Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Hepatic CYP1A levels and EROD activity in English sole: biomonitoring of marine contaminants in Vancouver Harbour.

PubMed

Miller, K A; Addison, R F; Bandiera, S M

2004-01-01

To assess chemical contaminant stress in the marine environment, ethoxyresorufin-O-deethylase (EROD) activity and cytochrome P450 1A (CYP1A) expression were measured in 88 English Sole (Pleuronectes vetulus) collected during May and June 1999 from four sites in Vancouver Harbour and at an expected reference site outside the harbour. Hepatic microsomes were prepared from the fish and analyzed for total CYP content, EROD activity, and CYP1A protein levels. Hepatic EROD activity and CYP1A protein levels were elevated in fish from two sites in the inner harbour. A comparison with sediment chemistry data showed that fish with increased EROD activity and CYP1A levels came from sites containing relatively high levels of polycyclic aromatic hydrocarbons and polychlorinated biphenyls. Unexpectedly high levels of EROD activity and CYP1A protein were also found in fish from a reference site near Gibsons, in Howe Sound. The elevated EROD activity and CYP1A expression in fish from this site cannot be explained by the chemical analysis data collected.

Comparison of Activity Determination of Radium 226 in FUSRAP Soil using Various Energy Lines - 12299

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

Tucker, Brian; Donakowski, Jough; Hays, David

2012-07-01

Gamma spectroscopy is used at the Formerly Utilized Sites Remedial Action Program (FUSRAP) Maywood Superfund Site as the primary radioanalytical tool for quantization of activities of the radionuclides of concern in site soil. When selecting energy lines in gamma spectroscopy, a number of factors are considered including assumptions concerning secondary equilibrium, interferences, and the strength of the lines. The case of the Maywood radionuclide of concern radium-226 (Ra-226) is considered in this paper. At the FUSRAP Maywood Superfund Site, one of the daughters produced from radioactive decay of Ra-226, lead-214 (Pb- 214), is used to quantitate Ra-226. Another Ra-226 daughter,more » bismuth-214 (Bi-214), also may be used to quantitate Ra-226. In this paper, a comparison of Ra-226 to Pb-214 activities and Ra-226 to Bi-214 activities, obtained using gamma spectrometry for a large number of soil samples, was performed. The Pb-214, Bi-214, and Ra-226 activities were quantitated using the 352 kilo electron volt (keV), 609 keV, and 186 keV lines, respectively. The comparisons were made after correcting the Ra-226 activities by a factor of 0.571 and both ignoring and accounting for the contribution of a U-235 interfering line to the Ra-226 line. For the Pb-214 and Bi-214 activities, a mean in-growth factor was employed. The gamma spectrometer was calibrated for efficiency and energy using a mixed gamma standard and an energy range of 59 keV to 1830 keV. The authors expect other sites with Ra-226 contamination in soil may benefit from the discussions and points in this paper. Proper use of correction factors and comparison of the data from three different gamma-emitting radionuclides revealed agreement with expectations and provided confidence that using such correction factors generates quality data. The results indicate that if contamination is low level and due to NORM, the Ra-226 can be measured directly if corrected to subtract the contribution from U-235. If there is any indication that technologically enhanced uranium may be present, the preferred measurement approach for quantitation of Ra-226 activity is detection of one of the Ra-226 daughters, Pb-214 or Bi-214, using a correction factor obtained from an in-growth curve. The results also show that the adjusted Ra-226 results compare very well with both the Pb-214 and Bi-214 results obtained using an in-growth curve correction factor. (authors)« less

Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory

NASA Astrophysics Data System (ADS)

Suydam, Ian T.; Snow, Christopher D.; Pande, Vijay S.; Boxer, Steven G.

2006-07-01

The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site. These shifts yield quantitative information on electric fields that can be directly compared with electrostatics calculations. We show that extensive molecular dynamics simulations and ensemble averaging are required to reproduce the observed changes in field.

Water vapor and aerosol lidar measurements within an atmospheric instrumental super site to study the aerosols and the tropospheric trace gases in rome

NASA Astrophysics Data System (ADS)

Dionisi, D.; Iannarelli, A. M.; Scoccione, A.; Liberti, G. L.; Cacciani, M.; Argentini, S.; Baldini, L.; Barnaba, F.; Campanelli, M.; Casasanta, G.; Diémoz, H.; Di Liberto, L.; Gobbi, G. P.; Petenko, I.; Siani, A. M.; Von Bismarck, J.; Casadio, S.

2018-04-01

A joint instrumental Super Site, combining observation in urban ("Sapienza" University) and semi-rural (ESA-ESRIN and CNR-ISAC) environment, for atmospheric studies and satellites Cal/Val activities, has been set-up in the Rome area (Italy). Ground based active and passive remote sensing instruments located in both sites are operating in synergy, offering information for a wide range of atmospheric parameters. In this work, a comparison of aerosol and water vapor measurements derived by the Rayleigh-Mie-Raman (RMR) lidars, operating simultaneously in both experimental sites, is presented.

[Roosting-site characteristics of wintering black-necked cranes (Grus nigricollis) at Napahai, Yunnan].

PubMed

He, Peng; Kong, De-Jun; Liu, Qiang; Yu, Hong-Zhong; Zhao, Jian-Lin; Yang, Xiao-Jun

2011-04-01

From November 2009 to April 2010, roosting-site characteristics of black-necked cranes (Grus nigricollis) were observed at Napahai Provincial Nature Reserve, Shangri-La, Yunnan, China. The positions of roosting-sites were determined by triangulation with markers and field correction. All of the 63 roosting-sites observed were located in patchy marshes with water, which contained some mud on the bottom and 81% of the roosting-sites were covered by plants. They also had a certain distance to areas of human activities and had a certain distance to the shore. A comparison of roosting sites and random sites showed that roosting-sites had thicker mud layers, a higher ratio of open water, longer distance to roads, villages, and farmland, and water depth. Another comparison of before and after usage of roosting-sites found a significant difference in area of marsh patch. Principal component analysis indicated that the usage of roosting-site of black-necked cranes was affected by human disturbance, area of marsh patch, and the condition of the shallow water environment.

Pseudomonas aeruginosa 4-Amino-4-Deoxychorismate Lyase: Spatial Conservation of an Active Site Tyrosine and Classification of Two Types of Enzyme

PubMed Central

O'Rourke, Patrick E. F.; Eadsforth, Thomas C.; Fyfe, Paul K.; Shepherd, Sharon M.; Hunter, William N.

2011-01-01

4-Amino-4-deoxychorismate lyase (PabC) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. This is an essential activity for the growth of Gram-negative bacteria, including important pathogens such as Pseudomonas aeruginosa. A high-resolution (1.75 Å) crystal structure of PabC from P. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. Residues around the pyridoxal 5′-phosphate cofactor are highly conserved adding support to aspects of a mechanism generic for enzymes carrying that cofactor. However, we suggest that PabC can be classified into two groups depending upon whether an active site and structurally conserved tyrosine is provided from the polypeptide that mainly forms an active site or from the partner subunit in the dimeric assembly. We considered that the conserved tyrosine might indicate a direct role in catalysis: that of providing a proton to reduce the olefin moiety of substrate as pyruvate is released. A threonine had previously been suggested to fulfill such a role prior to our observation of the structurally conserved tyrosine. We have been unable to elucidate an experimentally determined structure of PabC in complex with ligands to inform on mechanism and substrate specificity. Therefore we constructed a computational model of the catalytic intermediate docked into the enzyme active site. The model suggests that the conserved tyrosine helps to create a hydrophobic wall on one side of the active site that provides important interactions to bind the catalytic intermediate. However, this residue does not appear to participate in interactions with the C atom that undergoes an sp 2 to sp 3 conversion as pyruvate is produced. The model and our comparisons rather support the hypothesis that an active site threonine hydroxyl contributes a proton used in the reduction of the substrate methylene to pyruvate methyl in the final stage of the mechanism. PMID:21935381

A comparison of on-line and off-line bioaerosol measurements at a biowaste site.

PubMed

Feeney, Patrick; Rodríguez, Santiago Fernández; Molina, Rafael; McGillicuddy, Eoin; Hellebust, Stig; Quirke, Michael; Daly, Shane; O'Connor, David; Sodeau, John

2018-06-01

An air measurement campaign was carried out at a green-waste composting site in the South of Ireland during Spring 2016. The aim was to quantify and identify the levels of Primary Biological Aerosol Particles (PBAP) that were present using the traditional off-line, impaction/optical microscopy method alongside an on-line, spectroscopic approach termed WIBS (Wideband Integrated Bioaerosol Sensor), which can provide number concentrations, sizes and "shapes" of airborne PBAP in real-time by use of Light Induced Fluorescence (LIF). The results from the two techniques were compared in order to validate the use of the spectroscopic method for determining the releases of the wide-range of PBAP present there as a function of site activity and meteorological conditions. The seven-day monitoring period undertaken was much longer than any real-time studies that have been previously performed and allowed due comparison between weekday (working) activities at the site and weekend (closed) releases. The time-span also allowed relationships between site activities like turning, agitation or waste delivery and the WIBS data to be determined in a quantitative manner. This information cannot be obtained with the Andersen Sampling methods generally employed at green-waste management sites. Furthermore, few specific bioaerosol types other than Aspergillus fumigatus, are identified using the traditional protocols employed for site licensing purposes. Here though the co-location of WIBS with the impaction instrument made it possible to identify the real-time release behaviour of a specific plant pathogenic spore, Ustilago maydis, present after green-waste deliveries were made by a local distillery. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Comparison of the Output in Weighted Work Units of Installation Dental Laboratories with that of Regional Dental Activities. Part II.

DTIC Science & Technology

1980-07-01

at the study sites and compare it to the total production at each site. Orthodontics was excepted be- cause it is not done at all laboratories, nor is...DENTAC laboratories. It is sometimes tempting to relate productivity in terms of weighted work units to the type of work being done. Orthodontic laboratory...hypotheses. DENTAC Sites 2 and 3 both produce a heavy orthodontic workload, whereas Site 1 did very little in Month 1. In Month 2, when Site 1 reported a

Sustained Cutaneous Vasoconstriction during and Following Cyrotherapy Treatment: Role of Oxidative Stress and Rho Kinase

PubMed Central

Christmas, Kevin M.; Patik, Jordan C.; Khoshnevis, Sepideh; Diller, Kenneth R.; Brothers, R. Matthew

2016-01-01

Cryotherapy is a therapeutic technique using ice or cold water applied to the skin to reduce bleeding, inflammation, pain, and swelling following soft tissue trauma and injury. While beneficial, there are some side effects such as pronounced vasoconstriction and tissue ischemia that are sustained for hours post-treatment. This study tested the hypothesis that this vasoconstriction is mediated by 1) the Rho-kinase pathway and/or 2) elevated oxidative stress. 9 subjects were fitted with a commercially available cryotherapy unit with a water perfused bladder on the lateral portion of the right calf. Participants were instrumented with three microdialysis probes underneath the bladder. One site received lactated ringers (control site), one received the Rho-Kinase inhibitor Fasudil, and one received Ascorbic Acid. Skin temperature (Tskin) and cutaneous vascular conductance (CVC) was measured at each site. Subjects had 1 °C water perfused through the bladder for 30 min, followed by passive rewarming for 90 min. Tskin fell from ~ 34 °C to ~ 18.0 °C during active cooling across all sites and this response was similar for all sites (P>0.05 for all comparisons). During passive rewarming Tskin rose to a similar degree in all sites (P>0.05 relative to the end of cooling). %CVC was reduced during active cooling in all sites; however, the magnitude of this response was blunted in the Fasudil site relative to control (P<0.001 for all comparisons) and min 25 and 30 of cooling in the Ascorbic Acid site (P<0.05). During passive rewarming %CVC at the control and Ascorbic Acid sites did not change such that values were similar to the end of cooling (P>0.05 for each comparison). %CVC at the Fasudil site remained elevated during passive rewarming such that values were higher compared to the control and Ascorbic Acid sites throughout the 90 min of passive rewarming (P<0.001 main effect of Fasudi). These findings indicate that the Rho-kinase pathway contributes to pronounced vasoconstriction during cryotherapy as well as the sustained vasoconstriction during the subsequent rewarming period post treatment. PMID:27089823

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

PubMed Central

2016-01-01

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1.

PubMed

Blaha-Nelson, David; Krüger, Dennis M; Szeler, Klaudia; Ben-David, Moshe; Kamerlin, Shina Caroline Lynn

2017-01-25

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70-81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1's lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1's lactonase activity is minimal, whereas the k cat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1's active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar "gating loop" or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates.

[Substrate specificities of bile salt hydrolase 1 and its mutants from Lactobacillus salivarius].

