during the project. A new method for cost effectively treating soils was implemented - resulting in significant cost savings. Additional opportunities for minimizing waste streams and recycling were identified and effectively implemented by the project team. During the final phase of cleanup the project team applied lessons learned throughout the entire project to address the final, remaining source of chromium contamination. The C-7 cleanup now serves as a model for remediating extensive deep zone contamination sites at Hanford. (authors)« less

Extensive variation, but not local adaptation in an Australian alpine daisy.

PubMed

Hirst, Megan J; Sexton, Jason P; Hoffmann, Ary A

2016-08-01

Alpine plants often occupy diverse habitats within a similar elevation range, but most research on local adaptation in these plants has focused on elevation gradients. In testing for habitat-related local adaptation, local effects on seed quality and initial plant growth should be considered in designs that encompass multiple populations and habitats. We tested for local adaptation across alpine habitats in a morphologically variable daisy species, Brachyscome decipiens, in the Bogong High Plains in Victoria, Australia. We collected seed from different habitats, controlled for maternal effects through initial seed size estimates, and characterized seedling survival and growth in a field transplant experiment. We found little evidence for local adaptation for survival or plant size, based on three adaptation measures: Home versus Away, Local versus Foreign, and Sympatric versus Allopatric (SA). The SA measure controlled for planting site and population (site-of-origin) effects. There were significant differences due to site-of-origin and planting site effects. An important confounding factor was the size of plants directly after transplantation of seedlings, which had a large impact on subsequent seedling survival and growth. Initial differences in plant width and height influenced subsequent survival across the growing season but in opposing directions: wide plants had higher survival, but tall plants had lower survival. In an additional controlled garden experiment at Cranbourne Royal Botanic Gardens, site-of-origin effects detected in the field experiments disappeared under more benign homogeneous conditions. Although B. decipiens from different source areas varied significantly when grown across a range of alpine habitats, these differences did not translate into a local or habitat-related fitness advantage. This lack of local advantage may signal weak past selection, and/or weak adaptive transgeneration (plasticity) effects.

The Effect of Arc Proximity on Hydrothermal Activity Along Spreading Centers: New Evidence From the Mariana Back Arc (12.7°N-18.3°N)

NASA Astrophysics Data System (ADS)

Baker, Edward T.; Walker, Sharon L.; Resing, Joseph A.; Chadwick, William W.; Merle, Susan G.; Anderson, Melissa O.; Butterfield, David A.; Buck, Nathan J.; Michael, Susanna

2017-11-01

Back-arc spreading centers (BASCs) form a distinct class of ocean spreading ridges distinguished by steep along-axis gradients in spreading rate and by additional magma supplied through subduction. These characteristics can affect the population and distribution of hydrothermal activity on BASCs compared to mid-ocean ridges (MORs). To investigate this hypothesis, we comprehensively explored 600 km of the southern half of the Mariana BASC. We used water column mapping and seafloor imaging to identify 19 active vent sites, an increase of 13 over the current listing in the InterRidge Database (IRDB), on the bathymetric highs of 7 of the 11 segments. We identified both high and low (i.e., characterized by a weak or negligible particle plume) temperature discharge occurring on segment types spanning dominantly magmatic to dominantly tectonic. Active sites are concentrated on the two southernmost segments, where distance to the adjacent arc is shortest (<40 km), spreading rate is highest (>48 mm/yr), and tectonic extension is pervasive. Re-examination of hydrothermal data from other BASCs supports the generalization that hydrothermal site density increases on segments <90 km from an adjacent arc. Although exploration quality varies greatly among BASCs, present data suggest that, for a given spreading rate, the mean spatial density of hydrothermal activity varies little between MORs and BASCs. The present global database, however, may be misleading. On both BASCs and MORs, the spatial density of hydrothermal sites mapped by high-quality water-column surveys is 2-7 times greater than predicted by the existing IRDB trend of site density versus spreading rate.

Geological characterization of remote field sites using visible and infrared spectroscopy: Results from the 1999 Marsokhod field test

USGS Publications Warehouse

Johnson, J. R.; Ruff, S.W.; Moersch, J.; Roush, T.; Horton, K.; Bishop, J.; Cabrol, N.A.; Cockell, C.; Gazis, P.; Newsom, Horton E.; Stoker, C.

2001-01-01

Upcoming Mars Surveyor lander missions will include extensive spectroscopic capabilities designed to improve interpretations of the mineralogy and geology of landing sites on Mars. The 1999 Marsokhod Field Experiment (MFE) was a Mars rover simulation designed in part to investigate the utility of visible/near-infrared and thermal infrared field spectrometers to contribute to the remote geological exploration of a Mars analog field site in the California Mojave Desert. The experiment simultaneously investigated the abilities of an off-site science team to effectively analyze and acquire useful imaging and spectroscopic data and to communicate efficiently with rover engineers and an on-site field team to provide meaningful input to rover operations and traverse planning. Experiences gained during the MFE regarding effective communication between different mission operation teams will be useful to upcoming Mars mission teams. Field spectra acquired during the MFE mission exhibited features interpreted at the time as indicative of carbonates (both dolomitic and calcitic), mafic rocks and associated weathering products, and silicic rocks with desert varnish-like coatings. The visible/near-infrared spectra also suggested the presence of organic compounds, including chlorophyll in one rock. Postmission laboratory petrologic and spectral analyses of returned samples confirmed that all rocks identified as carbonates using field measurements alone were calc-silicates and that chlorophyll associated with endolithic organisms was present in the one rock for which it was predicted. Rocks classified from field spectra as silicics and weathered mafics were recognized in the laboratory as metamorphosed monzonites and diorite schists. This discrepancy was likely due to rock coatings sampled by the field spectrometers compared to fresh rock interiors analyzed petrographically, in addition to somewhat different surfaces analyzed by laboratory thermal spectroscopy compared to field spectra. Copyright 2001 by the American Geophysical Union.

Building dismantlement and site remediation at the Apollo Fuel Plant: When is technology the answer?

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

Walton, L.

1995-01-01

The Apollo fuel plant was located in Pennsylvania on a site known to have been used continuously for stell production from before the Civil War until after World War II. Then the site became a nuclear fuel chemical processing plants. Finally it was used to convert uranium hexafluoride to various oxide fuel forms. After the fuel manufacturing operations were teminated, the processing equipment was partially decontaminated, removed, packaged and shipped to a licensed low-level radioactive waste burial site. The work was completed in 1984. In 1990 a detailed site characterization was initiated to establishe the extent of contamination and tomore » plan the building dismantlement and soil remediation efforts. This article discusses the site characterization and remedial action at the site in the following subsections: characterization; criticality control; mobile containment; soil washing; in-process measurements; and the final outcome of the project.« less

The Savannah River Site's Groundwater Monitoring Program, third quarter 1991

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

Not Available

The Environmental Protection Department/Environmental Monitoring Section (EPD/EMS) administers the Savannah River Site's (SRS) Groundwater Monitoring Program. During third quarter 1991, EPD/EMS conducted extensive sampling of monitoring wells. Analytical results from third quarter 1991 are listed in this report.

Tunnel-Site Selection by Remote Sensing Techniques

DTIC Science & Technology

A study of the role of remote sensing for geologic reconnaissance for tunnel-site selection was commenced. For this study, remote sensing was defined...conventional remote sensing . Future research directions are suggested, and the extension of remote sensing to include airborne passive microwave

78 FR 29155 - Notice of Filing of Plats of Survey; Montana

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-17

..., representing the dependent resurvey of M.S. No. 551, Strawberry Lode; M.S. No. 780, Strawberry Lode; M.S. No.781, Strawberry Extension Lode; M.S. No. 2599B, Clipper Mill Site; M.S. No. 2617B, Rustler Mill Site...

SELECTING SITES FOR COMPARISON WITH CREATED WETLANDS

EPA Science Inventory

The paper describes the method used for selecting natural wetlands to compare with created wetlands. The results of the selection process and the advantages and disadvantages of the method are discussed. The random site selection method required extensive field work and may have ...

Use of Electrical Conductivity Logging to Characterize the Geological Context of Releases at UST Sites

EPA Science Inventory

Risk is the combination of hazard and exposure. Risk characterization at UST release sites has traditionally emphasized hazard (presence of residual fuel) with little attention to exposure. Exposure characterization often limited to a one-dimensional model such as the RBCA equa...

Extensive Loss of Islet Mass Beyond the First Day After Intraportal Human Islet Transplantation in a Mouse Model.

PubMed

Liljebäck, Hanna; Grapensparr, Liza; Olerud, Johan; Carlsson, Per-Ola

2016-01-01

Clinical islet transplantation is characterized by a progressive deterioration of islet graft function, which renders many patients once again dependent on exogenous insulin administration within a couple of years. In this study, we aimed to investigate possible engraftment factors limiting the survival and viability of experimentally transplanted human islets beyond the first day after their transplantation to the liver. Human islets were transplanted into the liver of nude mice and characterized 1 or 30 days after transplantation by immunohistochemistry. The factors assessed were endocrine mass, cellular death, hypoxia, vascular density and amyloid formation in the transplanted islets. One day posttransplantation, necrotic cells, as well as apoptotic cells, were commonly observed. In contrast to necrotic death, apoptosis rates remained high 1 month posttransplantation, and the total islet mass was reduced by more than 50% between 1 and 30 days posttransplantation. Islet mass at 30 days posttransplantation correlated negatively to apoptotic death. Vascular density within the transplanted islets remained less than 30% of that in native human islets up to 30 days posttransplantation and was associated with prevailing hypoxia. Amyloid formation was rarely observed in the 1-day-old transplants, but was commonly observed in the 30-day-old islet transplants. We conclude that substantial islet cell death occurs beyond the immediate posttransplantation phase, particularly through apoptotic events. Concomitant low vascularization with prevailing hypoxia and progressive amyloid development was observed in the human islet grafts. Strategies to improve engraftment at the intraportal site or change of implantation site in the clinical setting are needed.

Risk Factors for Hidradenitis Suppurativa in Patients with Inflammatory Bowel Disease.