PubMed

Bi, Jie; Fang, Fang; Qiu, Yuying; Yang, Qingli; Chen, Jian

2014-03-01

In order to analyze the correlation between critical residues in the catalytic centre of BSH and the enzyme substrate specificity, seven mutants of Lactobacillus salivarius bile salt hydrolase (BSH1) were constructed by using the Escherichia coli pET-20b(+) gene expression system, rational design and site-directed mutagenesis. These BSH1 mutants exhibited different hydrolytic activities against various conjugated bile salts through substrate specificities comparison. Among the residues being tested, Cys2 and Thr264 were deduced as key sites for BSH1 to catalyze taurocholic acid and glycocholic acid, respectively. Moreover, Cys2 and Thr264 were important for keeping the catalytic activity of BSH1. The high conservative Cys2 was not the only active site, other mutant amino acid sites were possibly involved in substrate binding. These mutant residues might influence the space and shape of the substrate-binding pockets or the channel size for substrate passing through and entering active site of BSH1, thus, the hydrolytic activity of BSH1 was changed to different conjugated bile salt.

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product.

PubMed

Boughton, Berin A; Dobson, Renwick C J; Hutton, Craig A

2012-08-01

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures. Copyright © 2012 Wiley Periodicals, Inc.

Operational Definition of Active and Healthy Aging (AHA): The European Innovation Partnership (EIP) on AHA Reference Site Questionnaire: Montpellier October 20-21, 2014, Lisbon July 2, 2015.

PubMed

Bousquet, Jean; Malva, Joao; Nogues, Michel; Mañas, Leocadio Rodriguez; Vellas, Bruno; Farrell, John

2015-12-01

A core operational definition of active and healthy aging (AHA) is needed to conduct comparisons. A conceptual AHA framework proposed by the European Innovation Partnership on Active and Healthy Ageing Reference Site Network includes several items such as functioning (individual capability and underlying body systems), well-being, activities and participation, and diseases (including noncommunicable diseases, frailty, mental and oral health disorders). The instruments proposed to assess the conceptual framework of AHA have common applicability and availability attributes. The approach includes core and optional domains/instruments depending on the needs and the questions. A major common domain is function, as measured by the World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0). WHODAS 2.0 can be used across all diseases and healthy individuals. It covers many of the AHA dimensions proposed by the Reference Site network. However, WHODAS 2.0 does not include all dimensions proposed for AHA assessment. The second common domain is health-related quality of life (HRQoL). A report of the AHA questionnaire in the form of a spider net has been proposed to facilitate usual comparisons across individuals and groups of interest. Copyright © 2015. Published by Elsevier Inc.

Conservation and Role of Electrostatics in Thymidylate Synthase.

PubMed

Garg, Divita; Skouloubris, Stephane; Briffotaux, Julien; Myllykallio, Hannu; Wade, Rebecca C

2015-11-27

Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.

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

Comparison of the fibrin-binding activities in the N- and C-termini of fibronectin.

PubMed

Rostagno, A A; Schwarzbauer, J E; Gold, L I

1999-03-01

Fibronectin (Fn) binds to fibrin in clots by covalent and non-covalent interactions. The N- and C-termini of Fn each contain one non-covalent fibrin-binding site, which are composed of type 1 (F1) structural repeats. We have previously localized the N-terminal site to the fourth and fifth F1 repeats (4F1.5F1). In the current studies, using proteolytic and recombinant proteins representing both the N- and C-terminal fibrin-binding regions, we localized and characterized the C-terminal fibrin-binding site, compared the relative fibrin-binding activities of both sites and determined the contribution of each site to the fibrin-binding activity of intact Fn. By fibrin-affinity chromatography, a protein composed of the 10F1 repeat through to the C-terminus of Fn (10F1-COOH), expressed in COS-1 cells, and 10F1-12F1, produced in Saccharomyces cerevisiae, displayed fibrin-binding activity. However, since 10F1 and 10F1.11F1 were not active, the presence of 12F1 is required for fibrin binding. A proteolytic fragment of 14.4 kDa, beginning 14 residues N-terminal to 10F1, was isolated from the fibrin-affinity matrix. Radio-iodinated 14.4 kDa fibrin-binding peptide/protein (FBP) demonstrated a dose-dependent and saturable binding to fibrin-coated wells that was both competitively inhibited and reversed by unlabelled 14.4 kDa FBP. Comparison of the fibrin-binding affinities of proteolytic FBPs from the N-terminus (25.9 kDa FBP), the C-terminus (14.4 kDa) and intact Fn by ELISA yielded estimated Kd values of 216, 18 and 2.1 nM, respectively. The higher fibrin-binding affinity of the N-terminus was substantiated by the ability of both a recombinant 4F1.5F1 and a monoclonal antibody (mAb) to this site to maximally inhibit biotinylated Fn binding to fibrin by 80%, and by blocking the 90% inhibitory activity of a polyclonal anti-Fn, by absorption with the 25.9 kDa FBP. We propose that whereas the N-terminal site appears to contribute to most of the binding activity of native Fn to fibrin, the specific binding of the C-terminal site may strengthen this interaction.

Comparison of the fibrin-binding activities in the N- and C-termini of fibronectin.

PubMed Central

Rostagno, A A; Schwarzbauer, J E; Gold, L I

1999-01-01

Fibronectin (Fn) binds to fibrin in clots by covalent and non-covalent interactions. The N- and C-termini of Fn each contain one non-covalent fibrin-binding site, which are composed of type 1 (F1) structural repeats. We have previously localized the N-terminal site to the fourth and fifth F1 repeats (4F1.5F1). In the current studies, using proteolytic and recombinant proteins representing both the N- and C-terminal fibrin-binding regions, we localized and characterized the C-terminal fibrin-binding site, compared the relative fibrin-binding activities of both sites and determined the contribution of each site to the fibrin-binding activity of intact Fn. By fibrin-affinity chromatography, a protein composed of the 10F1 repeat through to the C-terminus of Fn (10F1-COOH), expressed in COS-1 cells, and 10F1-12F1, produced in Saccharomyces cerevisiae, displayed fibrin-binding activity. However, since 10F1 and 10F1.11F1 were not active, the presence of 12F1 is required for fibrin binding. A proteolytic fragment of 14.4 kDa, beginning 14 residues N-terminal to 10F1, was isolated from the fibrin-affinity matrix. Radio-iodinated 14.4 kDa fibrin-binding peptide/protein (FBP) demonstrated a dose-dependent and saturable binding to fibrin-coated wells that was both competitively inhibited and reversed by unlabelled 14.4 kDa FBP. Comparison of the fibrin-binding affinities of proteolytic FBPs from the N-terminus (25.9 kDa FBP), the C-terminus (14.4 kDa) and intact Fn by ELISA yielded estimated Kd values of 216, 18 and 2.1 nM, respectively. The higher fibrin-binding affinity of the N-terminus was substantiated by the ability of both a recombinant 4F1.5F1 and a monoclonal antibody (mAb) to this site to maximally inhibit biotinylated Fn binding to fibrin by 80%, and by blocking the 90% inhibitory activity of a polyclonal anti-Fn, by absorption with the 25.9 kDa FBP. We propose that whereas the N-terminal site appears to contribute to most of the binding activity of native Fn to fibrin, the specific binding of the C-terminal site may strengthen this interaction. PMID:10024513

Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.

PubMed

Lahoda, Maryna; Mesters, Jeroen R; Stsiapanava, Alena; Chaloupkova, Radka; Kuty, Michal; Damborsky, Jiri; Kuta Smatanova, Ivana

2014-02-01

Haloalkane dehalogenases catalyze the hydrolytic cleavage of carbon-halogen bonds, which is a key step in the aerobic mineralization of many environmental pollutants. One important pollutant is the toxic and anthropogenic compound 1,2,3-trichloropropane (TCP). Rational design was combined with saturation mutagenesis to obtain the haloalkane dehalogenase variant DhaA31, which displays an increased catalytic activity towards TCP. Here, the 1.31 Å resolution crystal structure of substrate-free DhaA31, the 1.26 Å resolution structure of DhaA31 in complex with TCP and the 1.95 Å resolution structure of wild-type DhaA are reported. Crystals of the enzyme-substrate complex were successfully obtained by adding volatile TCP to the reservoir after crystallization at pH 6.5 and room temperature. Comparison of the substrate-free structure with that of the DhaA31 enzyme-substrate complex reveals that the nucleophilic Asp106 changes its conformation from an inactive to an active state during the catalytic cycle. The positions of three chloride ions found inside the active site of the enzyme indicate a possible pathway for halide release from the active site through the main tunnel. Comparison of the DhaA31 variant with wild-type DhaA revealed that the introduced substitutions reduce the volume and the solvent-accessibility of the active-site pocket.

Influence of rete testis fluid deprivation on the kinetic parameters of goat epididymal 5 alpha-reductase.

PubMed

Kelce, W R; Lubis, A M; Braun, W F; Youngquist, R S; Ganjam, V K

1990-01-01

A surgical technique to cannulate the rete testis of the goat was utilized to examine the effects of rete testis fluid (RTF) deprivation on the enzymatic activity of epididymal 5 alpha-reductase. Kinetic techniques were used to determine whether the regional enzymatic effect of RTF deprivation is to decrease the apparent number of 5 alpha-reductase active sites or the catalytic activity of each active site within the epididymal epithelium. Paired comparisons of (Vmax)app and (Km)app values between control and RTF-deprived epididymides indicated that RTF deprivation affected the value of (Vmax)app with no apparent change in the values of (Km)app in caput, corpus, and cauda epididymal regions. We conclude that RTF deprivation in the goat epididymis for 7 days results in a decreased number of apparent 5 alpha-reductase active sites within the epididymal epithelium.

The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

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

Gopal, B.; Madan, Lalima L.; Betz, Stephen F.

2010-11-10

Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s),more » whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.« less

Structure and Mechanism of a Eukaryotic FMN Adenylyltransferase

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

Huerta, Carlos; Borek, Dominika; Machius, Mischa

2009-12-01

Flavin mononucleotide adenylyltransferase (FMNAT) catalyzes the formation of the essential flavocoenzyme flavin adenine dinucleotide (FAD) and plays an important role in flavocoenzyme homeostasis regulation. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different sets of active-site residues to accomplish the same chemistry. Here we report the first structural characterization of a eukaryotic FMNAT from the pathogenic yeast Candida glabrata. Four crystal structures of C. glabrata FMNAT in different complexed forms were determined at 1.20-1.95 A resolutions, capturing the enzyme active-site states prior to and after catalysis. These structures reveal a novelmore » flavin-binding mode and a unique enzyme-bound FAD conformation. Comparison of the bacterial and eukaryotic FMNATs provides a structural basis for understanding the convergent evolution of the same FMNAT activity from different protein ancestors. Structure-based investigation of the kinetic properties of FMNAT should offer insights into the regulatory mechanisms of FAD homeostasis by FMNAT in eukaryotic organisms.« less

Purification and sequencing of the active site tryptic peptide from penicillin-binding protein 1b of Escherichia coli

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

Nicholas, R.A.; Suzuki, H.; Hirota, Y.

This paper reports the sequence of the active site peptide of penicillin-binding protein 1b from Escherichia coli. Purified penicillin-binding protein 1b was labeled with (/sup 14/C)penicillin G, digested with trypsin, and partially purified by gel filtration. Upon further purification by high-pressure liquid chromatography, two radioactive peaks were observed, and the major peak, representing over 75% of the applied radioactivity, was submitted to amino acid analysis and sequencing. The sequence Ser-Ile-Gly-Ser-Leu-Ala-Lys was obtained. The active site nucleophile was identified by digesting the purified peptide with aminopeptidase M and separating the radioactive products on high-pressure liquid chromatography. Amino acid analysis confirmed thatmore » the serine residue in the middle of the sequence was covalently bonded to the (/sup 14/C)penicilloyl moiety. A comparison of this sequence to active site sequences of other penicillin-binding proteins and beta-lactamases is presented.« less

Active sites for CO 2 hydrogenation to methanol on Cu/ZnO catalysts

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

Kattel, Shyam; Ramírez, Pedro J.; Chen, Jingguang G.

The active sites over commercial copper/zinc oxide/aluminum oxide (Cu/ZnO/Al 2O 3) catalysts for carbon dioxide (CO 2) hydrogenation to methanol, the Zn-Cu bimetallic sites or ZnO-Cu interfacial sites, have recently been the subject of intense debate. Here, we report a direct comparison between the activity of ZnCu and ZnO/Cu model catalysts for methanol synthesis. By combining x-ray photoemission spectroscopy, density functional theory, and kinetic Monte Carlo simulations, we can identify and characterize the reactivity of each catalyst. Both experimental and theoretical results agree that ZnCu undergoes surface oxidation under the reaction conditions so that surface Zn transforms into ZnO andmore » allows ZnCu to reach the activity of ZnO/Cu with the same Zn coverage. These results highlight a synergy of Cu and ZnO at the interface that facilitates methanol synthesis via formate intermediates.« less

Active sites for CO 2 hydrogenation to methanol on Cu/ZnO catalysts

DOE PAGES

Kattel, Shyam; Ramírez, Pedro J.; Chen, Jingguang G.; ...

2017-03-23

The active sites over commercial copper/zinc oxide/aluminum oxide (Cu/ZnO/Al 2O 3) catalysts for carbon dioxide (CO 2) hydrogenation to methanol, the Zn-Cu bimetallic sites or ZnO-Cu interfacial sites, have recently been the subject of intense debate. Here, we report a direct comparison between the activity of ZnCu and ZnO/Cu model catalysts for methanol synthesis. By combining x-ray photoemission spectroscopy, density functional theory, and kinetic Monte Carlo simulations, we can identify and characterize the reactivity of each catalyst. Both experimental and theoretical results agree that ZnCu undergoes surface oxidation under the reaction conditions so that surface Zn transforms into ZnO andmore » allows ZnCu to reach the activity of ZnO/Cu with the same Zn coverage. These results highlight a synergy of Cu and ZnO at the interface that facilitates methanol synthesis via formate intermediates.« less

A Systematic Comparison of Teaching Hospital and Remote-Site Clinical Education

ERIC Educational Resources Information Center

And Others; Friedman, Charles P.

1978-01-01

A methodology is presented for examining activities of medical students on multisite clinical clerkships in obstetrics and gynecology. Five variables are explored: distribution of student activities, type or class of clinical conditions encountered, degree of "esoterism" of those conditions, type of student role, and flexibility of student role.…

Newly identified essential amino acid residues affecting ^8-sphingolipid desaturase activity revealed by site-directed mutagenesis

USDA-ARS?s Scientific Manuscript database

In order to identify amino acid residues crucial for the enzymatic activity of ^8-sphingolipid desaturases, a sequence comparison was performed among ^8-sphingolipid desaturases and ^6-fatty acid desaturase from various plants. In addition to the known conserved cytb5 (cytochrome b5) HPGG motif and...

S28 peptidases: lessons from a seemingly 'dysfunctional' family of two.

PubMed

Kozarich, John W

2010-06-28

A recent paper in BMC Structural Biology reports the crystal structure of human prolylcarboxypeptidase (PRCP), one of the two members of the S28 peptidase family. Comparison of the substrate-binding site of PRCP with that of its family partner, dipeptidyl dipeptidase 7 (DPP7), helps to explain the different enzymatic activities of these structurally similar proteins, and also reveals a novel apparent charge-relay system in PRCP involving the active-site catalytic histidine. See research article: http://www.biomedcentral.com/1472-6807/10/16/

Comparison of natural resource issues on tropical pacific ranges

USGS Publications Warehouse

Helweg, D.A.; Jacobi, J.D.

2004-01-01

The natural resources issues on tropical Pacific ranges are compared. If active management plan is in place, FWS may exempt those spp. from critical Habitat Prevention and control or invasive species essential. Wetlands are low-hanging fruit for restoration, but birds present mgmt. challenge. Marine sites may offer less potential for precise mgmt. of natural resources than terrestrial sites such as, lack of knowledge, observational limits, ecosystem complexity, mobile biota. It has been suggested that the tremendus public interest in helping with conservation activities - volunteer opportunities may offset staffing shortfalls.

A global optimization algorithm for protein surface alignment

PubMed Central

2010-01-01

Background A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for the interaction with a specific ligand. Several matching strategies have been designed for the recognition of protein-ligand binding sites and of protein-protein interfaces but the problem cannot be considered solved. Results In this paper we propose a new method for local structural alignment of protein surfaces based on continuous global optimization techniques. Given the three-dimensional structures of two proteins, the method finds the isometric transformation (rotation plus translation) that best superimposes active regions of two structures. We draw our inspiration from the well-known Iterative Closest Point (ICP) method for three-dimensional (3D) shapes registration. Our main contribution is in the adoption of a controlled random search as a more efficient global optimization approach along with a new dissimilarity measure. The reported computational experience and comparison show viability of the proposed approach. Conclusions Our method performs well to detect similarity in binding sites when this in fact exists. In the future we plan to do a more comprehensive evaluation of the method by considering large datasets of non-redundant proteins and applying a clustering technique to the results of all comparisons to classify binding sites. PMID:20920230

Self-optimizing, highly surface-active layered metal dichalcogenide catalysts for hydrogen evolution

NASA Astrophysics Data System (ADS)

Liu, Yuanyue; Wu, Jingjie; Hackenberg, Ken P.; Zhang, Jing; Wang, Y. Morris; Yang, Yingchao; Keyshar, Kunttal; Gu, Jing; Ogitsu, Tadashi; Vajtai, Robert; Lou, Jun; Ajayan, Pulickel M.; Wood, Brandon C.; Yakobson, Boris I.

2017-09-01

Low-cost, layered transition-metal dichalcogenides (MX2) based on molybdenum and tungsten have attracted substantial interest as alternative catalysts for the hydrogen evolution reaction (HER). These materials have high intrinsic per-site HER activity; however, a significant challenge is the limited density of active sites, which are concentrated at the layer edges. Here we unravel electronic factors underlying catalytic activity on MX2 surfaces, and leverage the understanding to report group-5 MX2 (H-TaS2 and H-NbS2) electrocatalysts whose performance instead mainly derives from highly active basal-plane sites, as suggested by our first-principles calculations and performance comparisons with edge-active counterparts. Beyond high catalytic activity, they are found to exhibit an unusual ability to optimize their morphology for enhanced charge transfer and accessibility of active sites as the HER proceeds, offering a practical advantage for scalable processing. The catalysts reach 10 mA cm-2 current density at an overpotential of ˜50-60 mV with a loading of 10-55 μg cm-2, surpassing other reported MX2 candidates without any performance-enhancing additives.

Improving performance of Zambia Defence Force antiretroviral therapy providers: evaluation of a standards-based approach

PubMed Central

Kim, Young Mi; Banda, Joseph; Kanjipite, Webby; Sarkar, Supriya; Bazant, Eva; Hiner, Cyndi; Tholandi, Maya; Reinhardt, Stephanie; Njobvu, Panganani Dalisani; Kols, Adrienne; Benavides, Bruno

2013-01-01

ABSTRACT Background: The Zambia Defence Force (ZDF) has applied the Standards-Based Management and Recognition (SBM-R®) approach, which uses detailed performance standards, at some health facilities to improve HIV-related services offered to military personnel and surrounding civilian communities. This study examines the effectiveness of the SBM-R approach in improving facility readiness and provider performance at ZDF facilities. Methods: We collected data on facility readiness and provider performance before and after the 2010–2012 intervention at 4 intervention sites selected for their relatively poor performance and 4 comparison sites. Assessors observed whether each facility met 16 readiness standards and whether providers met 9 performance standards during consultations with 354 returning antiretroviral therapy (ART) clients. We then calculated the percentages of criteria achieved for each readiness and performance standard and conducted bivariate and multivariate analyses of provider performance data. Results: Facilities' ART readiness scores exceeded 80% before the intervention at both intervention and comparison sites. At endline, scores improved on 4 facility readiness standards in the intervention group but on only 1 standard in the comparison group. Multivariate analysis found that the overall provider performance score increased significantly in the intervention group (from 58% to 84%; P<.01) but not in the comparison group (from 62% to 70%). The before-and-after improvement in scores was significantly greater among intervention sites than among comparison sites for 2 standards—initial assessment of the client's condition and nutrition counseling. Conclusion: The standards-based approach, which involved intensive and mutually reinforcing intervention activities, showed modest improvements in some aspects of providers' performance during ART consultations. Further research is needed to determine whether improvements in provider performance affect client outcomes such as adherence to ART. PMID:25276534

Revealing the Double-Edged Sword Role of Graphene on Boosted Charge Transfer versus Active Site Control in TiO2 Nanotube Arrays@RGO/MoS2 Heterostructure.

PubMed

Quan, Quan; Xie, Shunji; Weng, Bo; Wang, Ye; Xu, Yi-Jun

2018-05-01

Charge separation/transfer is generally believed to be the most key factor affecting the efficiency of photocatalysis, which however will be counteracted if not taking the active site engineering into account for a specific photoredox reaction. Here, a 3D heterostructure composite is designed consisting of MoS 2 nanoplatelets decorated on reduced graphene oxide-wrapped TiO 2 nanotube arrays (TNTAs@RGO/MoS 2 ). Such a cascade configuration renders a directional migration of charge carriers and controlled immobilization of active sites, thereby showing much higher photoactivity for water splitting to H 2 than binary TNTAs@RGO and TNTAs/MoS 2 . The photoactivity comparison and mechanistic analysis reveal the double-edged sword role of RGO on boosted charge separation/transfer versus active site control in this composite system. The as-observed inconsistency between boosted charge transfer and lowered photoactivity over TNTAs@RGO is attributed to the decrease of active sites for H 2 evolution, which is significantly different from the previous reports in literature. The findings of the intrinsic relationship of balanced benefits from charge separation/transfer and active site control could promote the rational optimization of photocatalyst design by cooperatively manipulating charge flow and active site control, thereby improving the efficiency of photocatalysis for target photoredox processes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Carnivore activity in the Sima de los Huesos (Atapuerca, Spain) hominin sample

NASA Astrophysics Data System (ADS)

Sala, Nohemi; Arsuaga, Juan Luis; Martínez, Ignacio; Gracia-Téllez, Ana

2014-08-01

The Sima de los Huesos (SH) site is the largest accumulation of human remains from the Middle Pleistocene known to date. Studies in the last two decades have proposed different hypotheses to explain carnivore activity in the SH human sample. This study provides new data in order to test these different interpretations, and therefore to understand the role of the carnivores in site formation at SH. Carnivores are usually not the origin of large accumulations of hominin fossils in the Eurasian record. The results show that marks of carnivore activity in the SH sample appear very infrequently, which we interpret as indicating that carnivore activity was very sporadic at the site. This is in stark contrast with previous studies. The comparison of bone modification patterns at SH to actualistic carnivore data allows us to suggest that bears were likely to have been the carnivore responsible for the modification observed on both human and bear fossils.

Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations.

PubMed

Li, Jilai; Ryde, Ulf

2014-11-17

There are three families of mononuclear molybdenum enzymes that catalyze oxygen atom transfer (OAT) reactions, named after a typical example from each family, viz., dimethyl sulfoxide reductase (DMSOR), sulfite oxidase (SO), and xanthine oxidase (XO). These families differ in the construction of their active sites, with two molybdopterin groups in the DMSOR family, two oxy groups in the SO family, and a sulfido group in the XO family. We have employed density functional theory calculations on cluster models of the active sites to understand the selection of molybdenum ligands in the three enzyme families. Our calculations show that the DMSOR active site has a much stronger oxidative power than the other two sites, owing to the extra molybdopterin ligand. However, the active sites do not seem to have been constructed to make the OAT reaction as exergonic as possible, but instead to keep the reaction free energy close to zero (to avoid excessive loss of energy), thereby making the reoxidation (SO and XO) or rereduction of the active sites (DMSOR) after the OAT reaction facile. We also show that active-site models of the three enzyme families can all catalyze the reduction of DMSO and that the DMSOR model does not give the lowest activation barrier. Likewise, all three models can catalyze the oxidation of sulfite, provided that the Coulombic repulsion between the substrate and the enzyme model can be overcome, but for this harder reaction, the SO model gives the lowest activation barrier, although the differences are not large. However, only the XO model can catalyze the oxidation of xanthine, owing to its sulfido ligand.

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods.

PubMed

Bate, Paul; Warwicker, Jim

2004-07-02

Calculations of charge interactions complement analysis of a characterised active site, rationalising pH-dependence of activity and transition state stabilisation. Prediction of active site location through large DeltapK(a)s or electrostatic strain is relevant for structural genomics. We report a study of ionisable groups in a set of 20 enzymes, finding that false positives obscure predictive potential. In a larger set of 156 enzymes, peaks in solvent-space electrostatic properties are calculated. Both electric field and potential match well to active site location. The best correlation is found with electrostatic potential calculated from uniform charge density over enzyme volume, rather than from assignment of a standard atom-specific charge set. Studying a shell around each molecule, for 77% of enzymes the potential peak is within that 5% of the shell closest to the active site centre, and 86% within 10%. Active site identification by largest cleft, also with projection onto a shell, gives 58% of enzymes for which the centre of the largest cleft lies within 5% of the active site, and 70% within 10%. Dielectric boundary conditions emphasise clefts in the uniform charge density method, which is suited to recognition of binding pockets embedded within larger clefts. The variation of peak potential with distance from active site, and comparison between enzyme and non-enzyme sets, gives an optimal threshold distinguishing enzyme from non-enzyme. We find that 87% of the enzyme set exceeds the threshold as compared to 29% of the non-enzyme set. Enzyme/non-enzyme homologues, "structural genomics" annotated proteins and catalytic/non-catalytic RNAs are studied in this context.

Management practices that concentrate visitor activities: Camping impact management at Isle Royale National Park, USA

USGS Publications Warehouse

Marion, J.L.; Farrell, T.A.

2002-01-01

This study assessed campsite conditions and the effectiveness of campsite impact management strategies at Isle Royale National Park, USA. Protocols for assessing indicators of vegetation and soil conditions were developed and applied to 156 campsites and 88 shelters within 36 backcountry campgrounds. The average site was 68 m2 and 83% of sites lost vegetation over areas less than 47 m2. Results reveal that management actions to spatially concentrate camping activities and reduce camping disturbance have been highly successful. Comparisons of disturbed area/overnight stay among other protected areas reinforces this assertion. These reductions in area of camping disturbance are attributed to a designated site camping policy, limitation on site numbers, construction of sites in sloping terrain, use of facilities, and an ongoing program of campsite maintenance. Such actions are most appropriate in higher use backcountry and wilderness settings.