PubMed

Lukach, Alexis J; Saul, Melissa I; Ferris, Laura K; Swoger, Jason M

2018-03-01

Hidradenitis suppurativa (HS) is a chronic inflammatory skin disorder characterized by recurrent nodules, abscesses, and sinus tracts that can be debilitating and significantly impair quality of life. Small studies and case reports have suggested a possible association between HS and inflammatory bowel disease (IBD). We performed a case-control study to further characterize IBD patients with HS in terms of smoking status, BMI, sites affected by HS, IBD type and features, and IBD medication history. A total of 38 patients with HS and IBD were identified and matched on age, gender, and IBD type to 136 controls with IBD but not HS. Clinical characteristics of interest were obtained through extensive review of the electronic health record. Among patients with HS and IBD, the most common sites affected by HS were the inguinal, perianal, and axillary regions. Relative to patients with IBD alone, patients with HS and IBD were nearly six times more likely to be current smokers (p < 0.01) and nearly 11 times more likely to be obese (p < 0.01). Patients with HS and Crohn's were significantly more likely to have ileocolonic and perianal disease than patients with CD only (OR 8.31, 95% CI 2.90-23.80 and OR 2.85, 95% CI 1.19-6.81, respectively; p < 0.01 for both). Relative to patients with IBD who do not develop HS, patients with IBD and HS are more likely to be overweight or obese, to be former or current smokers, and to have ileocolonic and/or perianal disease.

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.

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.

PubMed

Cannistraci, Carlo Vittorio; Ravasi, Timothy; Montevecchi, Franco Maria; Ideker, Trey; Alessio, Massimo

2010-09-15

Nonlinear small datasets, which are characterized by low numbers of samples and very high numbers of measures, occur frequently in computational biology, and pose problems in their investigation. Unsupervised hybrid-two-phase (H2P) procedures-specifically dimension reduction (DR), coupled with clustering-provide valuable assistance, not only for unsupervised data classification, but also for visualization of the patterns hidden in high-dimensional feature space. 'Minimum Curvilinearity' (MC) is a principle that-for small datasets-suggests the approximation of curvilinear sample distances in the feature space by pair-wise distances over their minimum spanning tree (MST), and thus avoids the introduction of any tuning parameter. MC is used to design two novel forms of nonlinear machine learning (NML): Minimum Curvilinear embedding (MCE) for DR, and Minimum Curvilinear affinity propagation (MCAP) for clustering. Compared with several other unsupervised and supervised algorithms, MCE and MCAP, whether individually or combined in H2P, overcome the limits of classical approaches. High performance was attained in the visualization and classification of: (i) pain patients (proteomic measurements) in peripheral neuropathy; (ii) human organ tissues (genomic transcription factor measurements) on the basis of their embryological origin. MC provides a valuable framework to estimate nonlinear distances in small datasets. Its extension to large datasets is prefigured for novel NMLs. Classification of neuropathic pain by proteomic profiles offers new insights for future molecular and systems biology characterization of pain. Improvements in tissue embryological classification refine results obtained in an earlier study, and suggest a possible reinterpretation of skin attribution as mesodermal. https://sites.google.com/site/carlovittoriocannistraci/home.

Epigenetic signatures of familial cancer are characteristic of tumor type and family category.

PubMed

Joensuu, Emmi I; Abdel-Rahman, Wael M; Ollikainen, Miina; Ruosaari, Salla; Knuutila, Sakari; Peltomäki, Päivi

2008-06-15

Tumor suppressor genes (TSG) may be inactivated by methylation of critical CpG sites in their promoter regions, providing targets for early detection and prevention. Although sporadic cancers, especially colorectal carcinoma (CRC), have been characterized for epigenetic changes extensively, such information in familial/hereditary cancer is limited. We studied 108 CRCs and 63 endometrial carcinomas (EC) occurring as part of hereditary nonpolyposis CRC, as separate familial site-specific entities or sporadically, for promoter methylation of 24 TSGs. Eleven genes in CRC and 6 in EC were methylated in at least 15% of tumors and together accounted for 89% and 82% of promoter methylation events in CRC and EC, respectively. Some genes (e.g., CDH13, APC, GSTP1, and TIMP3) showed frequent methylation in both cancers, whereas promoter methylation of ESR1, CHFR, and RARB was typical of CRC and that of RASSF1(A) characterized EC. Among CRCs, sets of genes with methylation characteristic of familial versus sporadic tumors appeared. A TSG methylator phenotype (methylation of at least 5 of 24 genes) occurred in 37% of CRC and 18% of EC (P = 0.013), and the presence versus absence of MLH1 methylation divided the tumors into high versus low methylation groups. In conclusion, inactivation of TSGs by promoter methylation followed patterns characteristic of tumor type (CRC versus EC) and family category and was strongly influenced by MLH1 promoter methylation status in all categories. Paired normal tissues or blood displayed negligible methylation arguing against a constitutional methylation abnormality in familial cases.

The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae.

PubMed

de Santana Lopes, Amanda; Gomes Pacheco, Túlio; Nimz, Tabea; do Nascimento Vieira, Leila; Guerra, Miguel P; Nodari, Rubens O; de Souza, Emanuel Maltempi; de Oliveira Pedrosa, Fábio; Rogalski, Marcelo

2018-04-01

The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.

Field evidence of biodegradation of N-Nitrosodimethylamine (NDMA) in groundwater with incidental and active recycled water recharge.

PubMed

Zhou, Quanlin; McCraven, Sally; Garcia, Julio; Gasca, Monica; Johnson, Theodore A; Motzer, William E

2009-02-01

Biodegradation of N-Nitrosodimethylamine (NDMA) has been found through laboratory incubation in unsaturated and saturated soil samples under both aerobic and anaerobic conditions. However, direct field evidence of in situ biodegradation in groundwater is very limited. This research aimed to evaluate biodegradation of NDMA in a large-scale groundwater system receiving recycled water as incidental and active recharge. NDMA concentrations in 32 monitoring and production wells with different screen intervals were monitored over a period of seven years. Groundwater monitoring was used to characterize changes in the magnitude and extent of NDMA in groundwater in response to seasonal hydrogeologic conditions and, more importantly, to significant concentration variations in effluent from water reclamation plants (associated with treatment-process changes). Extensive monitoring of NDMA concentrations and flow rates at effluent discharge locations and surface-water stations was also conducted to reasonably estimate mass loading through unlined river reaches to underlying groundwater. Monitoring results indicate that significant biodegradation of NDMA occurred in groundwater, accounting for an estimated 90% mass reduction over the seven-year monitoring period. In addition, a discrete effluent-discharge and groundwater-extraction event was extensively monitored in a well-characterized, localized groundwater subsystem for 626 days. Analysis of the associated NDMA fate and transport in the subsystem indicated that an estimated 80% of the recharged mass was biodegraded. The observed field evidence of NDMA biodegradation is supported by groundwater transport modeling accounting for various dilution mechanisms and first-order decay for biodegradation, and by a previous laboratory study on soil samples collected from the study site [Bradley, P.M., Carr, S.A., Baird, R.B., Chapelle, F.H., 2005. Biodegradation of N-Nitrosodimethylamine in soil from a water reclamation facility. Bioremediat. J. 9 (2), 115-120.].

Lunar site characterization and mining

NASA Technical Reports Server (NTRS)

Glass, Charles E.

1992-01-01

Lunar mining requirements do not appear to be excessively demanding in terms of volume of material processed. It seems clear, however, that the labor-intensive practices that characterize terrestrial mining will not suffice at the low-gravity, hard-vacuum, and inaccessible sites on the Moon. New research efforts are needed in three important areas: (1) to develop high-speed, high-resolution through-rock vision systems that will permit more detailed and efficient mine site investigation and characterization; (2) to investigate the impact of lunar conditions on our ability to convert conventional mining and exploration equipment to lunar prototypes; and (3) to develop telerobotic or fully robotic mining systems for operations on the Moon and other bodies in the inner solar system. Other aspects of lunar site characterization and mining are discussed.

Fidelity of bats to forest sites revealed from mist-netting recaptures

Treesearch

Roger W. Perry

2011-01-01

Although site fidelity to permanent roost structures by bats is generally known, long-term fidelity to areas such as foraging or drinking sites is unknown. Furthermore, mist-net recaptures of bats over multiple years are rarely reported. Extensive mist-net surveys were conducted over the course of 8 y in the Ouachita National Forest of central Arkansas, United States...

Sustainability, Participatory Culture, and the Performance of Democracy: Ascendant Sites of Theory and Practice in Art Education

ERIC Educational Resources Information Center

Blandy, Doug

2011-01-01

Art education is a systemic and extensive network within which children, youth, and adults make and learn about material culture. This lecture considers three sites of theory and practice that I see as ascendant in circulating through this network. These sites are sustainability, participatory culture, and performing democracy. I argue that…

Numerical simulations of water flow and tracer transport in soils at the USDA-ARS Beltsville OPE3 field site

USDA-ARS?s Scientific Manuscript database

The objective of this study was to develop a realistic model to simulate the complex processes of flow and tracer transport in USDA-ARS OPE3 field site and to compare simulation results with the detailed monitoring observations. The site has been studied for over 10 years with the extensive availabl...

The stable isotopes of site wide waters at an oil sands mine in northern Alberta, Canada

NASA Astrophysics Data System (ADS)

Baer, Thomas; Barbour, S. Lee; Gibson, John J.

2016-10-01

Oil sands mines have large disturbance footprints and contain a range of new landforms constructed from mine waste such as shale overburden and the byproducts of bitumen extraction such as sand and fluid fine tailings. Each of these landforms are a potential source of water and chemical release to adjacent surface and groundwater, and consequently, the development of methods to track water migration through these landforms is of importance. The stable isotopes of water (i.e. 2H and 18O) have been widely used in hydrology and hydrogeology to characterize surface water/groundwater interactions but have not been extensively applied in mining applications, or specifically to oil sands mining in northern Alberta. A prerequisite for applying these techniques is the establishment of a Local Meteoric Water Line (LMWL) to characterize precipitation at the mine sites as well as the development of a 'catalogue' of the stable water isotope signatures of various mine site waters. This study was undertaken at the Mildred Lake Mine Site, owned and operated by Syncrude Canada Ltd. The LMWL developed from 2 years (2009/2012) of sample collection is shown to be consistent with other LMWLs in western Canada. The results of the study highlight the unique stable water isotope signatures associated with hydraulically placed tailings (sand or fluid fine tailings) and overburden shale dumps relative to natural surface water and groundwater. The signature associated with the snow melt water on reclaimed landscapes was found to be similar to ground water recharge in the region. The isotopic composition of the shale overburden deposits are also distinct and consistent with observations made by other researchers in western Canada on undisturbed shales. The process water associated with the fine and coarse tailings streams has highly enriched 2H and 18O signatures. These signatures are developed through the non-equilibrium fractionation of imported fresh river water during evaporation from cooling towers used within the raw water process circuit. This highly fractionated surface water eventually becomes part of the recycled tailings water circuit, and as a consequence it undergoes further non-equilibrium fractionation as a result of surface evaporation, leading to additional enrichment along local evaporation lines.

Summer Ephemeroptera, Plecoptera, and Trichoptera (EPT) species richness and community structure in the lower Illinois River basin of Illinois

USGS Publications Warehouse

DeWalt, R.E.; Webb, D.W.; Harris, M.A.

1999-01-01

Ephemeroptera, Plecoptera, and Trichoptera (EPT) species richness is useful for monitoring stream health, but no published studies in Illinois quantitatively document EPT richness or assemblage structure. The objectives of this study were to characterize adult EPT richness and structure and relate these to relative water quality at eight stream sites (160-69,300 km3 area) in the lower Illinois River basin. Adults were ultra-violet light trapped in June, July, and August 1997. Nutrient enrichment by nitrate and nitrite nitrogen was strongly evident, especially in smaller drainages, while critical loss of stable habitat was observed in larger water bodies. Seventy EPT species were identified from 17,889 specimens. Trichoptera were by far the most speciose (41 species), followed by Ephemeroptera (26), and Plecoptera (3). Caddisflies also dominated species richness across sites, contributing 18.0 of the average 28.9 total EPT species collected. Site EPT richness varied significantly (F = 5.51, p = 0.003, df = 7), with smaller drainages supporting greater richness, generally. Differences were also evident for months (F = 21.7, p = 0.0001, df = 2), with June being lower (11.8 average) than either July (20.6) or August (18.1) values. Hilsenhoff biotic index (HBI) scores did not vary significantly across sites (F = 0.7, p = 0.7, df = 7), but were different across months (F = 5.4, p = 0.02, df = 2). June (4.23) and July (4.53) means were not different, but both were lower (of better quality) than August (5.33) scores. The relationship of EPT to HBI scores was not investigated statistically due to problems of sample size and interdependence of monthly samples, but graphical analysis suggested no consistent relationship. This suggested a decoupling of the HBI from the EPT and implied that the gain in taxonomic resolution achieved by using adults outstripped the resolution of the HBI. Use of the HBI to characterize adult aquatic insect communities is discouraged. New state records and range extensions for Ephemeroptera and Trichoptera are presented and possible loss of sensitive Plecoptera in the drainage is discussed.

Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi

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

Fernández-Fueyo, Elena; Acebes, Sandra; Ruiz-Dueñas, Francisco J.

2014-12-01

The variable C-terminal tail of manganese peroxidases, a group of enzymes involved in lignin degradation, is implicated in their catalytic and stability properties, as shown by new crystal structures, molecular-simulation and directed-mutagenesis data. Based on this structural–functional evaluation, short and long/extralong manganese peroxidase subfamilies have been accepted; the latter are characterized by exceptional stability, while it is shown for the first time that the former are able to oxidize other substrates at the same site where manganese(II) is oxidized. The genome of Ceriporiopsis subvermispora includes 13 manganese peroxidase (MnP) genes representative of the three subfamilies described in ligninolytic fungi, whichmore » share an Mn{sup 2+}-oxidation site and have varying lengths of the C-terminal tail. Short, long and extralong MnPs were heterologously expressed and biochemically characterized, and the first structure of an extralong MnP was solved. Its C-terminal tail surrounds the haem-propionate access channel, contributing to Mn{sup 2+} oxidation by the internal propionate, but prevents the oxidation of 2, 2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), which is only oxidized by short MnPs and by shortened-tail variants from site-directed mutagenesis. The tail, which is anchored by numerous contacts, not only affects the catalytic properties of long/extralong MnPs but is also associated with their high acidic stability. Cd{sup 2+} binds at the Mn{sup 2+}-oxidation site and competitively inhibits oxidation of both Mn{sup 2+} and ABTS. Moreover, mutations blocking the haem-propionate channel prevent substrate oxidation. This agrees with molecular simulations that position ABTS at an electron-transfer distance from the haem propionates of an in silico shortened-tail form, while it cannot reach this position in the extralong MnP crystal structure. Only small differences exist between the long and the extralong MnPs, which do not justify their classification as two different subfamilies, but they significantly differ from the short MnPs, with the presence/absence of the C-terminal tail extension being implicated in these differences.« less

Genomic organization and chromosomal localization of the gene TCF15 encoding the early mesodermal basic helix-loop-helix factor bHLH-EC2

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

Hidai, H.; Quertermous, E.E.; Quertermous, T.

1995-12-10

bHLH-EC2 is a recently characterized member of a growing family of basic helix-loop-helix transcription factors. This family includes bHLH factors such as twist, which appear to be primarily involved in early mesodermal differentiation, and bHLH factors such as TAL-1, which have been characterized through their association with chromosomal breakpoints associated with T-cell leukemias. To provide for studies aimed at understanding the genetic regulation of bHLH-EC2, we have characterized the organization of this gene and conducted preliminary studies of the transcriptional activity of the upstream promoter region. The mouse bHLH-EC2 gene was found to consist of two exons separated by amore » 5-kb intron, an organization pattern similar to the mouse twist gene. The transcription initiation site was identified by RNase protection assay and primer extension analysis. Linked promoter-reporter gene transfection experiments in cultured cells indicated that while the identified upstream sequence can function to promote transcription, it does not function in a cell-specific fashion. To investigate the possible association of bHLH-EC2 with hematological malignancy, the chromosomal location of this gene in the human was mapped by fluorescence in situ hybridization and assigned to chromosome band 20p13. 16 refs., 3 figs.« less

Geomorphological mapping of ice-free areas using polarimetric RADARSAT-2 data on Fildes Peninsula and Ardley Island, Antarctica

NASA Astrophysics Data System (ADS)

Schmid, T.; López-Martínez, J.; Guillaso, S.; Serrano, E.; D'Hondt, O.; Koch, M.; Nieto, A.; O'Neill, T.; Mink, S.; Durán, J. J.; Maestro, A.

2017-09-01

Satellite-borne Synthetic Aperture Radar (SAR) has been used for characterizing and mapping in two relevant ice-free areas in the South Shetland Islands. The objective has been to identify and characterize land surface covers that mainly include periglacial and glacial landforms, using fully polarimetric SAR C band RADARSAT-2 data, on Fildes Peninsula that forms part of King George Island, and Ardley Island. Polarimetric parameters obtained from the SAR data, a selection of field based training and validation sites and a supervised classification approach, using the support vector machine were chosen to determine the spatial distribution of the different landforms. Eight periglacial and glacial landforms were characterized according to their scattering mechanisms using a set of 48 polarimetric parameters. The mapping of the most representative surface covers included colluvial deposits, stone fields and pavements, patterned ground, glacial till and rock outcrops, lakes and glacier ice. The overall accuracy of the results was estimated at 81%, a significant value when mapping areas that are within isolated regions where access is limited. Periglacial surface covers such as stone fields and pavements occupy 25% and patterned ground over 20% of the ice-free areas. These are results that form the basis for an extensive monitoring of the ice-free areas throughout the northern Antarctic Peninsula region.

Deep Borehole Field Test Research Activities at LBNL

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

Dobson, Patrick; Tsang, Chin-Fu; Kneafsey, Timothy

The goal of the U.S. Department of Energy Used Fuel Disposition’s (UFD) Deep Borehole Field Test is to drill two 5 km large-diameter boreholes: a characterization borehole with a bottom-hole diameter of 8.5 inches and a field test borehole with a bottom-hole diameter of 17 inches. These boreholes will be used to demonstrate the ability to drill such holes in crystalline rocks, effectively characterize the bedrock repository system using geophysical, geochemical, and hydrological techniques, and emplace and retrieve test waste packages. These studies will be used to test the deep borehole disposal concept, which requires a hydrologically isolated environment characterizedmore » by low permeability, stable fluid density, reducing fluid chemistry conditions, and an effective borehole seal. During FY16, Lawrence Berkeley National Laboratory scientists conducted a number of research studies to support the UFD Deep Borehole Field Test effort. This work included providing supporting data for the Los Alamos National Laboratory geologic framework model for the proposed deep borehole site, conducting an analog study using an extensive suite of geoscience data and samples from a deep (2.5 km) research borehole in Sweden, conducting laboratory experiments and coupled process modeling related to borehole seals, and developing a suite of potential techniques that could be applied to the characterization and monitoring of the deep borehole environment. The results of these studies are presented in this report.« less

Assessment of remote sensing technologies to discover and characterize waste sites

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

NONE

1992-03-11

This report presents details about waste management practices that are being developed using remote sensing techniques to characterize DOE waste sites. Once the sites and problems have been located and characterized and an achievable restoration and remediation program have been established, efforts to reclaim the environment will begin. Special problems to be considered are: concentrated waste forms in tanks and pits; soil and ground water contamination; ground safety hazards for workers; and requirement for long-term monitoring.

Bottom-up low molecular weight heparin analysis using liquid chromatography-Fourier transform mass spectrometry for extensive characterization.

PubMed

Li, Guoyun; Steppich, Julia; Wang, Zhenyu; Sun, Yi; Xue, Changhu; Linhardt, Robert J; Li, Lingyun

2014-07-01

Low molecular weight heparins (LMWHs) are heterogeneous, polydisperse, and highly negatively charged mixtures of glycosaminoglycan chains prescribed as anticoagulants. The detailed characterization of LMWH is important for the drug quality assurance and for new drug research and development. In this study, online hydrophilic interaction chromatography (HILIC) Fourier transform mass spectrometry (FTMS) was applied to analyze the oligosaccharide fragments of LMWHs generated by heparin lyase II digestion. More than 40 oligosaccharide fragments of LMWH were quantified and used to compare LMWHs prepared by three different manufacturers. The quantified fragment structures included unsaturated disaccharides/oligosaccharides arising from the prominent repeating units of these LMWHs, 3-O-sulfo containing tetrasaccharides arising from their antithrombin III binding sites, 1,6-anhydro ring-containing oligosaccharides formed during their manufacture, saturated uronic acid oligosaccharides coming from some chain nonreducing ends, and oxidized linkage region oligosaccharides coming from some chain reducing ends. This bottom-up approach provides rich detailed structural analysis and quantitative information with high accuracy and reproducibility. When combined with the top-down approach, HILIC LC-FTMS based analysis should be suitable for the advanced quality control and quality assurance in LMWH production.