The use of biotic and abiotic components of Red Sea coastal areas as indicators of ecosystem health.

PubMed

Omar, Wael A; Saleh, Yousef S; Marie, Mohamed-Assem S

2016-03-01

A biomonitoring study was conducted using some biotic (Pomadasys hasta and Lutjanus russellii fish) and abiotic (water and sediment) components of the Red Sea coast of Hodeida, Yemen Republic along two polluted sites (Al-Dawar beach and Urj village) in comparison to a reference site (Al-Nukhailah beach). The studied fish biomarkers included hepatosomatic index (HSI), condition factor (K), scaled mass index (SMI), catalase, glutathione-S-transferase (GST), malondialdehyde (MDA), total protein and albumin. In addition, metals (Fe, Cu, Zn, Pb and Cd) concentrations in water and sediment were measured and sediment pollution assessment was carried out using contamination factor (CF), geoaccumulation index (Igeo), pollution load index (PLI) and enrichment factor (EF). The studied metals concentration in water and sediment samples showed significant increase among the polluted sites in comparison to the reference site. Sediment pollution assessment generally confirmed that Urj village was the most contaminated site followed by Al-Dawar beach. Catalase, GST and MDA proved to be the most responsive biomarkers with increased values of GST and MDA at sites influenced by agricultural, urban and industrial activities while catalase, HSI, K, SMI, total protein and albumin showed the opposite trend. This study recommends monitoring of sediment Igeo and EF values as well as SMI, catalase, GST and MDA as sensitive indicators of different anthropogenic activities and their effects on aquatic ecosystems under complex and different gradients of metal pollution. In addition, P. hasta proved to be more sensitive towards the detected pollution condition.

Neural learning rules for the vestibulo-ocular reflex

NASA Technical Reports Server (NTRS)

Raymond, J. L.; Lisberger, S. G.

1998-01-01

Mechanisms for the induction of motor learning in the vestibulo-ocular reflex (VOR) were evaluated by recording the patterns of neural activity elicited in the cerebellum by a range of stimuli that induce learning. Patterns of climbing-fiber, vestibular, and Purkinje cell simple-spike signals were examined during sinusoidal head movement paired with visual image movement at stimulus frequencies from 0.5 to 10 Hz. A comparison of simple-spike and vestibular signals contained the information required to guide learning only at low stimulus frequencies, and a comparison of climbing-fiber and simple-spike signals contained the information required to guide learning only at high stimulus frequencies. Learning could be guided by comparison of climbing-fiber and vestibular signals at all stimulus frequencies tested, but only if climbing fiber responses were compared with the vestibular signals present 100 msec earlier. Computational analysis demonstrated that this conclusion is valid even if there is a broad range of vestibular signals at the site of plasticity. Simulations also indicated that the comparison of vestibular and climbing-fiber signals across the 100 msec delay must be implemented by a subcellular "eligibility" trace rather than by neural circuits that delay the vestibular inputs to the site of plasticity. The results suggest two alternative accounts of learning in the VOR. Either there are multiple mechanisms of learning that use different combinations of neural signals to drive plasticity, or there is a single mechanism tuned to climbing-fiber activity that follows activity in vestibular pathways by approximately 100 msec.

Regional Air Quality in central México and emissions inventories

NASA Astrophysics Data System (ADS)

Gerardo Ruiz-Suarez, Luis; Torres-Jardón, Ricardo; Agustín García-Reynoso, José; Santos García-Yee, José; Barrera-Huertas, Hugo; Alejandro Torres-Jaramillo, Jorge; Robles-Roldán, Miguel Angel; Gutierrez López, Wilfrido; García-Espinoza, Manuel; Castro-Romero, Telma

2014-05-01

Four air quality field campaigns, from 2009 to 2012, during March-April were carried out in several sites in urban, rural and semi-rural sites in Central México. One of the sites was in the Chalco Gap southeast of MCMA (2011), another in the state of Morelos (2011), other two in the state of Puebla (2009 and 2012). All these sites are South and East of the Mexico Basin. The main object of those campaigns was to document regional air quality, mainly in rural and periurban sites, including the photochemical age of regional polluted plumes as they were transported away from the main metropolitan areas within the region. In this paper, we focus on comparisons between observed CO/NOx, and CO/SO2 ratios with those from the National Emissions Inventory and form local inventories reported in state air quality management programs. Comparisons were made with data between 05:00 to 08:00 h to minimize effects photochemical activity and the fast evolution of MLH occurring between 08:00 and 09:00 due to high insolation. Comparisons among observed ratios show a fairly consistent ratio, whereas ratios from emissions inventory are widely variable and only in few sites compare reasonable well with observed ones, indicating the need for homologation of emissions inventories in the country. Also Ozone, CO, NOx and NOy observed time series are compared with WRF-Chem model results for the same campaign periods to evaluate its performance outside MCMA. In addition, observed surface wind speeds and early morning MLH obtained with a tethered balloon are also compared with modeled values to help understanding discrepancies in the trace gases comparisons.

New insights into the interaction between pyrrolyl diketoacids and HIV-1 integrase active site and comparison with RNase H.

PubMed

Corona, Angela; di Leva, Francesco Saverio; Rigogliuso, Giuseppe; Pescatori, Luca; Madia, Valentina Noemi; Subra, Frederic; Delelis, Olivier; Esposito, Francesca; Cadeddu, Marta; Costi, Roberta; Cosconati, Sandro; Novellino, Ettore; di Santo, Roberto; Tramontano, Enzo

2016-10-01

HIV-1 integrase (IN) inhibitors are one of the most recent innovations in the treatment of HIV infection. The selection of drug resistance viral strains is however a still open issue requiring constant efforts to identify new anti-HIV-1 drugs. Pyrrolyl diketo acid (DKA) derivatives inhibit HIV-1 replication by interacting with the Mg 2+ cofactors within the HIV-1 IN active site or within the HIV-1 reverse-transcriptase associated ribonuclease H (RNase H) active site. While the interaction mode of pyrrolyl DKAs with the RNase H active site has been recently reported and substantiated by mutagenesis experiments, their interaction within the IN active site still lacks a detailed understanding. In this study, we investigated the binding mode of four pyrrolyl DKAs to the HIV-1 IN active site by molecular modeling coupled with site-directed mutagenesis studies showing that the DKA pyrrolyl scaffold primarily interacts with the IN amino residues P145, Q146 and Q148. Importantly, the tested DKAs demonstrated good effectiveness against HIV-1 Raltegravir resistant Y143A and N155H INs, thus showing an interaction pattern with relevant differences if compared with the first generation IN inhibitors. These data provide precious insights for the design of new HIV inhibitors active on clinically selected Raltegravir resistant variants. Furthermore, this study provides new structural information to modulate IN and RNase H inhibitory activities for development of dual-acting anti-HIV agents. Copyright © 2016 Elsevier B.V. All rights reserved.

Remedial action plan and site design for stabilization of the inactive Uranium Mill Tailing site Maybell, Colorado. Attachment 3, ground water hydrology report, Attachment 4, water resources protection strategy. Final report

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

Not Available

1994-06-01

The U.S. Environmental Protection Agency (EPA) has established health and environmental regulations to correct and prevent ground water contamination resulting from former uranium processing activities at inactive uranium processing sites (40 CFR Part 192 (1993)) (52 FR 36000 (1978)). According to the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978 (42 USC {section} 7901 et seq.), the U.S. Department of Energy (DOE) is responsible for assessing the inactive uranium processing sites. The DOE has decided that each assessment will include information on hydrogeologic site characterization. The water resources protection strategy that describes the proposed action compliance with the EPAmore » ground water protection standards is presented in Attachment 4, Water Resources Protection Strategy. Site characterization activities discussed in this section include the following: (1) Definition of the hydrogeologic characteristics of the environment, including hydrostratigraphy, aquifer parameters, areas of aquifer recharge and discharge, potentiometric surfaces, and ground water velocities. (2) Definition of background ground water quality and comparison with proposed EPA ground water protection standards. (3) Evaluation of the physical and chemical characteristics of the contaminant source and/or residual radioactive materials. (4) Definition of existing ground water contamination by comparison with the EPA ground water protection standards. (5) Description of the geochemical processes that affect the migration of the source contaminants at the processing site. (6) Description of water resource use, including availability, current and future use and value, and alternate water supplies.« less

Crystal Structure of Bacillus subtilis α-Amylase in Complex with Acarbose

PubMed Central

Kagawa, Masayuki; Fujimoto, Zui; Momma, Mitsuru; Takase, Kenji; Mizuno, Hiroshi

2003-01-01

The crystal structure of Bacillus subtilis α-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process. PMID:14617662

Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM-1 β-lactamase

PubMed Central

Marciano, David C; Brown, Nicholas G; Palzkill, Timothy

2009-01-01

A large number of β-lactamases have emerged that are capable of conferring bacterial resistance to β-lactam antibiotics. Comparison of the structural and functional features of this family has refined understanding of the catalytic properties of these enzymes. An arginine residue present at position 244 in TEM-1 β-lactamase interacts with the carboxyl group common to penicillin and cephalosporin antibiotics and thereby stabilizes both the substrate and transition state complexes. A comparison of class A β-lactamase sequences reveals that arginine at position 244 is not conserved, although a positive charge at this structural location is conserved and is provided by an arginine at positions 220 or 276 for those enzymes lacking arginine at position 244. The plasticity of the location of positive charge in the β-lactamase active site was experimentally investigated by relocating the arginine at position 244 in TEM-1 β-lactamase to positions 220, 272, and 276 by site-directed mutagenesis. Kinetic analysis of the engineered β-lactamases revealed that removal of arginine 244 by alanine mutation reduced catalytic efficiency against all substrates tested and restoration of an arginine at positions 272 or 276 partially suppresses the catalytic defect of the Arg244Ala substitution. These results suggest an evolutionary mechanism for the observed divergence of the position of positive charge in the active site of class A β-lactamases. PMID:19672877

Using mass spectrometry to study the photo-affinity labeling of protein tyrosine phosphatase 1B

NASA Astrophysics Data System (ADS)

Leriche, Tammy; Skorey, Kathryn; Roy, Patrick; McKay, Dan; Bateman, Kevin P.

2004-11-01

Protein tyrosine phosphatase 1B (PTP1B) is a potential target for the treatment of Type II diabetes and several companies are developing small molecule inhibitors of this enzyme. Part of the characterization of these compounds as PTP1B inhibitors is the understanding of how they bind in the enzyme active site. The use of photo-activated inhibitors that target the active site can provide such insight. This paper describes the characterization of a photoprobe directed at the active site of PTP1B. Mass spectrometry revealed the specific binding of the probe to the intact protein. Digestion of the labeled protein followed by LC-MS and LC-MS/MS was used to show that the photoprobe binds to a specific active site amino acid. This was confirmed by comparison with the X-ray structure of PTP1B with a PTP1B inhibitor. The probe labels a conserved acidic residue (Asp) that is required for catalytic activity. This photoprobe may prove to be a useful tool for the development of a PTP1B inhibitor or for the study of PTPs in general.

Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site.

PubMed

Prado, R A; Barbosa, J A; Ohmiya, Y; Viviani, V R

2011-07-01

The structural origin and evolution of bioluminescent activity of beetle luciferases from AMP/CoA ligases remains a mystery. Previously we cloned the luciferase-like enzyme from Zophobas morio mealworm, a reasonable protoluciferase model that could shine light on this mystery. Kinetic characterization and studies with D- and L-luciferin and their adenylates showed that stereoselectivity constitutes a critical feature for the origin of luciferase activity in AMP/CoA ligases. Comparison of the primary structures and modeling studies of this protoluciferase and the three main families of beetle luciferases showed that the carboxylic acid substrate binding site of this enzyme is smaller and more hydrophobic than the luciferin binding site of beetle luciferases, showing several substitutions of otherwise conserved residues. Thus, here we performed a site-directed mutagenesis survey of the carboxylic binding site motifs of the protoluciferase by replacing their residues by the respective conserved ones found in beetle luciferases in order to identify the structural determinants of luciferase/oxygenase activity. Although most of the substitutions had negative impact on the luminescence activity of the protoluciferase, only the substitution I327T improved the luminescence activity, resulting in a broad and 15 nm blue-shifted luminescence spectrum. Such substitution indicates the importance of the loop motif 322YGMSEI327 (341YGLTETT347 in Photinus pyralis luciferase) for luciferase activity, and indicates a possible route for the evolution of bioluminescence function of beetle luciferases.

Bimetallic Effect of Single Nanocatalysts Visualized by Super-Resolution Catalysis Imaging

DOE PAGES

Chen, Guanqun; Zou, Ningmu; Chen, Bo; ...