Visualized Characterization for Cerebral Response of Acupuncture Deqi: Paradox Underway

PubMed Central

Yang, Ming-Xiao; Zeng, Fang; Wu, Xi; Chen, Jiao; Liu, Yan-Qin; Feng, Yue; Liang, Fan-Rong

2013-01-01

Acupuncture as an oriental natural healing therapy with prolonged history has been extensively utilized in the management of great numbers of disorders. Deqi, a renowned acupuncture needling sensation, is profoundly regarded as the predictor and also the prerequisite of a preferable acupuncture treatment efficacy. Till now, there is still no consistency being reached towards the mechanism of acupuncture Deqi as a result of the discrepancy for publicly acknowledged evidence. Recent visualized research on Deqi using modern technologies has demonstrated possible central mechanism towards it. However, there is a conspicuous paradox underway in the research of cerebral response to acupuncture Deqi. This paper provided a view of up-to-date studies using visualized tools to characterize the brain response to acupuncture Deqi, such as functional magnetic resonance imaging (fMRI) and positron emission tomography/computed tomography (PET/CT). The paradox was extruded to highlight certain reasons from a TCM view. It is hypothesized that acupoints located at different dermal sites, state of participant, and needling manipulation can all contribute to the current paradox. Hence, further studies on acupuncture Deqi should pay more attention to the strategy of experiment design with generalized measurement, valid sham control methods, and more to subjects in diseased condition. PMID:23935686

Unresolved issues in the understanding of the pathogenesis of local tissue damage induced by snake venoms.

PubMed

Gutiérrez, José María; Rucavado, Alexandra; Escalante, Teresa; Herrera, Cristina; Fernández, Julián; Lomonte, Bruno; Fox, Jay W

2018-06-15

Snakebite envenoming by viperid species, and by some elapids, is characterized by a complex pattern of tissue damage at the anatomical site of venom injection. In severe cases, tissue destruction may be so extensive as to lead to permanent sequelae, with serious pathophysiological, social and psychological consequences. Significant advances have been performed in the study of venom-induced tissue damage, including identification and characterization of the toxins involved, insights into the mechanisms of action of venoms and toxins, and study of tissue responses to venom-induced injury. Nevertheless, much remains to be known and understood on the pathogenesis of these alterations. This review focuses on some of the pending issues in the topic of snake venom-induced local tissue damage. The traditional 'reductionist' approach, which has predominated in the study of snake venoms and their actions, needs to be complemented by more integrative and holistic perspectives aimed at capturing the complexity of these pathological alterations. Future advances in the study of these topics will certainly pave the way for innovative therapeutic interventions, with the goal of reducing the impact of this aspect of snakebite envenoming. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Mobile laboratory measurements of atmospheric emissions from agriculture, oil, and natural gas activities in northeastern Colorado

NASA Astrophysics Data System (ADS)

Eilerman, S. J.; Peischl, J.; Neuman, J. A.; Ryerson, T. B.; Wild, R. J.; Perring, A. E.; Brown, S. S.; Aikin, K. C.; Holloway, M.; Roberts, O.

2014-12-01

Atmospheric emissions from agriculture are important to air quality and climate, yet their representation in inventories is incomplete. Increased fertilizer use has lead to increased emissions of nitrogen compounds, which can adversely affect ecosystems and contribute to the formation of fine particulates. Furthermore, extraction and processing of oil and natural gas continues to expand throughout northeastern Colorado; emissions from these operations require ongoing measurement and characterization. This presentation summarizes initial data and analysis from a summer 2014 campaign to study emissions of nitrogen compounds, methane, and other species in northeastern Colorado using a new mobile laboratory. A van was instrumented to measure NH3, N2O, NOx, NOy, CH4, CO, CO2, O3, and bioaerosols with high time resolution. By sampling in close proximity to a variety of emissions sources, the mobile laboratory facilitated accurate source identification and quantification of emissions ratios. Measurements were obtained near agricultural sites, natural gas and oil operations, and other point sources. Additionally, extensive measurements were obtained downwind from urban areas and along roadways. The relationship between ammonia and other trace gases is used to characterize sources and constrain emissions inventories.

A shift in the spatial pattern of Iberian droughts during the 17th century

NASA Astrophysics Data System (ADS)

Domínguez-Castro, F.; García-Herrera, R.; Ribera, P.; Barriendos, M.

2010-09-01

In this paper, series of drought occurrence and drought extension in the Iberian Peninsula are constructed for the 1600-1750 period from seven rogation series. These rogation ceremony records come from Bilbao, Catalonia, Zamora, Zaragoza, Toledo, Murcia and Seville. They are distributed across the Peninsula and include the areas with the most characteristic Iberian climate types, influenced by the Atlantic and the Mediterranean conditions, described from modern data. A seasonal division of the series shows that spring is a critical season for rogation series in most of Iberia, being Bilbao the only site were the highest number of rogations is detected for a different season. The annual analysis of the series shows a dramatic difference between the first half of the 17th century when droughts are characterized by its local character; and the rest of the period, when they affect to broader regions or even to the whole Peninsula. The analysis of spring series confirms the existence of the two periods detected in the annual analysis. Finally, secondary documentary sources are used to further characterise the two most extended droughts in the period, 1664 and 1680, and to verify the extension of the areas affected by droughts recorded through rogation series.

Evolution of nonspectral rhodopsin function at high altitudes.

PubMed

Castiglione, Gianni M; Hauser, Frances E; Liao, Brian S; Lujan, Nathan K; Van Nynatten, Alexander; Morrow, James M; Schott, Ryan K; Bhattacharyya, Nihar; Dungan, Sarah Z; Chang, Belinda S W

2017-07-11

High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.

Rooting Characteristics of Vegetation Near Areas 3 and 5 Radioactive Waste Management Sites at the Nevada Test Site--Part 1

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

D. J. Hansen

2003-09-30

The U.S. Department of Energy emplaced high-specific-activity low-level radioactive wastes and limited quantities of classified transuranic wastes in Greater Confinement Disposal (GCD) boreholes from 1984 to 1989. The boreholes are located at the Area 5 Radioactive Waste Management Site (RWMS) on the Nevada Test Site (NTS) in southern Nevada. The boreholes were backfilled with native alluvium soil. The surface of these boreholes and trenches is expected to be colonized by native vegetation in the future. Considering the long-term performance of the disposal facilities, bioturbation (the disruption of buried wastes by biota) is considered a primary release mechanism for radionuclides disposedmore » in GCD boreholes as well as trenches at both Areas 3 and 5 RWMSs. This report provides information about rooting characteristics of vegetation near Areas 3 and 5 RWMSs. Data from this report are being used to resolve uncertainties involving parameterization of performance assessment models used to characterize the biotic mixing of soils and radionuclide transport processes by biota. The objectives of this study were to: (1) survey the prior ecological literature on the NTS and identify pertinent information about the vegetation, (2) conduct limited field studies to describe the current vegetation in the vicinity of Areas 3 and 5 RWMSs so as to correlate findings with more extensive vegetation data collected at Yucca Mountain and the NTS, ( 3 ) review prior performance assessment documents and evaluate model assumptions based on current ecological information, and (4) identify data deficiencies and make recommendations for correcting such deficiencies.« less

NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors

PubMed Central

Fleming, Joseph D.; Pavesi, Giulio; Benatti, Paolo; Imbriano, Carol; Mantovani, Roberto; Struhl, Kevin

2013-01-01

NF-Y, a trimeric transcription factor (TF) composed of two histone-like subunits (NF-YB and NF-YC) and a sequence-specific subunit (NF-YA), binds to the CCAAT motif, a common promoter element. Genome-wide mapping reveals 5000–15,000 NF-Y binding sites depending on the cell type, with the NF-YA and NF-YB subunits binding asymmetrically with respect to the CCAAT motif. Despite being characterized as a proximal promoter TF, only 25% of NF-Y sites map to promoters. A comparable number of NF-Y sites are located at enhancers, many of which are tissue specific, and nearly half of the NF-Y sites are in select subclasses of HERV LTR repeats. Unlike most TFs, NF-Y can access its target DNA motif in inactive (nonmodified) or polycomb-repressed chromatin domains. Unexpectedly, NF-Y extensively colocalizes with FOS in all genomic contexts, and this often occurs in the absence of JUN and the AP-1 motif. NF-Y also coassociates with a select cluster of growth-controlling and oncogenic TFs, consistent with the abundance of CCAAT motifs in the promoters of genes overexpressed in cancer. Interestingly, NF-Y and several growth-controlling TFs bind in a stereo-specific manner, suggesting a mechanism for cooperative action at promoters and enhancers. Our results indicate that NF-Y is not merely a commonly used proximal promoter TF, but rather performs a more diverse set of biological functions, many of which are likely to involve coassociation with FOS. PMID:23595228

Effects of Submarine Groundwater Discharge (SGD) on the Growth of the Lobe Coral Porites lobata in Maunalua Bay, Hawaii.

NASA Astrophysics Data System (ADS)

Lubarsky, K.

2016-02-01

Submarine groundwater discharge (SGD) constitutes a large percentage of the freshwater inputs onto coastal coral reefs on high islands such as the Hawaiian Islands, although the impact of SGD on coral reef health is currently understudied. In Maunalua Bay, on Oahu, Hawaii, SGD is discharged onto shallow reef flats from discrete seeps, creating natural gradients of water chemistry across the reef flat. We used this system to investigate rates of growth of the lobe coral Porites lobata across a gradient of SGD influence at two study sites within the bay, and to characterize the variation in water chemistry gradient over space and time due to SGD. SGD input at these sites is tidally modulated, and the groundwater itself is brackish and extremely nutrient-rich (mean=190 μM NO3- at the Black Point study site, mean=40 μM NO3- at Wailupe Beach Park), with distinct carbonate signatures at both study sites. Coral nubbins were placed across the gradient for 6 months, and growth was measured using three metrics: surface area (photo analysis), buoyant weight, and linear extension. Various chemical parameters, including pH, salinity, total alkalinity, nutrients, and chlorphyll were sampled at the same locations across the gradient over 24 hour periods in the spring and fall in order to capture spatial and temporal variation in water chemistry due to the SGD plume. Spatial patterns and temporal variation in water chemistry were correlated with the observed spatial patterns in coral growth across the SGD gradient.