2017-11-01

Compared with their monometallic counterparts, bimetallic nanoparticles often show enhanced catalytic activity associated with the bimetallic interface. Direct quantitation of catalytic activity at the bimetallic interface is important for understanding the enhancement mechanism, but challenging experimentally. Here using single-molecule super-resolution catalysis imaging in correlation with electron microscopy, we report the first quantitative visualization of enhanced bimetallic activity within single bimetallic nanoparticles. We focus on heteronuclear bimetallic PdAu nanoparticles that present a well-defined Pd–Au bimetallic interface in catalyzing a photodriven fluorogenic disproportionation reaction. Our approach also enables a direct comparison between the bimetallic and monometallic regions within the same nanoparticle. Theoreticalmore » calculations further provide insights into the electronic nature of N–O bond activation of the reactant (resazurin) adsorbed on bimetallic sites. Subparticle activity correlation between bimetallic enhancement and monometallic activity suggests that the favorable locations to construct bimetallic sites are those monometallic sites with higher activity, leading to a strategy for making effective bimetallic nanocatalysts. Furthermore, the results highlight the power of super-resolution catalysis imaging in gaining insights that could help improve nanocatalysts.« less

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

Chen, Guanqun; Zou, Ningmu; Chen, Bo

Compared with their monometallic counterparts, bimetallic nanoparticles often show enhanced catalytic activity associated with the bimetallic interface. Direct quantitation of catalytic activity at the bimetallic interface is important for understanding the enhancement mechanism, but challenging experimentally. Here using single-molecule super-resolution catalysis imaging in correlation with electron microscopy, we report the first quantitative visualization of enhanced bimetallic activity within single bimetallic nanoparticles. We focus on heteronuclear bimetallic PdAu nanoparticles that present a well-defined Pd–Au bimetallic interface in catalyzing a photodriven fluorogenic disproportionation reaction. Our approach also enables a direct comparison between the bimetallic and monometallic regions within the same nanoparticle. Theoreticalmore » calculations further provide insights into the electronic nature of N–O bond activation of the reactant (resazurin) adsorbed on bimetallic sites. Subparticle activity correlation between bimetallic enhancement and monometallic activity suggests that the favorable locations to construct bimetallic sites are those monometallic sites with higher activity, leading to a strategy for making effective bimetallic nanocatalysts. Furthermore, the results highlight the power of super-resolution catalysis imaging in gaining insights that could help improve nanocatalysts.« less

Brownian aggregation rate of colloid particles with several active sites

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

Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V., E-mail: chern@ns.kinetics.nsc.ru

2014-08-14

We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shownmore » to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.« less

Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

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

Chen, Chuanying; Beck, Brian W.; Krause, Kurt

2007-02-15

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we showmore » that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.« less

Characterization of Missouri surface waters near point sources of pollution reveals potential novel atmospheric route of exposure for bisphenol A and wastewater hormonal activity pattern.

PubMed

Kassotis, Christopher D; Alvarez, David A; Taylor, Julia A; vom Saal, Frederick S; Nagel, Susan C; Tillitt, Donald E

2015-08-15

Surface water contamination by chemical pollutants increasingly threatens water quality around the world. Among the many contaminants found in surface water, there is growing concern regarding endocrine disrupting chemicals, based on their ability to interfere with some aspect of hormone action in exposed organisms, including humans. This study assessed water quality at several sites across Missouri (near wastewater treatment plants and airborne release sites of bisphenol A) based on hormone receptor activation potencies and chemical concentrations present in the surface water. We hypothesized that bisphenol A and ethinylestradiol would be greater in water near permitted airborne release sites and wastewater treatment plant inputs, respectively, and that these two compounds would be responsible for the majority of activities in receptor-based assays conducted with water collected near these sites. Concentrations of bisphenol A and ethinylestradiol were compared to observed receptor activities using authentic standards to assess contribution to total activities, and quantitation of a comprehensive set of wastewater compounds was performed to better characterize each site. Bisphenol A concentrations were found to be elevated in surface water near permitted airborne release sites, raising questions that airborne releases of BPA may influence nearby surface water contamination and may represent a previously underestimated source to the environment and potential for human exposure. Estrogen and androgen receptor activities of surface water samples were predictive of wastewater input, although the lower sensitivity of the ethinylestradiol ELISA relative to the very high sensitivity of the bioassay approaches did not allow a direct comparison. Wastewater-influenced sites also had elevated anti-estrogenic and anti-androgenic equivalence, while sites without wastewater discharges exhibited no antagonist activities. Published by Elsevier B.V.

Characterization of Missouri surface waters near point sources of pollution reveals potential novel atmospheric route of exposure for bisphenol A and wastewater hormonal activity pattern

USGS Publications Warehouse

Kassotis, Christopher D.; Alvarez, David A.; Taylor, Julia A.; vom Saal, Frederick S.; Nagel, Susan C.; Tillitt, Donald E.

2015-01-01

Surface water contamination by chemical pollutants increasingly threatens water quality around the world. Among the many contaminants found in surface water, there is growing concern regarding endocrine disrupting chemicals, based on their ability to interfere with some aspect of hormone action in exposed organisms, including humans. This study assessed water quality at several sites across Missouri (near wastewater treatment plants and airborne release sites of bisphenol A) based on hormone receptor activation potencies and chemical concentrationspresent in the surface water. We hypothesized that bisphenol A and ethinylestradiol would be greater in water near permitted airborne release sites and wastewater treatment plant inputs, respectively, and that these two compounds would be responsible for the majority of activities in receptor-based assays conducted with water collected near these sites. Concentrations of bisphenol A and ethinylestradiol were compared to observed receptor activities using authentic standards to assess contribution to total activities, and quantitation of a comprehensive set of wastewater compounds was performed to better characterize each site. Bisphenol A concentrations were found to be elevated in surface water near permitted airborne release sites, raising questions that airborne releases of BPA may influence nearby surface water contamination and may represent a previously underestimated source to the environment and potential for human exposure. Estrogen and androgen receptor activities of surface water samples were predictive of wastewater input, although the lower sensitivity of the ethinylestradiol ELISA relative to the very high sensitivity of the bioassay approaches did not allow a direct comparison. Wastewater-influenced sites also had elevated anti-estrogenic and anti-androgenic equivalence, while sites without wastewater discharges exhibited no antagonist activities.

High Concentrations of Organic Contaminants in Air from Ship Breaking Activities in Chittagong, Bangladesh.

PubMed

Nøst, Therese H; Halse, Anne K; Randall, Scott; Borgen, Anders R; Schlabach, Martin; Paul, Alak; Rahman, Atiqur; Breivik, Knut

2015-10-06

The beaches on the coast of Chittagong in Bangladesh are one of the most intense ship breaking areas in the world. The aim of the study was to measure the concentrations of organic contaminants in the air in the city of Chittagong, including the surrounding ship breaking areas using passive air samplers (N = 25). The compounds detected in the highest amounts were the polycyclic aromatic hydrocarbons (PAHs) and short-chain chlorinated paraffins (SCCPs), whereas dichlorodiphenyltrichloroethanes (DDTs), hexachlorobenzene (HCB), and polychlorinated biphenyls (PCBs) were several orders of magnitude lower in comparison. PCBs, PAHs, and HCB were highest at sites near the ship breaking activities, whereas DDTs and SCCPs were higher in the urban areas. Ship breaking activities likely act as atmospheric emission sources of PCBs, PAHs, and HCB, thus adding to the international emphasis on responsible recycling of ships. Concentrations of PAHs, PCBs, DDTs, HCB, and SCCPs in ambient air in Chittagong are high in comparison to those found in similar studies performed in other parts of Asia. Estimated toxic equivalent quotients indicate elevated human health risks caused by inhalation of PAHs at most sites.

Archaeology of Void Spaces

NASA Astrophysics Data System (ADS)

Look, Cory

The overall goal of this research is to evaluate the efficacy of pXRF for the identification of ancient activity areas at Pre-Columbian sites in Antigua that range across time periods, geographic regions, site types with a variety of features, and various states of preservation. These findings have important implications for identifying and reconstructing places full of human activity but void of material remains. A synthesis for an archaeology of void spaces requires the construction of new ways of testing anthrosols, and identifying elemental patterns that can be used to connect people with their places and objects. This research begins with an exploration of rich middens in order to study void spaces. Midden archaeology has been a central focus in Caribbean research, and consists of an accumulation of discarded remnants from past human activities that can be tested against anthrosols. The archaeological collections visited for this research project involved creating new databases to generate a comprehensive inventory of sites, materials excavated, and assemblages available for study. Of the more than 129 Pre-Columbian sites documented in Antigua, few sites have been thoroughly surveyed or excavated. Twelve Pre-Columbian sites, consisting of thirty-six excavated units were selected for study; all of which contained complete assemblages for comparison and soil samples for testing. These excavations consisted almost entirely of midden excavations, requiring new archaeological investigations to be carried out in spaces primarily void of material remains but within the village context. Over the course of three seasons excavations, shovel test pits, and soil augers were used to obtain a variety of anthrosols and archaeological assemblages in order to generate new datasets to study Pre-Columbian activity areas. The selection of two primary case study sites were used for comparison: Indian Creek and Doigs. Findings from this research indicate that accounting for the variety of activity areas that make up a site can imbue a site with an identity of purpose and shed light on how different sites may have served different purposes within a regional framework. Excavations at the site of Indian Creek identified a series of raised middens that enclosed an open space for approximately 1500 years. This research explores this open space, and questions the meaning of 'void' and 'empty' with respect to past human activities. While archaeologists recognize that areas void of material remains are certainly part of the larger site, the question remains, without an understand of these spaces; what aspects of past life are we possibly masking? The integration of anthrosols alongside archaeological excavations and spatial analysis indicate that the site of Indian Creek contained a ceremonial plaza that formed early on and was maintained until abandonment. The spatial distribution of material objects combined with anthrosol studies provided additional evidence of ritual deposits concentrated in one part of the plaza associated with a nearby creek-bed. The second site, Doigs represents one of the last intact undisturbed Early Ceramic Age site of its kind in the Eastern Caribbean. Since its discovery in the 1970's, Doig's has been partially surveyed and excavated. The identification of residential activity areas including several potential structures, bead manufacturing loci, and cooking hearths were used to help test chemical signatures with archaeologically defined activity areas. Findings from this site illustrated the uniqueness of elemental patterns associated with activity areas, and also generated new questions regarding void spaces enriched with elemental patterns associated with concentrations of plant and vegetation debris. It is the hope of this study to contribute to our general knowledge for the identification of ancient activity areas as well as the different places that give sites their identity. These assemblages of activity areas can provide Caribbeanists with an alternative approach to studying social organization at a village scale and generate new discussions regarding island wide-community relationships.

Amino acid sequence of human cholinesterase. Annual report, 30 September 1984-30 September 1985

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

Lockridge, O.

1985-10-01

The active-site serine residue is located 198 amino acids from the N-terminal. The active-site peptide was isolated from three different genetic types of human serum cholinesterase: from usual, atypical, and atypical-silent genotypes. It was found that the amino acid sequence of the active-site peptide was identical in all three genotypes. Comparison of the complete sequences of cholinesterase from human serum and acetylcholinesterase from the electric organ of Torpedo californica shows an identity of 53%. Cholinesterase is of interest to the Department of Defense because cholinesterase protects against organophosphate poisons of the type used in chemical warfare. The structural results presentedmore » here will serve as the basis for cloning the gene for cholinesterase. The potential uses of large amounts of cholinesterase would be for cleaning up spills of organophosphates and possibly for detoxifying exposed personnel.« less

Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

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

Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong

2009-11-10

The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenzamore » H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.« less

Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

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

Buhrman, Greg; O; #8242

2012-09-17

We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the 'off' and 'on' allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond themore » active site. Comparison of FTMaps for the H and K isoforms reveals essentially identical hot spots. Furthermore, using NMR measurements of spin relaxation, we determined that K-Ras exhibits global conformational dynamics very similar to those we previously reported for H-Ras. We thus hypothesize that the global conformational rearrangement serves as a mechanism for allosteric coupling between the effector interface and remote hot spots in all Ras isoforms. At least with respect to the binding sites involving the G domain, H-Ras is an excellent model for K-Ras and probably N-Ras as well. Ras has so far been elusive as a target for drug design. The present work identifies various unexplored hot spots throughout the entire surface of Ras, extending the focus from the disordered active site to well-ordered locations that should be easier to target.« less

Evolution of the herpes thymidine kinase: identification and comparison of the equine herpesvirus 1 thymidine kinase gene reveals similarity to a cell-encoded thymidylate kinase.

PubMed Central

Robertson, G R; Whalley, J M

1988-01-01

We have identified the equine herpesvirus 1 (EHV-1) thymidine kinase gene (TK) by DNA-mediated transformation and by DNA sequencing. Alignment of the amino acid sequence of the EHV-1 TK with the TKs from 3 other herpesviruses revealed regions of homology, some of which correspond to the previously identified substrate binding sites, while others have as yet, no assigned function. In particular, the strict conservation of an aspartate within the proposed nucleoside binding site suggests a role in ATP binding for this residue. Comparison of 5 herpes TKs with the thymidylate kinase of yeast revealed significant similarity which was strongest in those regions important to catalytic activity of the herpes TKs, and, therefore we propose that the herpes TK may be derived from a cellular thymidylate kinase. The implications for the evolution of enzyme activities within a pathway of nucleotide metabolism are discussed. PMID:2849761

The glycoprotein character of multiple forms of Aspergillus polygalacturonase.