10 CFR 60.18 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... IN GEOLOGIC REPOSITORIES Licenses Preapplication Review § 60.18 Review of site characterization... its progress in developing the design of a geologic repository operations area appropriate for the...

SITE CHARACTERIZATION TO SUPPORT DEVELOPMENT OF CONCEPTUAL SITE MODELS AND TRANSPORT MODELS FOR MONITORING CONTAMINANTS IN GROUND WATER

EPA Science Inventory

The development of conceptual and predictive models is an important tool to guide site characterization in support of monitoring contaminants in ground water. The accuracy of predictive models is limited by the adequacy of the input data and the assumptions made to constrain mod...

New methods to characterize site amplification

USGS Publications Warehouse

Safak, Erdal

1993-01-01

Methods alternative to spectral ratios are introduced to characterize site amplification. The methods are developed by using a range of models, from the simple constant amplification model to the time-varying filter model. Examples are given for each model by using a pair of rock- and soil-site recordings from the Loma Prieta earthquake.

Late Miocene extension partitioning in the eastern Betics: from W- to E-directed extension between the Sorbas and Vera basins (SE Spain).

NASA Astrophysics Data System (ADS)

Giaconia, Flavio; Booth-Rea, Guillermo; Martínez-Martínez, Jose Miguel; Azañon, Jose Miguel

2014-05-01

Late Miocene westward-directed extension in the Betics produced elongated core-complexes like Sierra Nevada and the Sierra de Filabres, tilted-block domains and associated basins. This extension represents the superficial manifestation of the rupture of the Tethyan slab and associated edge delamination along a lithospheric transform fault beneath the northern branch of the Gibraltar Arc orogenic system. However, crustal thinning at the eastern Betics occurs progressively towards the east suggesting an eastward-directed extension, probably related to the late Miocene opening of the Algero-Balearic basin. In order to define the kinematics and timing of such a heterogeneous extension at the eastern Betics we have carefully mapped a key area at the transition between the Sorbas and Vera basins. Field data indicate that extension in the area started at the southern margin of the Vera basin during the Serravallian (13.8 Ma) and continued until the Tortonian (approximately 8 Ma). This extension was characterized by a set of NE- to E-directed normal faults to the east, in the Vera basin, and a set of SW-directed normal faults to the west, towards the Sorbas basin. This opposite-directed extension is segmented by E-W to WNW-ESE strike-slip faults like the North Cabrera dextral transfer fault that accommodates NE- to E-directed extension to the north and SW-directed extension to the south. This structure resulted in westward tilted blocks that lead to Serravallian-Tortonian depocenters deepening towards the east at the Vera basin along the northern side of Sierra Cabrera. Meanwhile, at the western termination of Sierra Cabrera, westward-directed extension migrated SW-ward forming the Sorbas basin during the Tortonian (approximately 9-7.24 Ma). This extension was characterized by a listric fan of SW-directed normal faults highly segmented by E-W to NE-SW transfer. This extensional system produced tiled-blocks defining a Tortonian depocenter at the eastern margin of the Sorbas basin. This westward migration of extension followed very closely the apatite fission track cooling ages obtained from Nevado-Filabride samples exhumed at the Sierra de Filabres core-complex, to the north. These ages range between 15 and 11 Ma, to the east, and between 9.5 and 7.5 Ma, to the west. The westward migration of extension continued during the Messinian and the Quaternary affecting the Níjar basin where a SW-directed normal-fault system occurs. Heterogeneous extension in the region resulted in different extensional domains both in extension direction and style. These domains are separated by transfer faults as the North Cabrera dextral fault, which accommodated opposite tilted-block domains at the southern margin of the Vera basin. Similarly, the Carboneras sinistral fault separates the Níjar tilted-block domain, to the north, from the Cabo de Gata domain characterized by magmatic accretion upon previously thinned continental crust, to the south.

Chemical climatology of the southeastern United States, 1999-2013

NASA Astrophysics Data System (ADS)

Hidy, G. M.; Blanchard, C. L.; Baumann, K.; Edgerton, E.; Tanenbaum, S.; Shaw, S.; Knipping, E.; Tombach, I.; Jansen, J.; Walters, J.

2014-11-01

A series of experiments (the Southern Oxidant and Aerosol Study - SOAS) took place in central Alabama in June-July, 2013 as part of the broader Southern Atmosphere Study (SAS). These projects were aimed at studying oxidant photochemistry and formation and impacts of aerosols at a detailed process level in a location where high biogenic organic vapor emissions interact with anthropogenic emissions, and the atmospheric chemistry occurs in a subtropical climate in North America. The majority of the ground-based experiments were located at the Southeastern Aerosol Research and Characterization (SEARCH) Centreville (CTR) site near Brent, Alabama, where extensive, unique aerometric measurements of trace gases and particles and meteorology were made beginning in the early 1990s through 2013. The SEARCH network data permits a characterization of the temporal and spatial context of the SOAS findings. Our earlier analyses of emissions and air quality trends are extended through 2013 to provide a perspective for continued decline in ambient concentrations, and the implications of these changes to regional sulfur oxide, nitrogen-ozone, and carbon chemistry. The narrative supports the SAS program in terms of long-term average chemistry (chemical climatology) and short-term comparisons of early summer average spatial variability across the southeastern US at high temporal (hourly) resolution. The long-term measurements show that the SOAS experiments took place during the second wettest and coolest year in the 2000-2013 period, with lower than average solar radiation. The pollution levels at CTR and other SEARCH sites were the lowest since full measurements began in 1999. Changes in anthropogenic gas and particle emissions between 1999 and 2013 account for the decline in pollutant concentrations at the monitoring sites in the region. The data provide an opportunity to contrast SOAS results with temporally and spatially variable conditions in support of the development of tests for the robustness of SOAS findings.

The road to Yucca Mountain—Evolution of nuclear waste disposal in the United States

USGS Publications Warehouse

Stuckless, John S.; Levich, Robert A.

2016-01-01

The generation of electricity by nuclear power and the manufacturing of atomic weapons have created a large amount of spent nuclear fuel and high-level radioactive waste. There is a world-wide consensus that the best way to protect mankind and the environment is to dispose of this waste in a deep geologic repository. Initial efforts focused on salt as the best medium for disposal, but the heat generated by the radioactive waste led many earth scientists to examine other rock types. In 1976, the director of the U.S. Geological Survey (USGS) wrote to the U.S. Energy Research and Development Administration (ERDA), predecessor agency of the U.S. Department of Energy (DOE), suggesting that there were several favorable environments at the Nevada Test Site (NTS), and that the USGS already had extensive background information on the NTS. Later, in a series of communications and one publication, the USGS espoused the favorability of the thick unsaturated zone. After the passage of the Nuclear Waste Policy Act (1982), the DOE compiled a list of nine favorable sites and settled on three to be characterized. In 1987, as the costs of characterizing three sites ballooned, Congress amended the Nuclear Waste Policy Act directing the DOE to focus only on Yucca Mountain in Nevada, with the proviso that if anything unfavorable was discovered, work would stop immediately. The U.S. DOE, the U.S. DOE national laboratories, and the USGS developed more than 100 detailed plans to study various earth-science aspects of Yucca Mountain and the surrounding area, as well as materials studies and engineering projects needed for a mined geologic repository. The work, which cost more than 10 billion dollars and required hundreds of man-years of work, culminated in a license application submitted to the U.S. Nuclear Regulatory Commission (NRC) in 2008.

Drupal Done Right

ERIC Educational Resources Information Center

Coombs, Karen

2009-01-01

Drupal is a PHP-and MySQL-based system for managing web sites, developed in 2000 and released in 2001 under the open GNU General Public License (GPL). It is modular, extensible, and scalable. In recent years, Drupal has gained a huge following within libraries as a content management system (CMS). Probably the best-known extension of Drupal in the…

78 FR 54756 - Extension of Expiration Dates for Two Body System Listings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-06

... SOCIAL SECURITY ADMINISTRATION 20 CFR Part 404 [Docket No. SSA-2013-0039] RIN 0960-AH60 Extension of Expiration Dates for Two Body System Listings AGENCY: Social Security Administration. ACTION... national toll-free number, 1-800-772-1213, or TTY 1-800-325-0778, or visit our Internet site, Social...

REMEDIAL COSTS FOR MTBE IN SOIL AND GROUND WATER

EPA Science Inventory

The extensive contamination of methyl tertiary butyl ether (MTBE) in ground water has introduced concerns about the increased cost of remediation of MTBE releases compared to sites with BTEX only contamination. In an attempt to evaluate these costs, cost information for 311 site...

Molecular structure of human KATP in complex with ATP and ADP

PubMed Central

Lee, Kenneth Pak Kin

2017-01-01

In many excitable cells, KATP channels respond to intracellular adenosine nucleotides: ATP inhibits while ADP activates. We present two structures of the human pancreatic KATP channel, containing the ABC transporter SUR1 and the inward-rectifier K+ channel Kir6.2, in the presence of Mg2+ and nucleotides. These structures, referred to as quatrefoil and propeller forms, were determined by single-particle cryo-EM at 3.9 Å and 5.6 Å, respectively. In both forms, ATP occupies the inhibitory site in Kir6.2. The nucleotide-binding domains of SUR1 are dimerized with Mg2+-ATP in the degenerate site and Mg2+-ADP in the consensus site. A lasso extension forms an interface between SUR1 and Kir6.2 adjacent to the ATP site in the propeller form and is disrupted in the quatrefoil form. These structures support the role of SUR1 as an ADP sensor and highlight the lasso extension as a key regulatory element in ADP’s ability to override ATP inhibition. PMID:29286281

Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme.

PubMed

Brown, Breann L; Kardon, Julia R; Sauer, Robert T; Baker, Tania A

2018-04-03

5-Aminolevulinic acid synthase (ALAS) catalyzes the first step in heme biosynthesis. We present the crystal structure of a eukaryotic ALAS from Saccharomyces cerevisiae. In this homodimeric structure, one ALAS subunit contains covalently bound cofactor, pyridoxal 5'-phosphate (PLP), whereas the second is PLP free. Comparison between the subunits reveals PLP-coupled reordering of the active site and of additional regions to achieve the active conformation of the enzyme. The eukaryotic C-terminal extension, a region altered in multiple human disease alleles, wraps around the dimer and contacts active-site-proximal residues. Mutational analysis demonstrates that this C-terminal region that engages the active site is important for ALAS activity. Our discovery of structural elements that change conformation upon PLP binding and of direct contact between the C-terminal extension and the active site thus provides a structural basis for investigation of disruptions in the first step of heme biosynthesis and resulting human disorders. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ground penetrating radar survey and lineament analysis of the West Pearl Queen carbon sequestration pilot site, New Mexico

NASA Astrophysics Data System (ADS)

Wilson, T. H.; Wells, A. W.; Diehl, R. R.; Bromhal, G. S.; Carpenter, W.; Smith, D. H.

2004-05-01

The potential for leakage of injected CO2 at carbon sequestration sites is a significant concern in the design and deployment of long term carbon sequestration efforts. Effective and reliable monitoring of near-surface environments in the vicinity of these sites is essential to ensure the viability of sequestration activities as well as long term public and environmental safety. This study reports on near-surface geological and geophysical characterization efforts conducted at the NETL West Pearl Queen carbon sequestration pilot site in southeastern New Mexico and their use in uncovering possible mechanisms facilitating escape of small amounts (10e-13 liters) of tracer injected with the CO2. In this pilot test, a small amount of CO2 (2100 tonnes) was injected into the Shattuck sandstone member of the Permian Queen Formation early in 2003. Tracers injected with the CO2 were detected within a few days of injection and continued to escape for several months following injection. Geological and geophysical characterization of the near-surface environment in the vicinity of the injection well incorporated lineament interpretations and a detailed ground penetrating radar survey conducted over a circular area extending out 300 meters from the injection well. The near-surface geology consists of a few-feet thick veneer of late Pleistocene and Holocene sand dunes covering the middle Pleistocene Mescalero caliche. The lineament study incorporated interpretation of black and white aerial photos from 1949, digital orthophotos, and Landsat TM imagery. Analysis reveals distinct northeast and northwest trending lineament sets. The GPR survey defines the presence of a nearly continuous blanket of caliche beneath the area. However, the thickness of the caliche zone varies significantly, and it is disrupted by numerous fault-like features, amplitude anomalies, and reflection gaps. Some of these disruptions are traceable over distances of 25 to 200 meters and their aerial distribution shows some association with the distribution of tracers detected in the near-surface across the site. The observations suggest that the caliche has undergone significant karstification and could provide pathways along which CO2 could migrate through the near-surface from a leaky well casing or, less likely, along more extensive vertical migration pathways.

Characterization of human translesion DNA synthesis across a UV-induced DNA lesion

PubMed Central

Hedglin, Mark; Pandey, Binod; Benkovic, Stephen J

2016-01-01

Translesion DNA synthesis (TLS) during S-phase uses specialized TLS DNA polymerases to replicate a DNA lesion, allowing stringent DNA synthesis to resume beyond the offending damage. Human TLS involves the conjugation of ubiquitin to PCNA clamps encircling damaged DNA and the role of this post-translational modification is under scrutiny. A widely-accepted model purports that ubiquitinated PCNA recruits TLS polymerases such as pol η to sites of DNA damage where they may also displace a blocked replicative polymerase. We provide extensive quantitative evidence that the binding of pol η to PCNA and the ensuing TLS are both independent of PCNA ubiquitination. Rather, the unique properties of pols η and δ are attuned to promote an efficient and passive exchange of polymerases during TLS on the lagging strand. DOI: http://dx.doi.org/10.7554/eLife.19788.001 PMID:27770570

Identification of genetic elements in metabolism by high-throughput mouse phenotyping.

PubMed

Rozman, Jan; Rathkolb, Birgit; Oestereicher, Manuela A; Schütt, Christine; Ravindranath, Aakash Chavan; Leuchtenberger, Stefanie; Sharma, Sapna; Kistler, Martin; Willershäuser, Monja; Brommage, Robert; Meehan, Terrence F; Mason, Jeremy; Haselimashhadi, Hamed; Hough, Tertius; Mallon, Ann-Marie; Wells, Sara; Santos, Luis; Lelliott, Christopher J; White, Jacqueline K; Sorg, Tania; Champy, Marie-France; Bower, Lynette R; Reynolds, Corey L; Flenniken, Ann M; Murray, Stephen A; Nutter, Lauryl M J; Svenson, Karen L; West, David; Tocchini-Valentini, Glauco P; Beaudet, Arthur L; Bosch, Fatima; Braun, Robert B; Dobbie, Michael S; Gao, Xiang; Herault, Yann; Moshiri, Ala; Moore, Bret A; Kent Lloyd, K C; McKerlie, Colin; Masuya, Hiroshi; Tanaka, Nobuhiko; Flicek, Paul; Parkinson, Helen E; Sedlacek, Radislav; Seong, Je Kyung; Wang, Chi-Kuang Leo; Moore, Mark; Brown, Steve D; Tschöp, Matthias H; Wurst, Wolfgang; Klingenspor, Martin; Wolf, Eckhard; Beckers, Johannes; Machicao, Fausto; Peter, Andreas; Staiger, Harald; Häring, Hans-Ulrich; Grallert, Harald; Campillos, Monica; Maier, Holger; Fuchs, Helmut; Gailus-Durner, Valerie; Werner, Thomas; Hrabe de Angelis, Martin

2018-01-18

Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome.

Glycyl radical activating enzymes: structure, mechanism, and substrate interactions.

PubMed

Shisler, Krista A; Broderick, Joan B

2014-03-15

The glycyl radical enzyme activating enzymes (GRE-AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe-4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE-AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE-AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE-AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes. Copyright © 2014. Published by Elsevier Inc.

The cutting mechanism of the electrosurgical scalpel

NASA Astrophysics Data System (ADS)

Gjika, Eda; Pekker, Mikhail; Shashurin, Alexey; Shneider, Mikhail; Zhuang, Taisen; Canady, Jerome; Keidar, Michael

2017-01-01

Electrosurgical cutting is a well-known technique for creating incisions often used for the removal of benign and malignant tumors. The proposed mathematical model suggests that incisions are created due to the localized heating of the tissue. The model estimates a volume of tissue heating in the order of 2 · 10-4 mm3. This relatively small predicted volume explains why the heat generated from the very tip of the scalpel is unable to cause extensive damage to the tissue adjacent to the incision site. The scalpel exposes the target region to an RF field in 60 ms pulses until a temperature of around 100 °C is reached. This process leads to desiccation where the tissue is characterized by a significantly low electrical conductivity, which prevents further heating and charring. Subsequently, the incision is created from the mechanical scraping process that follows.

A 3400 year paleolimnological record of prehispanic human–environment interactions in the Holmul region of the southern Maya lowlands

USGS Publications Warehouse

Wahl, David B.; Estrada-Belli, Francisco; Anderson, Lysanna

2015-01-01

The timing, magnitude and drivers of late Holocene environmental change in the Holmul region of the southern Maya lowlands are examined by combining paleoenvironmental and archeological data. Environmental proxy analyses on a ~ 3350 cal yr lacustrine sediment record include pollen, charcoal, loss on ignition, magnetic suscep- tibility, and elemental geochemistry. Archeological evidence is derived from extensive settlement surveys conducted near the study site. Results indicate nearby settlement and agricultural activity taking place in an environment characterized by open forest from around 3350 to 950 cal yr BP. The fire history shows a dramatic increase in burning during the Classic period, possibly reflecting changing agricultural strategies. A distinct band of carbonate deposited from 1270 to 1040 cal yr BP suggests decreased hydrologic input associated with drier conditions. Abrupt changes in proxy data around 940 cal yr BP indicate a cessation of human disturbance and local abandonment of the area.

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

Sunden, Fanny; Peck, Ariana; Salzman, Julia

Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called ‘catalytic residues’ are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modesmore » of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.« less

Production of Primary Amines by Reductive Amination of Biomass-Derived Aldehydes/Ketones.

PubMed

Liang, Guanfeng; Wang, Aiqin; Li, Lin; Xu, Gang; Yan, Ning; Zhang, Tao

2017-03-06

Transformation of biomass into valuable nitrogen-containing compounds is highly desired, yet limited success has been achieved. Here we report an efficient catalyst system, partially reduced Ru/ZrO 2 , which could catalyze the reductive amination of a variety of biomass-derived aldehydes/ketones in aqueous ammonia. With this approach, a spectrum of renewable primary amines was produced in good to excellent yields. Moreover, we have demonstrated a two-step approach for production of ethanolamine, a large-market nitrogen-containing chemical, from lignocellulose in an overall yield of 10 %. Extensive characterizations showed that Ru/ZrO 2 -containing multivalence Ru association species worked as a bifunctional catalyst, with RuO 2 as acidic promoter to facilitate the activation of carbonyl groups and Ru as active sites for the subsequent imine hydrogenation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural characterizations of human periostin dimerization and cysteinylation.

PubMed

Liu, Jianmei; Zhang, Junying; Xu, Fei; Lin, Zhaohan; Li, Zhiqiang; Liu, Heli

2018-05-12

Human periostin plays a multifaceted role in remodeling the extracellular matrix milieu by interacting with other proteins and itself in both a heterophilic and homophilic manner. However, the structural mechanism for its extensive interactions has remained elusive. Here, we report the crystal structures of human periostin (EMI-Fas1 I- IV ) and its Cys60Ala mutant. In combination with multi-angle light scattering analysis and biochemical assays, the crystal structures reveal that periostin mainly exists as a dimer in solution and its homophilic interaction is mainly mediated by the EMI domain. Furthermore, Cys60 undergoes cysteinylation as confirmed by mass spectroscopy, and this site hardly affects the homophilic interaction. Also, the structures yield insights into how periostin forms heterophilic interactions with other proteins under physiological or pathological conditions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The Microstructure of Lunar Micrometeorite Impact Craters

NASA Technical Reports Server (NTRS)

Noble, S. K.; Keller, L. P.; Christoffersen, R.; Rahman, Z.