PubMed

Stratilová, E; Mislovicová, D; Kacuráková, M; Machová, E; Kolarová, N; Markovic, O; Jörnvall, H

1998-02-01

Comparisons of known primary structures of polygalacturonases show that extent and localization of potential N-glycosylation sites differ. Some sites are similar in position and adjacent to strictly conserved residues at the potential active site. The presence of N-acetylglucosamine and mannose in the molecules of two homogeneous, major Aspergillus sp. polygalacturonase forms was confirmed by IR spectroscopy. The purification method, based on interaction of the carbohydrate part with concanavalin A immobilized on chlorotriazine bead cellulose, was optimized. Deglycosylation with N-glycosidase F under denaturating and nondenaturating conditions led to molecular mass decreases followed by complete inactivation of the polygalacturonase enzyme activity. These results show the importance of glycosylation in these protein forms, while the comparative patterns establish both variability and some similarities in overall glycosylation architectures.

Site-index comparisons for tree species in northern Minnesota.

Treesearch

Willard H. Carmean; Alexander Vasilevsky

1971-01-01

Presents site-index comparisons for the following forest species in northern Minnesota: quaking aspen, paper birch, basswood, red oak, black ash, jack pine, red pine, white pine, white spruce, black spruce, balsam fir, white-cedar, and tamarack. Shows site-index relationships among these species by using site-index ratios and species-comparison graphs.

Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site.

PubMed

Adamczyk, Katrin; Simpson, Niall; Greetham, Gregory M; Gumiero, Andrea; Walsh, Martin A; Towrie, Michael; Parker, Anthony W; Hunt, Neil T

2015-01-01

Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H 2 O and D 2 O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump-probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.

Design, synthesis and evaluation of some N-methylenebenzenamine derivatives as selective acetylcholinesterase (AChE) inhibitor and antioxidant to enhance learning and memory.

PubMed

Shrivastava, Sushant K; Srivastava, Pavan; Upendra, T V R; Tripathi, Prabhash Nath; Sinha, Saurabh K

2017-02-15

Series of some 3,5-dimethoxy-N-methylenebenzenamine and 4-(methyleneamino)benzoic acid derivatives comprising of N-methylenebenzenamine nucleus were designed, synthesized, characterized, and assessed for their acetylcholinesterase (AChE), butyrylcholinesterase (BChE) inhibitory, and antioxidant activity thereby improving learning and memory in rats. The IC 50 values of all the compound along with standard were determined on AChE and BChE enzyme. The free radical scavenging activity was also assessed by in vitro DPPH (2,2-diphenyl-1-picryl-hydrazyl) and hydrogen peroxide radical scavenging assay. The selective inhibitions of all compounds were observed against AChE in comparison with standard donepezil. The enzyme kinetic study of the most active compound 4 indicated uncompetitive AChE inhibition. The docking studies of compound 4 exhibited the worthy interaction on active-site gorge residues Phe330 and Trp279 responsible for its high affinity towards AChE, whereas lacking of the BChE inhibition was observed due to a wider gorge binding site and absence of important aromatic amino acids interactions. The ex vivo study confirmed AChE inhibition abilities of compound 4 at brain site. Further, a considerable decrease in escape latency period of the compound was observed in comparison with standard donepezil through in vivo Spatial Reference Memory (SRM) and Spatial Working Memory (SWM) models which showed the cognition-enhancing potential of compound 4. The in vivo reduced glutathione (GSH) estimation on rat brain tissue homogenate was also performed to evaluate free radical scavenging activity substantiated the antioxidant activity in learning and memory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis

NASA Astrophysics Data System (ADS)

Woolfrey, John R.; Avery, Mitchell A.; Doweyko, Arthur M.

1998-03-01

Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.

Biochemical identification of residues that discriminate between 3,4-dihydroxyphenylalanine decarboxylase and 3,4-dihydroxyphenylacetaldehyde synthase-mediated reactions.

PubMed

Liang, Jing; Han, Qian; Ding, Haizhen; Li, Jianyong

2017-12-01

In available insect genomes, there are several L-3,4-dihydroxyphenylalanine (L-dopa) decarboxylase (DDC)-like or aromatic amino acid decarboxylase (AAAD) sequences. This contrasts to those of mammals whose genomes contain only one DDC. Our previous experiments established that two DDC-like proteins from Drosophila actually mediate a complicated decarboxylation-oxidative deamination process of dopa in the presence of oxygen, leading to the formation of 3,4-dihydroxyphenylacetaldehyde (DHPA), CO 2 , NH 3, and H 2 O 2 . This contrasts to the typical DDC-catalyzed reaction, which produces CO 2 and dopamine. These DDC-like proteins were arbitrarily named DHPA synthases based on their critical role in insect soft cuticle formation. Establishment of reactions catalyzed by these AAAD-like proteins solved a puzzle that perplexed researchers for years, but to tell a true DHPA synthase from a DDC in the insect AAAD family remains problematic due to high sequence similarity. In this study, we performed extensive structural and biochemical comparisons between DHPA synthase and DDC. These comparisons identified several target residues potentially dictating DDC-catalyzed and DHPA synthase-catalyzed reactions, respectively. Comparison of DHPA synthase homology models with crystal structures of typical DDC proteins, particularly residues in the active sites, provided further insights for the roles these identified target residues play. Subsequent site-directed mutagenesis of the tentative target residues and activity evaluations of their corresponding mutants determined that active site His192 and Asn192 are essential signature residues for DDC- and DHPA synthase-catalyzed reactions, respectively. Oxygen is required in DHPA synthase-mediated process and this oxidizing agent is reduced to H 2 O 2 in the process. Biochemical assessment established that H 2 O 2 , formed in DHPA synthase-mediated process, can be reused as oxidizing agent and this active oxygen species is reduced to H 2 O; thereby avoiding oxidative stress by H 2 O 2 . Results of our structural and functional analyses provide a reasonable explanation of mechanisms involved in DHPA synthase-mediated reactions. Based on the key active site residue Asn192, identified in Drosophila DHPA synthase, we were able to distinguish all available insect DHPA synthases from DDC sequences primarily. Copyright © 2017. Published by Elsevier Ltd.

Interactive flare sites within an active region complex

NASA Technical Reports Server (NTRS)

Poletto, G.; Gary, G. A.; Machado, M. E.

1993-01-01

We examine here a set of images of an active region complex, acquired on June 24-25, 1980, by the Hard X-ray Imaging Spectrometer on SMM, with the purpose of establishing whether there was any interplay between the frequent activity observed at different sites in the activity center and, in such a case, how the interaction was established. By analyzing both quiet and active orbits we show that, as a rule, activity originating in one region triggers the other region's activity. However, we find little unambiguous evidence for the presence of large-scale interconnecting loops. A comparison of X-ray images with magnetic field observations suggested that we interpret the active region behavior in terms of the interaction between different loop systems, in a scenario quite analogous to the interacting bipole representation of individual flares. We conclude that active region interplay provides an easily observable case to study the time-dependent topology and the mechanisms for the spreading of activity in transient events over all energy scales.

Comparison of ligand migration and binding in heme proteins of the globin family

NASA Astrophysics Data System (ADS)

Karin, Nienhaus; Ulrich Nienhaus, G.

2015-12-01

The binding of small diatomic ligands such as carbon monoxide or dioxygen to heme proteins is among the simplest biological processes known. Still, it has taken many decades to understand the mechanistic aspects of this process in full detail. Here, we compare ligand binding in three heme proteins of the globin family, myoglobin, a dimeric hemoglobin, and neuroglobin. The combination of structural, spectroscopic, and kinetic experiments over many years by many laboratories has revealed common properties of globins and a clear mechanistic picture of ligand binding at the molecular level. In addition to the ligand binding site at the heme iron, a primary ligand docking site exists that ensures efficient ligand binding to and release from the heme iron. Additional, secondary docking sites can greatly facilitate ligand escape after its dissociation from the heme. Although there is only indirect evidence at present, a preformed histidine gate appears to exist that allows ligand entry to and exit from the active site. The importance of these features can be assessed by studies involving modified proteins (via site-directed mutagenesis) and comparison with heme proteins not belonging to the globin family.

A Rapid and Quantitative Recombinase Activity Assay

USDA-ARS?s Scientific Manuscript database

We present here a comparison between the recombinase systems FLP-FRT and Cre-loxP. A transient excision based dual luciferase expression assay is used for its rapid and repeatable nature. The detection system was designed within an intron to remove the remaining recombinase recognition site and no...

Dual evaluation of some novel 2-amino-substituted coumarinylthiazoles as anti-inflammatory-antimicrobial agents and their docking studies with COX-1/COX-2 active sites.

PubMed

Chandak, Navneet; Kumar, Pawan; Kaushik, Pawan; Varshney, Parul; Sharma, Chetan; Kaushik, Dhirender; Jain, Sudha; Aneja, Kamal R; Sharma, Pawan K

2014-08-01

Synthesis of total eighteen 2-amino-substituted 4-coumarinylthiazoles including sixteen new compounds (3a-o and 5b) bearing the benzenesulfonamide moiety is described in the present report. All the synthesized target compounds were examined for their in vivo anti-inflammatory (AI) activity and in vitro antimicrobial activity. Results revealed that six compounds (3 d, 3 f, 3 g, 3 h, 3 j and 3 n) exhibited pronounced anti-inflammatory activity comparable to the standard drug indomethacin. AI results were further confirmed by the docking studies of the most active (3n) and the least active compound (3a) with COX-1 and COX-2 active sites. In addition, most of the compounds exhibited moderate antimicrobial activity against Gram-positive bacteria as well as fungal yeast, S. cervisiae. Comparison between 3 and 5 indicated that incorporation of additional substituted pyrazole nucleus into the scaffold significantly enhanced AI activity.

Mechanism of the asymmetric activation of the MinD ATPase by MinE

PubMed Central

Park, Kyung-Tae; Wu, Wei; Lovell, Scott; Lutkenhaus, Joe

2012-01-01

Summary MinD is a component of the Min system involved in the spatial regulation of cell division. It is an ATPase in the MinD/ParA/Mrp deviant Walker A motif family which is within the P loop GTPase superfamily. Its ATPase activity is stimulated by MinE, however, the mechanism of this activation is unclear. MinD forms a symmetric dimer with two binding sites for MinE, however, a recent model suggested that MinE occupying one site was sufficient for ATP hydrolysis. By generating heterodimers with one binding site for MinE we show that one binding site is sufficient for stimulation of the MinD ATPase. Furthermore, comparison of structures of MinD and related proteins led us to examine the role of N45 in the switch I region. An asparagine at this position is conserved in four of the deviant Walker A motif subfamilies (MinD, chromosomal ParAs, Get3 and FleN) and we find that N45 in MinD is essential for MinE stimulated ATPase activity and suggest that it is a key residue affected by MinE binding. PMID:22651575

Crystal Structure of Phosphatidylglycerophosphatase (PGPase), a Putative Membrane-Bound Lipid Phosphatase, Reveals a Novel Binuclear Metal Binding Site and Two Proton Wires

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

Kumaran,D.; Bonnano, J.; Burley, S.

2006-01-01

Phosphatidylglycerophosphatase (PGPase), an enzyme involved in lipid metabolism, catalyzes formation of phosphatidylglycerol from phosphatidylglycerophosphate. Phosphatidylglycerol is a multifunctional phospholipid, found in the biological membranes of many organisms. Here, we report the crystal structure of Listeria monocytogenes PGPase at 1.8 Angstroms resolution. PGPase, an all-helical molecule, forms a homotetramer. Each protomer contains an independent active site with two metal ions, Ca{sup 2+} and Mg{sup 2+}, forming a hetero-binuclear center located in a hydrophilic cavity near the surface of the molecule. The binuclear center, conserved ligands, metal-bound water molecules, and an Asp-His dyad form the active site. The catalytic mechanism of thismore » enzyme is likely to proceed via binuclear metal activated nucleophilic water. The binuclear metal-binding active-site environment of this structure should provide insights into substrate binding and metal-dependent catalysis. A long channel with inter-linked linear water chains, termed 'proton wires', is observed at the tetramer interface. Comparison of similar water chain structures in photosynthetic reaction centers (RCs), Cytochrome f, gramicidin, and bacteriorhodopsin, suggests that PGPase may conduct protons via proton wires.« less

Publicly available hospital comparison web sites: determination of useful, valid, and appropriate information for comparing surgical quality.