2016-01-01

The peak of the mass flux of impactors striking the lunar surface is made up of objects approximately 200 micrometers in diameter that erode rocks, comminute regolith grains, and produce agglutinates. The effects of these micro-scale impacts are still not fully understood. Much effort has focused on evaluating the physical and optical effects of micrometeorite impacts on lunar and meteoritic material using pulsed lasers to simulate the energy deposited into a substrate in a typical hypervelocity impact. Here we characterize the physical and chemical changes that accompany natural micrometeorite impacts into lunar rocks with long surface exposure to the space environment (12075 and 76015). Transmission electron microscope (TEM) observations were obtained from cross-sections of approximately 10-20 micrometers diameter craters that revealed important micro-structural details of micrometeorite impact processes, including the creation of npFe (sup 0) in the melt, and extensive deformation around the impact site.

SITE CHARACTERIZATION OF AREA 6, DOVER AIR FORCE BASE, IN SUPPORT OF NATURAL ATTENUATION AND ENHANCED ANAEROBIC BIOREMEDIATION PROJECTS

EPA Science Inventory

A field program for site characterization of targeted study areas at the Dover Air Force Base was conducted between January 16, 1995, and March 9, 1995. The stated objectives of the investigation, "to characterize the stratigraphy, depth to groundwater, groundwater flow directio...

IODP Expedition 338: Riser and Riserless Drilling Along the NanTroSEIZE Transect

NASA Astrophysics Data System (ADS)

Strasser, M.; Moore, G. F.; Dugan, B.; Kanagawa, K.; Toczko, S.

2013-12-01

Integrated Ocean Drilling Program (IODP) Expedition 338 provided new constraints on the Kumano Basin sediments, the accretionary prism inner wedge, the seaward extension of the megasplay fault, the architecture and mechanics of landslides, and the alteration of oceanic basement of the incoming Philippine Sea plate. This was accomplished through riser and riserless drilling, logging while drilling (LWD), and cuttings and core analysis. Cuttings and LWD analyses at Hole C0002F reveal two lithologic units in the prism inner wedge which are separated by a prominent fault zone at ~1640 mbsf. Mud-gases from the inner prism show high concentrations at the top of the wedge that decrease, but become more thermogenic, with depth. These data are from the previously unaccessed deeper part of the Nankai accretionary prism. Riserless coring at Site C0002 provided data across the gas hydrate zone of the Kumano Basin, across the Kumano Basin-accretionary prism unconformity, and in the uppermost accretionary prism. Within the Kumano basin section, gas and porewater geochemistry documents microbial methane gas in hydrates that are disseminated in sandy layers. Multiple penetrations of the Kumano Basin-accretionary prism boundary and 3D seismic data show that the boundary is erosive and complex. LWD (Site C0018) and coring and LWD (Site C0021) augment existing data to better understand submarine landslide dynamics and mass-transport deposit (MTD) emplacement processes. Previous coring at Site C0018 identified six MTDs, but only two MTD intervals were detected in resistivity images that show high angle, randomly oriented bedding. Site C0021, located more proximal to the MTD source, provides constraint on MTD variability. Correlation across the sites reveals a thick MTD with an erosional base characterized by a shear zone in muddy sediments vs. a translational basal surface within coarse volcaniclastic sand in the proximal and distal/lateral areas, respectively. LWD data and cores from Site C0022 characterize the uppermost 400 m of sediment near the tip of the megasplay fault zone where it approaches the seafloor. This fault zone is inferred to be located at the interval of 80-145 mbsf, based on biostratigraphic reversals, bedding dips >20°, porosity anomalies and a change in trend of interstitial water chemistry data. LWD at Site C0012 primarily yielded insights into the nature of the incoming oceanic crust. Two crustal units were identified based on LWD data. The upper unit had gamma ray variations that may indicate changes in the crustal alteration or sediment-basalt interlayering. The deeper unit has little variation in log properties, suggesting the presence of uniform or fresh basalt. Together these data provide new constraints on the overall architecture and mechanics of the Nankai subduction zone.

10 CFR 60.7 - License not required for certain preliminary activities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.7 License not required for certain preliminary... repository: (a) For purposes of site characterization; or (b) For use, during site characterization or...

Spectral Induced Polarization monitoring of the groundwater physico-chemical parameters daily variations for stream-groundwater interactions

NASA Astrophysics Data System (ADS)

Jougnot, Damien; Camerlynck, Christian; Robain, Henri; Tallec, Gaëlle; Ribolzi, Olivier; Gaillardet, Jérôme

2017-04-01

During the last decades, geophysical methods have been attracting an increasing interest in hydrology and environmental sciences given their sensitivity to parameters of interests and their non-intrusive nature. The Spectral Induced Polarization (SIP) is a low frequency electro-magnetic method that allows the characterization of the subsurface through its complex electrical conductivity. It reports the modulus of the conductivity and the phase between an injected current and a measured voltage over a rather large frequency range (from few millihertz to few tens of kilohertz). The real part of the conductivity is sensitive to lithological (porosity, specific surface area) and hydrological (water saturation, water salinity) parameters, while the imaginary part is linked to electrochemical polarizations, that have been shown to be largely influenced by the chemistry of the pore water. In the present contribution, we aim at better characterizing the exchanges between a stream and the surrounding groundwater using the SIP method and its sensitivity to pore water changes over time. Two sites from the OZCAR Research Infrastructure (French Critical Zone observatories) have been chosen for this study: the Houay Pano catchment (Laos) and the Orgeval catchment (France). These two sites have a good existing infrastructure and have been already studied extensively in terms of hydrology, geophysics, and hydrochemistry. They constitute perfect experimental sites to develop novel methodologies for the assessment of stream-groundwater exchanges. We propose to obtain a vertical description of the changes in complex electrical conductivity with depth based on SIP soundings undertaken with the multi-channel system SIP Fuchs III. We conducted a high-frequency monitoring close to a river stream (one vertical profiles every 30 min). In parallel, a high frequency monitoring of the physico-chemical parameters (temperature, conductivity, ionic concentrations) in the river stream has been performed. Relating the daily fluctuations of the groundwater complex conductivity and the river physico-chemical parameters could therefore establish a new proxy to characterize stream-groundwater interactions. In parallel to the field measurements, laboratory experiments have been conducted on soil samples from the two sites. These measurements provide a better understanding of the complex conductivity signature of the samples submitted to saturation and pore water physico-chemical changes. This work is in progress but the first results already show that the method has a real interest for the monitoring of daily variations of the physico-chemistry properties of the groundwater and their relations to those of the stream.

Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites

PubMed Central

Ye, Wenjie; Paul, Debamita; Gao, Lina; Seckute, Jolita; Jayaraj, Karupiah; Zhang, Zhenfa; Kaminski, P. Alexandre

2014-01-01

Deoxyribosyl transferases and functionally related purine nucleoside phosphorylases are used extensively for synthesis of non-natural deoxynucleosides as pharmaceuticals or standards for characterizing and quantitating DNA adducts. Hence exploring the conformational tolerance of the active sites of these enzymes is of considerable practical interest. We have determined the crystal structure at 2.1 Å resolution of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N 2,3-ethenoguanine) at the active site. The active site electron density map was compatible with four orientations, two consistent with sites for deoxyribosylation and two appearing to be unproductive. In accord with the crystal structure, Lactobacillus helveticus PDT glycosylates the 8,9-dihydro-9-oxoimidazo[2,1-b]purine at N7 and N1, with a marked preference for N7. The activity of Lactobacillus helveticus PDT was compared with that of the nucleoside 2′-deoxyribosyltransferase enzymes (DRT Type II) from Lactobacillus leichmannii and Lactobacillus fermentum, which were somewhat more effective in the deoxyribosylation than Lactobacillus helveticus PDT, glycosylating the substrate with product profiles dependent on the pH of the incubation. The purine nucleoside phosphorylase of Escherichia coli, also commonly used in ribosylation of non-natural bases, was an order of magnitude less efficient than the transferase enzymes. Modeling based on published active-site structures as templates suggests that in all cases, an active site Phe is critical in orienting the molecular plane of the purine derivative. Adventitious hydrogen bonding with additional active site residues appears to result in presentation of multiple nucleophilic sites on the periphery of the acceptor base for ribosylation to give a distribution of nucleosides. Chemical glycosylation of O 9-benzylated 8,9-dihydro-9-oxoimidazo[2,1-b]purine also resulted in N7 and N1 ribosylation. Absent from the enzymatic and chemical glycosylations is the natural pattern of N3 ribosylation, verified by comparison of spectroscopic and chromatographic properties with an authentic standard synthesized by an unambiguous route. PMID:25521390

Environmental assessment: Davis Canyon site, Utah

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

none,

1986-05-01

In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOEmore » prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considering for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization.« less

Diurnal warming in shallow coastal seas: Observations from the Caribbean and Great Barrier Reef regions

NASA Astrophysics Data System (ADS)

Zhu, X.; Minnett, P. J.; Berkelmans, R.; Hendee, J.; Manfrino, C.

2014-07-01

A good understanding of diurnal warming in the upper ocean is important for the validation of satellite-derived sea surface temperature (SST) against in-situ buoy data and for merging satellite SSTs taken at different times of the same day. For shallow coastal regions, better understanding of diurnal heating could also help improve monitoring and prediction of ecosystem health, such as coral reef bleaching. Compared to its open ocean counterpart which has been studied extensively and modeled with good success, coastal diurnal warming has complicating localized characteristics, including coastline geometry, bathymetry, water types, tidal and wave mixing. Our goal is to characterize coastal diurnal warming using two extensive in-situ temperature and weather datasets from the Caribbean and Great Barrier Reef (GBR), Australia. Results showed clear daily warming patterns in most stations from both datasets. For the three Caribbean stations where solar radiation is the main cause of daily warming, the mean diurnal warming amplitudes were about 0.4 K at depths of 4-7 m and 0.6-0.7 K at shallower depths of 1-2 m; the largest warming value was 2.1 K. For coral top temperatures of the GBR, 20% of days had warming amplitudes >1 K, with the largest >4 K. The bottom warming at shallower sites has higher daily maximum temperatures and lower daily minimum temperatures than deeper sites nearby. The averaged daily warming amplitudes were shown to be closely related to daily average wind speed and maximum insolation, as found in the open ocean. Diurnal heating also depends on local features including water depth, location on different sections of the reef (reef flat vs. reef slope), the relative distance from the barrier reef chain (coast vs. lagoon stations vs. inner barrier reef sites vs. outer rim sites); and the proximity to the tidal inlets. In addition, the influence of tides on daily temperature changes and its relative importance compared to solar radiation was quantified by calculating the ratio of power spectrum densities at the principal lunar semidiurnal M2 tide versus 24-hour cycle frequency representing mainly solar radiation forcing, i.e., (PSDM2/PSD24). Despite the fact that GBR stations are generally located at regions with large tidal changes, the tidal effects were modest: 80% of stations showed value of (PSDM2/PSD24) of less than 10%.