PubMed

Leonardi, Michael J; McGory, Marcia L; Ko, Clifford Y

2007-09-01

To explore hospital comparison Web sites for general surgery based on: (1) a systematic Internet search, (2) Web site quality evaluation, and (3) exploration of possible areas of improvement. A systematic Internet search was performed to identify hospital quality comparison Web sites in September 2006. Publicly available Web sites were rated on accessibility, data/statistical transparency, appropriateness, and timeliness. A sample search was performed to determine ranking consistency. Six national hospital comparison Web sites were identified: 1 government (Hospital Compare [Centers for Medicare and Medicaid Services]), 2 nonprofit (Quality Check [Joint Commission on Accreditation of Healthcare Organizations] and Hospital Quality and Safety Survey Results [Leapfrog Group]), and 3 proprietary sites (names withheld). For accessibility and data transparency, the government and nonprofit Web sites were best. For appropriateness, the proprietary Web sites were best, comparing multiple surgical procedures using a combination of process, structure, and outcome measures. However, none of these sites explicitly defined terms such as complications. Two proprietary sites allowed patients to choose ranking criteria. Most data on these sites were 2 years old or older. A sample search of 3 surgical procedures at 4 hospitals demonstrated significant inconsistencies. Patients undergoing surgery are increasingly using the Internet to compare hospital quality. However, a review of available hospital comparison Web sites shows suboptimal measures of quality and inconsistent results. This may be partially because of a lack of complete and timely data. Surgeons should be involved with quality comparison Web sites to ensure appropriate methods and criteria.

Cost And Performance Report Evaluating the Longevity and Hydraulic Performance of Permeable Reactive Barriers at Department of Defense Sites

DTIC Science & Technology

2003-12-01

construction methods, such as jetting, hydraulic fracturing , and vibratory beam, have been demonstrated at some sites, as they offer some cost... hydraulic fracturing , are available, but there is not as much widespread experience yet with these techniques for PRBs. Also, these innovative... hydraulic fracturing ) can be used at relatively higher cost. The cost comparison of a PRB versus an active remedy, such as a pump-and-treat system, often

Collection of LAI and FPAR Data Over The Terra Core Sites

NASA Technical Reports Server (NTRS)

Myneni, Ranga B.; Knjazihhin, J.; Tian, Y.; Wang, Y.

2001-01-01

The objective of our effort was to collect and archive data on LAI (leaf area index) and FPAR (Fraction of Photosynthetically active Radiation absorbed by vegetation) at the EOS Core validation sites as well as to validate and evaluate global fields of LAI and FPAR derived from atmospherically corrected MODIS (Moderate Resolution Imaging Spectrometer) surface reflectance data by comparing these fields with the EOS Core validation data set. The above has been accomplished by: (a) the participation in selected field campaigns within the EOS Validation Program; (b) the processing of the collected data so that suitable comparison between field measurements and the MODIS LAI/FPAR fields can be made; (c) the comparison of the MODAS LAI/FRAM fields with the EOS Terra Core validation data set.

Effects of microwaves (900 MHz) on peroxidase systems: A comparison between lactoperoxidase and horseradish peroxidase.

PubMed

Barteri, Mario; De Carolis, Roberta; Marinelli, Fiorenzo; Tomassetti, Goliardo; Montemiglio, Linda Celeste

2016-01-01

This work shows the effects of exposure to an electromagnetic field at 900 MHz on the catalytic activity of the enzymes lactoperoxidase (LPO) and horseradish peroxidase (HRP). Experimental evidence that irradiation causes conformational changes of the active sites and influences the formation and stability of the intermediate free radicals is documented by measurements of enzyme kinetics, circular dichroism spectroscopy (CD) and cyclic voltammetry.

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The concentration of some metals (Pb, Cd, Zn and Cu) and delta aminolevulinic acid dehydratase activity of fruit fly (Drosophila melanogaster) living near lead and zinc smelter ``Trepça'' in Kosova

NASA Astrophysics Data System (ADS)

Elezaj, I. R.; Letaj, K. Rr.; Selimi, Q. I.; Zhushi-Etemi, F.

2003-05-01

The concentration of Pb, Cd, Zn and Cu, δ-aminolevulinic acid dehydratase activity (ALA-D: EC.4.2.1.24) hemoglobin and protein amount have been determined in three different populations of fruit fly (Drosophila melanogaster) caught at two urban sites (Mitrovica town, which is situated close to smelter of “Trepça” don close and Prishtina the capital of Kosova) and in Luki village as uncontaminated area. The results show that in the fruit fly of Mitrovica the concentration of Pb, Cd and Zn was significantly higher (P<0.00l) in comparison with that on the f-Liit fly of Prishtina and Luki. The concentration of Pb of fruit fly from Mitrovica was 3.1 times higher in comparison with that on fruit fly of Prishtina and 4.9 times higher in comparison with uncontaminated group of fruit fly. The ALA-D activity was significantly inhibited in the homogenate of fruit fly from Mitrovica in comparison with Prishtina and Luki localities (P<0.00l). ALA-D activity was also inhibited in the homogenate of Prishtina fruit fly in comparison with Luki group (P<0.00l). The amount of proteins was significantly lower in Mitrovica fruit fly in comparison with that in control and Prishtina group. The hemoglobin value was relatively unchanged.

Comparison of CCD astrolabe multi-site solar diameter observations

NASA Astrophysics Data System (ADS)

Andrei, A. H.; Boscardin, S. C.; Chollet, F.; Delmas, C.; Golbasi, O.; Jilinski, E. G.; Kiliç, H.; Laclare, F.; Morand, F.; Penna, J. L.; Reis Neto, E.

2004-11-01

Results are presented of measured variations of the photospheric solar diameter, as concurrently observed at three sites of the R2S3 (Réseau de Suivi au Sol du Rayon Solaire) consortium in 2001. Important solar flux variations appeared in that year, just after the maximum of solar activity cycle 23, make that time stretch particularly promising for a comparison of the multi-site results. The sites are those in Turkey, France and Brasil. All observations are made with similar CCD solar astrolabes, and at nearby effective wavelengths. The data reductions share algorithms, that are alike, the outcomes of which are here treated after applying a normalization correction using the Fried parameter. Since the sites are geographically quite far, atmospheric conditions are dismissed as possible causes of the large common trend found. Owing to particularities of each site, the common continuous observational period extends from April to September. The standard deviation for the daily averages is close to 0.47 arcsec for the three sites. Accordingly, the three series are smoothed by a low-pass-band Fourier filter of 150 observations (typically one month). The main common features found are a declining linear trend, of the order of 0.7 mas/day, and a relative maximum, around MJD 2120, of the order of 100 mas. Standard statistical tests endorse the correlation of the three series.

Plant uptake of 238U, 235U, 232Th, 226Ra, 210Pb and 40K from a coal ash and slag disposal site and control soil under field conditions: A preliminary study.

PubMed

Skoko, Božena; Marović, Gordana; Babić, Dinko; Šoštarić, Marko; Jukić, Mirela

2017-06-01

The aim of this study was to investigate the uptake of 238 U, 235 U, 232 Th, 226 Ra, 210 Pb and 40 K by plants that grow on a coal ash and slag disposal site known for its higher content of naturally occurring radionuclides. Plant species that were sampled are common for the Mediterranean flora and can be divided as follows: grasses & herbs, shrubs and trees. To compare the activity concentrations and the resultant concentration ratios of the disposal site with those in natural conditions, we used control data specific for the research area, obtained for plants growing on untreated natural soil. Radionuclide activity concentrations were determined by high resolution gamma-ray spectrometry. Media parameters (pH, electrical conductivity and organic matter content) were also analysed. We confirmed significantly higher activity concentrations of 238 U, 235 U, 226 Ra and 210 Pb in ash and slag compared to control soil. However, a significant increase in the radionuclide activity concentration in the disposal site's vegetation was observed only for 226 Ra. On the contrary, a significantly smaller activity concentration of 40 K in ash and slag had no impact on its activity concentration in plant samples. The calculated plant uptake of 238 U, 235 U, 226 Ra and 210 Pb is significantly smaller in comparison with the uptake at the control site, while it is vice versa for 40 K. No significant difference was observed between the disposal site and the control site's plant uptake of 232 Th. These results can be the foundation for further radioecological assessment of this disposal site but also, globally, they can contribute to a better understanding of nature and long-term management of such disposal sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

Studies on the regulation of the human E1 subunit of the 2-oxoglutarate dehydrogenase complex, including the identification of a novel calcium-binding site.

PubMed

Armstrong, Craig T; Anderson, J L Ross; Denton, Richard M

2014-04-15

The regulation of the 2-oxoglutarate dehydrogenase complex is central to intramitochondrial energy metabolism. In the present study, the active full-length E1 subunit of the human complex has been expressed and shown to be regulated by Ca2+, adenine nucleotides and NADH, with NADH exerting a major influence on the K0.5 value for Ca2+. We investigated two potential Ca2+-binding sites on E1, which we term site 1 (D114ADLD) and site 2 (E139SDLD). Comparison of sequences from vertebrates with those from Ca2+-insensitive non-vertebrate complexes suggest that site 1 may be the more important. Consistent with this view, a mutated form of E1, D114A, shows a 6-fold decrease in sensitivity for Ca2+, whereas variant ∆site1 (in which the sequence of site 1 is replaced by A114AALA) exhibits an almost complete loss of Ca2+ activation. Variant ∆site2 (in which the sequence is replaced with A139SALA) shows no measurable change in Ca2+ sensitivity. We conclude that site 1, but not site 2, forms part of a regulatory Ca2+-binding site, which is distinct from other previously described Ca2+-binding sites.

The Utility of Geographical Information Systems (GIS) in Systems-Oriented Obesity Intervention Projects: The Selection of Comparable Study Sites for a Quasi-Experimental Intervention Design—TX CORD

PubMed Central

Byars, Allison; Byrd-Williams, Courtney; Sharma, Shreela V.; Durand, Casey; Hoelscher, Deanna M.; Butte, Nancy F.; Kelder, Steven H.

2015-01-01

Abstract Background: The Texas Childhood Obesity Research Demonstration project (TX CORD) uses a systems-oriented approach to address obesity that includes individual and family interventions, community-level action, as well as environmental and policy initiatives. Given that randomization is seldom possible in community-level intervention studies, TX CORD uses a quasi-experimental design. Comparable intervention and comparison study sites are needed to address internal validity bias. Methods: TX CORD was designed to be implemented in low-income, ethnically diverse communities in Austin and Houston, Texas. A three-stage Geographical Information System (GIS) methodology was used to establish and ascertain the comparability of the intervention and comparison study sites. Census tract (stage 1) and school (stage 2) data were used to identify spatially exclusive geographic areas that were comparable. In stage 3, study sites were compared on demographic characteristics, socioeconomic status (SES), food assets, and physical activity (PA) assets. Student's t-test was used to examine significant differences between the selected sites. Results: The methodology that was used resulted in the selection of catchment areas with demographic and socioeconomic characteristics that fit the target population: ethnically diverse population; lower-median household income; and lower home ownership rates. Additionally, the intervention and comparison sites were statistically comparable on demographic and SES variables, as well as food assets and PA assets. Conclusions: This GIS approach can provide researchers, program evaluators, and policy makers with useful tools for both research and practice. Area-level information that allows for robust understanding of communities can enhance analytical procedures in community health research and offer significant contributions in terms of community assessment and engagement. PMID:25587670

The utility of Geographical Information Systems (GIS) in systems-oriented obesity intervention projects: the selection of comparable study sites for a quasi-experimental intervention design--TX CORD.

PubMed

Oluyomi, Abiodun O; Byars, Allison; Byrd-Williams, Courtney; Sharma, Shreela V; Durand, Casey; Hoelscher, Deanna M; Butte, Nancy F; Kelder, Steven H

2015-02-01

The Texas Childhood Obesity Research Demonstration project (TX CORD) uses a systems-oriented approach to address obesity that includes individual and family interventions, community-level action, as well as environmental and policy initiatives. Given that randomization is seldom possible in community-level intervention studies, TX CORD uses a quasi-experimental design. Comparable intervention and comparison study sites are needed to address internal validity bias. TX CORD was designed to be implemented in low-income, ethnically diverse communities in Austin and Houston, Texas. A three-stage Geographical Information System (GIS) methodology was used to establish and ascertain the comparability of the intervention and comparison study sites. Census tract (stage 1) and school (stage 2) data were used to identify spatially exclusive geographic areas that were comparable. In stage 3, study sites were compared on demographic characteristics, socioeconomic status (SES), food assets, and physical activity (PA) assets. Student's t-test was used to examine significant differences between the selected sites. The methodology that was used resulted in the selection of catchment areas with demographic and socioeconomic characteristics that fit the target population: ethnically diverse population; lower-median household income; and lower home ownership rates. Additionally, the intervention and comparison sites were statistically comparable on demographic and SES variables, as well as food assets and PA assets. This GIS approach can provide researchers, program evaluators, and policy makers with useful tools for both research and practice. Area-level information that allows for robust understanding of communities can enhance analytical procedures in community health research and offer significant contributions in terms of community assessment and engagement.

Anthropogenic disturbance homogenizes seagrass fish communities.