Yucca Mountain Biological Resources Monitoring Program. Progress report, January 1994--December 1994

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

NONE

1995-07-01

The US Department of Energy (DOE) is required by the Nuclear Waste Policy Act of 1982 (as amended in 1987) to study and characterize the suitability of Yucca Mountain as a potential geological repository for high-level nuclear waste. During site characterization, the DOE will conduct a variety of geotechnical, geochemical, geological, and hydrological studies to determine the suitability of Yucca Mountain as a potential repository. To ensure that site characterization activities do not adversely affect the environment at Yucca Mountain, a program has been implemented to monitor and mitigate potential impacts and ensure activities comply with applicable environmental regulations. Thismore » report describes the activities and accomplishments of EG and G Energy Measurements, Inc. (EG and G/EM) from January 1994 through December 1994 for six program areas within the Terrestrial Ecosystem component of the environmental program for the Yucca Mountain Site Characterization Project (YMP): Site Characterization Effects, Desert Tortoises (Gopherus agassizii), Habitat Reclamation, Monitoring and Mitigation, Radiological Monitoring, and Biological Support.« less

Social Studies. [SITE 2001 Section].

ERIC Educational Resources Information Center

White, Cameron, Ed.

This document contains the following papers on social studies from the SITE (Society for Information Technology & Teacher Education) 2001 conference: (1) "Teacher's Guide to the Holocaust: An Extensive Online Resource for Teachers" (Ann E. Barron and others); (2) "Preparing a Virtual Field Trip To Teach Value of Community and…

TREATMENT OF ARSENIC AND METALS IN GROUND WATER USING A COMPOST/ZVI PRB

EPA Science Inventory

One of Region 4's Regional Applied Research Efforts (RARE) projects resulted in two different studies on cleaning up the Columbia Nitrogen Superfund Site located in Charleston, SC. This site is extensively contaminated with pyrite and elemental sulfur used in phosphate fertilize...

Comparison of mesospheric sodium layers at different latitudes

NASA Astrophysics Data System (ADS)

Liu, Yingjie

With the support of the Chinese Meridional project in the eastern hemisphere, two brand new sodium fluorescence lidars with the same configuration were respectively set up at Yanqing (40.46(°) N, 115.98(°) E) and Haikou (20.04(°) N, 110.34(°) E) in April, 2010. Based on the observations obtained from 2010 to 2012, comparison of the Na layer at these two latitudes was performed. It reveals a strong correlation in the topside layer between these two sites. Independently of their seasonal characteristics at lower altitudes, they both show an extension to 120 km and above, predominantly during summer. Simultaneous observations at these two sites show that the correlation above 102 km is remarkable in contrast to their different seasonal characteristics below 98 km. It indicates that different processes dominate different height ranges in the Na layer. Meanwhile, it indicates that the topside extension effect is global, combined with the observations at other latitudes. Besides, when the topside layer has an extension, the bottom side layer extends slightly downward, too. Comparison with known meteor showers shows that most of these extensions correspond well to one or more meteor showers, although not one by one. Meteor showers with velocities less than 35 km/s appear to have more influence on these extensions.

Poincare inequalities, uniform domains and extension properties for Newton-Sobolev functions in metric spaces

NASA Astrophysics Data System (ADS)

Bjorn, Jana; Shanmugalingam, Nageswari

2007-08-01

In the setting of metric measure spaces equipped with a doubling measure supporting a weak p-Poincare inequality with 1[less-than-or-equals, slant]p<[infinity], we show that any uniform domain [Omega] is an extension domain for the Newtonian space N1,p([Omega]) and that [Omega], together with the metric and the measure inherited from X, supports a weak p-Poincare inequality. For p>1, we obtain a near characterization of N1,p-extension domains with local estimates for the extension operator.

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

Code of Federal Regulations, 2010 CFR

2010-01-01

... POTENTIAL SITES FOR A NUCLEAR WASTE REPOSITORY Implementation Guidelines § 960.3-2-3 Recommendation of sites... characterization for the selection of the first repository, the Secretary shall recommend in writing to the..., and, after the first repository, consideration of regionality in §§ 960.3-1-1, 960.3-1-2, and 960.3-1...

Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.

PubMed Central

Allawi, H T; Dong, F; Ip, H S; Neri, B P; Lyamichev, V I

2001-01-01

A rapid and simple method for determining accessible sites in RNA that is independent of the length of target RNA and does not require RNA labeling is described. In this method, target RNA is allowed to hybridize with sequence-randomized libraries of DNA oligonucleotides linked to a common tag sequence at their 5'-end. Annealed oligonucleotides are extended with reverse transcriptase and the extended products are then amplified by using PCR with a primer corresponding to the tag sequence and a second primer specific to the target RNA sequence. We used the combination of both the lengths of the RT-PCR products and the location of the binding site of the RNA-specific primer to determine which regions of the RNA molecules were RNA extendible sites, that is, sites available for oligonucleotide binding and extension. We then employed this reverse transcription with the random oligonucleotide libraries (RT-ROL) method to determine the accessible sites on four mRNA targets, human activated ras (ha-ras), human intercellular adhesion molecule-1 (ICAM-1), rabbit beta-globin, and human interferon-gamma (IFN-gamma). Our results were concordant with those of other researchers who had used RNase H cleavage or hybridization with arrays of oligonucleotides to identify accessible sites on some of these targets. Further, we found good correlation between sites when we compared the location of extendible sites identified by RT-ROL with hybridization sites of effective antisense oligonucleotides on ICAM-1 mRNA in antisense inhibition studies. Finally, we discuss the relationship between RNA extendible sites and RNA accessibility. PMID:11233988

Cultured allogeneic keratinocyte sheets accelerate healing compared to Op-site treatment of donor sites in burns.

PubMed

Duinslaeger, L A; Verbeken, G; Vanhalle, S; Vanderkelen, A

1997-01-01

Donor site treatment is a crucial issue in the treatment of extensive burns. In this single-blind, randomized study treatment of donor sites with a polyurethane dressing, Op-Site (Smith & Nephew, York, U.K.) is compared to treatment with allogeneic cultured keratinocyte sheets. Results show a mean healing time of 6.7 days with use of cultured keratinocyte sheets compared to mean healing time of 13.6 days with Op-Site treatment. Also, improvement in the comfort of patients as the result of less exudate formation and pain attenuation was noted.

CHARACTERIZING SITE HYDROLOGY (REGION 5)

EPA Science Inventory

Hydrogeology is the foundation of subsurface site characterization for evaluations of monitored natural attenuation (MNA). Three case studies are presented. Examples of the potentially detrimental effects of drilling additives on ground-water samples from monitoring wells are d...

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data.

PubMed

Ye, Congting; Long, Yuqi; Ji, Guoli; Li, Qingshun Quinn; Wu, Xiaohui

2018-06-01

Alternative polyadenylation (APA) has been increasingly recognized as a crucial mechanism that contributes to transcriptome diversity and gene expression regulation. As RNA-seq has become a routine protocol for transcriptome analysis, it is of great interest to leverage such unprecedented collection of RNA-seq data by new computational methods to extract and quantify APA dynamics in these transcriptomes. However, research progress in this area has been relatively limited. Conventional methods rely on either transcript assembly to determine transcript 3' ends or annotated poly(A) sites. Moreover, they can neither identify more than two poly(A) sites in a gene nor detect dynamic APA site usage considering more than two poly(A) sites. We developed an approach called APAtrap based on the mean squared error model to identify and quantify APA sites from RNA-seq data. APAtrap is capable of identifying novel 3' UTRs and 3' UTR extensions, which contributes to locating potential poly(A) sites in previously overlooked regions and improving genome annotations. APAtrap also aims to tally all potential poly(A) sites and detect genes with differential APA site usages between conditions. Extensive comparisons of APAtrap with two other latest methods, ChangePoint and DaPars, using various RNA-seq datasets from simulation studies, human and Arabidopsis demonstrate the efficacy and flexibility of APAtrap for any organisms with an annotated genome. Freely available for download at https://apatrap.sourceforge.io. liqq@xmu.edu.cn or xhuister@xmu.edu.cn. Supplementary data are available at Bioinformatics online.

Cone penetrometer testing and discrete-depth ground water sampling techniques: A cost-effective method of site characterization in a multiple-aquifer setting

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

Zemo, D.A.; Pierce, Y.G.; Gallinatti, J.D.

Cone penetrometer testing (CPT), combined with discrete-depth ground water sampling methods, can significantly reduce the time and expense required to characterize large sites that have multiple aquifers. Results from the screening site characterization can then be used to design and install a cost-effective monitoring well network. At a site in northern California, it was necessary to characterize the stratigraphy and the distribution of volatile organic compounds (VOCs). To expedite characterization, a five-week field screening program was implemented that consisted of a shallow ground water survey, CPT soundings and pore-pressure measurements, and discrete-depth ground water sampling. Based on continuous lithologic informationmore » provided by the CPT soundings, four predominantly coarse-grained, water yielding stratigraphic packages were identified. Seventy-nine discrete-depth ground water samples were collected using either shallow ground water survey techniques, the BAT Enviroprobe, or the QED HydroPunch I, depending on subsurface conditions. Using results from these efforts, a 20-well monitoring network was designed and installed to monitor critical points within each stratigraphic package. Good correlation was found for hydraulic head and chemical results between discrete-depth screening data and monitoring well data. Understanding the vertical VOC distribution and concentrations produced substantial time and cost savings by minimizing the number of permanent monitoring wells and reducing the number of costly conductor casings that had to be installed. Additionally, significant long-term cost savings will result from reduced sampling costs, because fewer wells comprise the monitoring network. The authors estimate these savings to be 50% for site characterization costs, 65% for site characterization time, and 60% for long-term monitoring costs.« less