PubMed

Iacarella, Josephine C; Adamczyk, Emily; Bowen, Dan; Chalifour, Lia; Eger, Aaron; Heath, William; Helms, Sibylla; Hessing-Lewis, Margot; Hunt, Brian P V; MacInnis, Andrew; O'Connor, Mary I; Robinson, Clifford L K; Yakimishyn, Jennifer; Baum, Julia K

2018-05-01

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat-forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta-diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance- and incidence-based beta-diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within-region comparisons using abundance- and incidence-based measures of beta-diversity, and in across-region comparisons using incidence-based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta-diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land- and seascapes, as well as managing anthropogenic impacts in high activity areas. © 2018 John Wiley & Sons Ltd.

The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation.

PubMed

Blankenship, Elise; Vahedi-Faridi, Ardeschir; Lodowski, David T

2015-12-01

Rhodopsin, a light-activated G protein coupled receptor (GPCR), has been the subject of numerous biochemical and structural investigations, serving as a model receptor for GPCRs and their activation. We present the 2.3-Å resolution structure of native source rhodopsin stabilized in a conformation competent for G protein binding. An extensive water-mediated hydrogen bond network linking the chromophore binding site to the site of G protein binding is observed, providing connections to conserved motifs essential for GPCR activation. Comparison of this extensive solvent-mediated hydrogen-bonding network with the positions of ordered solvent in earlier crystallographic structures of rhodopsin photointermediates reveals both static structural and dynamic functional water-protein interactions present during the activation process. When considered along with observations that solvent occupies similar positions in the structures of other GPCRs, these analyses strongly support an integral role for this dynamic ordered water network in both rhodopsin and GPCR activation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine

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

DeVore, Natasha M.; Meneely, Kathleen M.; Bart, Aaron G.

2013-11-20

Human xenobiotic-metabolizing cytochrome P450 (CYP) enzymes can each bind and monooxygenate a diverse set of substrates, including drugs, often producing a variety of metabolites. Additionally, a single ligand can interact with multiple CYP enzymes, but often the protein structural similarities and differences that mediate such overlapping selectivity are not well understood. Even though the CYP superfamily has a highly canonical global protein fold, there are large variations in the active site size, topology, and conformational flexibility. We have determined how a related set of three human CYP enzymes bind and interact with a common inhibitor, the muscarinic receptor agonist drugmore » pilocarpine. Pilocarpine binds and inhibits the hepatic CYP2A6 and respiratory CYP2A13 enzymes much more efficiently than the hepatic CYP2E1 enzyme. To elucidate key residues involved in pilocarpine binding, crystal structures of CYP2A6 (2.4 {angstrom}), CYP2A13 (3.0 {angstrom}), CYP2E1 (2.35 {angstrom}), and the CYP2A6 mutant enzyme, CYP2A6 I208S/I300F/G301A/S369G (2.1 {angstrom}) have been determined with pilocarpine in the active site. In all four structures, pilocarpine coordinates to the heme iron, but comparisons reveal how individual residues lining the active sites of these three distinct human enzymes interact differently with the inhibitor pilocarpine.« less

Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin.

PubMed

Fry, John C; Webster, Gordon; Cragg, Barry A; Weightman, Andrew J; Parkes, R John

2006-10-01

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R(2)=55-100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community.

Insights into the binding mode of sulphamates and sulphamides to hCA II: crystallographic studies and binding free energy calculations.

PubMed

De Simone, Giuseppina; Langella, Emma; Esposito, Davide; Supuran, Claudiu T; Monti, Simona Maria; Winum, Jean-Yves; Alterio, Vincenzo

2017-12-01

Sulphamate and sulphamide derivatives have been largely investigated as carbonic anhydrase inhibitors (CAIs) by means of different experimental techniques. However, the structural determinants responsible for their different binding mode to the enzyme active site were not clearly defined so far. In this paper, we report the X-ray crystal structure of hCA II in complex with a sulphamate inhibitor incorporating a nitroimidazole moiety. The comparison with the structure of hCA II in complex with its sulphamide analogue revealed that the two inhibitors adopt a completely different binding mode within the hCA II active site. Starting from these results, we performed a theoretical study on sulphamate and sulphamide derivatives, demonstrating that electrostatic interactions with residues within the enzyme active site play a key role in determining their binding conformation. These findings open new perspectives in the design of effective CAIs using the sulphamate and sulphamide zinc binding groups as lead compounds.

Evaluation of operating room suite efficiency in the Veterans Health Administration system by using data-envelopment analysis.

PubMed

Basson, Marc D; Butler, Timothy

2006-11-01

Operating room (OR) activity transcends single ratios such as cases/room, but weighting multiple inputs and outputs may be arbitrary. Data-envelopment analysis (DEA) is a novel technique by which each facility is analyzed by the weightings that optimize its score. We performed DEA analysis of 23 Veterans Health Administration annual OR activity; 87,180 cases were performed, 24 publications generated, and 560 trainee-years of education delivered, in 168 ORs over 166,377 hours by 1,384 full-time equivalents of surgical and anesthesia providers and 523 nonproviders. Varying analyzed parameters produced similar efficiency rankings, with individual differences suggesting possible inefficiencies. We characterized returns to scale for efficient sites, suggesting whether patient flow might be efficiently further increased through these sites. We matched inefficient sites to similar efficient sites for comparison and suggested resource alterations to increase efficiency. Broader DEA application might characterize OR efficiency more informatively than conventional single-ratio rank ordering.

Field Demonstration of Biologically Active Zone Enhancement (BAZE) for In Situ RDX Degradation in Groundwater

DTIC Science & Technology

2010-07-01

Used Defense Site GAC granular activated carbon HA health advisory HFCS high fructose corn syrup HMX octahydro-1,3,5,7-tetranitro 1,3,5,7... fructose corn syrup (HFCS) by injection is another innovative alternative and was demonstrated at Milan Army Ammunition Plant. Data needed for comparison...tetrazocine HPLC high pressure liquid chromatograph HVAC heating, ventilation, and air conditioning ID inside diameter IW injection well MNX

The Sim-SEQ Project: Comparison of Selected Flow Models for the S-3 Site

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

Mukhopadhyay, Sumit; Doughty, Christine A.; Bacon, Diana H.

Sim-SEQ is an international initiative on model comparison for geologic carbon sequestration, with an objective to understand and, if possible, quantify model uncertainties. Model comparison efforts in Sim-SEQ are at present focusing on one specific field test site, hereafter referred to as the Sim-SEQ Study site (or S-3 site). Within Sim-SEQ, different modeling teams are developing conceptual models of CO2 injection at the S-3 site. In this paper, we select five flow models of the S-3 site and provide a qualitative comparison of their attributes and predictions. These models are based on five different simulators or modeling approaches: TOUGH2/EOS7C, STOMP-CO2e,more » MoReS, TOUGH2-MP/ECO2N, and VESA. In addition to model-to-model comparison, we perform a limited model-to-data comparison, and illustrate how model choices impact model predictions. We conclude the paper by making recommendations for model refinement that are likely to result in less uncertainty in model predictions.« less

An aerial radiological survey of the Robert Emmett Ginna Nuclear Power Plant and surrounding area, Ontario, New York

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

Proctor, A.E.

1997-06-01

Terrestrial radioactivity surrounding the Robert Emmett Ginna Nuclear Power Plant was measured using aerial radiological surveying techniques. The purpose of this survey was to document exposure rates near the plant and to identify unexpected, man-made radiation sources within the survey area. The surveyed area included land areas within a three-mile radius of the plant site. Data were acquired using an airborne detection system that employed sodium iodide, thallium-activated detectors. Exposure-rate and photopeak counts were computed from these data and plotted on aerial photographs of the survey area. Several ground-based exposure measurements were made for comparison with the aerial survey results.more » Exposure rates in the area surrounding the plant site varied from 6 to 10 microroentgens per hour. Man-made radiation (cobalt-60 within the plant site and cesium-1 37 directly over the reactor) was found at the plant site. In addition, small areas of suspected cesium-137 activity were found within the survey areas. Other than these small sites, the survey area was free of man-made radioac- tivity.« less

Great gulf wilderness use estimation: comparisons from 1976, 1989, and 1999

Treesearch

Chad P. Dawson; Mark Simon; Rebecca Oreskes; Gary Davis

2001-01-01

Wilderness visitor monitoring techniques can provide important baseline information on recreational use and assist managers in making recreation use management decisions. A demonstration project was conducted in the Great Gulf Wilderness using active infra-red beam type trail counters and brief on-site interviews to obtain information about visitor travel patterns,...

77 FR 34961 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-12

... the Child Welfare Sector and Comparison Study with an administrative record review form to lessen... in the study is up to 24 months. The outcome measures include the following: Child symptomatology and... site informants......... 1081 3 1.00 3,243 649 Child and Family Outcome Study Caregiver Information...

The Effect of Intravenous Infiltration Management Program for Hospitalized Children.

PubMed

Park, Soon Mi; Jeong, Ihn Sook; Kim, Kyoung Lae; Park, Kyung Ju; Jung, Moon Ju; Jun, Seong Suk

2016-01-01

This study aimed to identify the effect of IV infiltration management program among hospitalized children. This was a quasi-experimental study with history comparison group design with 2,894 catheters inserted during 3 months comparison phase and 3,651 catheters inserted during 4 months experimental phase. The intervention was composed of seven activities including applying poster, documentation of catheter insertion, parents education, making infiltration report, assessment of vein condition before inserting catheter, appropriate site selection, and documentation of catheter insertion, and assessment of peripheral catheter insertion site every shift. Data were analyzed using of X2-test, Fisher's exact test. The infiltration incidence rate was 0.9% for experimental group and 4.4% for comparison group, which was significantly different (x2=80.42, p<.001). The catheter maintenance period (p=.035) and infiltration state (p=.039) were significantly different among participants with infiltration between comparison and experimental groups. IV Infiltration management program was founded to be effective in reducing the IV infiltration incidence rate and increasing early detection of IV infiltration. Considering the effect of IV Infiltration management program, we recommend that this infiltration management program would be widely used in the clinical settings. Copyright © 2016 Elsevier Inc. All rights reserved.

Fabrication of efficient TiO2-RGO heterojunction composites for hydrogen generation via water-splitting: Comparison between RGO, Au and Pt reduction sites

NASA Astrophysics Data System (ADS)

El-Bery, Haitham M.; Matsushita, Yoshihisa; Abdel-moneim, Ahmed

2017-11-01

A facile one-step synthesis approach of M/TiO2/RGO (M = Au or Pt) ternary composite by hydrothermal treatment for hydrogen generation via water-splitting was investigated. Photocurrent response measurements revealed that TiO2 (P25) nanoparticles anchored on the reduced graphene oxide (RGO) surface exhibited a p-n heterojunction interface by changing the photocurrent direction with the applied bias from reverse to forward potential. H2 evolution rate of TiO2/RGO (5 wt.%) composite was substantially enhanced by 12-fold in comparison to bare TiO2 under simulated solar light irradiation. Cyclic volatmmetry measurements manifested, that the optimized 0.3 wt.% of platinum metal loaded on TiO2/RGO composite was the most active catalytic reduction sites for hydrogen generation reaction with an initial hydrogen rate of 670 μmol h-1. This study sheds the light on the tunable semiconductor type of TiO2/RGO composite fabricated by solution mixing pathway and its merits to improve the photocatalytic activity.

Down-regulation of tryptamine binding sites following chronic molindone administration. A comparison with responses of dopamine and 5-hydroxytryptamine receptors.

PubMed

Nguyen, T V; Juorio, A V

1989-10-01

The present study assessed changes of tryptamine, dopamine D2, 5-HT1 and 5-HT2 binding sites in rat brain following chronic treatment with low (5 mg/kg/day) and high (40 mg/kg/day) doses of molindone, a clinically effective psychotropic drug. The high-dose molindone treatment produced a decrease in the number of tryptamine binding sites while both high and low doses caused an increase in the number of dopamine D2 binding sites in the striatum. No significant changes were observed in either 5-HT1 or 5-HT2 binding sites in the cerebral cortex. Competition binding experiments showed that molindone was a potent inhibitor at dopamine D2 but less effective at tryptamine, 5-HT1 and 5-HT2 binding sites. The inhibition activity of molindone towards type A monoamine oxidase produced a significant increase in endogenous tryptamine accumulation rate which was much higher than that of dopamine and 5-HT. These findings suggest that the reduction in the number of tryptamine binding sites produced by chronic molindone administration is related to monoamine oxidase inhibition and that the increase in the number of dopamine D2 binding sites is correlated to receptor blocking activity of the drug.

Effects of urbanization, construction activity, management practices, and impoundments on suspended-sediment transport in Johnson County, northeast Kansas, February 2006 through November 2008

USGS Publications Warehouse

Lee, Casey J.; Ziegler, Andrew C.

2010-01-01

The U.S. Geological Survey, in cooperation with the Johnson County, Kansas, Stormwater Management Program, investigated the effects of urbanization, construction activity, management practices, and impoundments on suspended-sediment transport in Johnson County from February 2006 through November 2008. Streamgages and continuous turbidity sensors were operated at 15 sites within the urbanizing 57-square-mile Mill Creek Basin, and 4 sites downstream from the other largest basins (49 to 66 square miles) in Johnson County. The largest sediment yields in Johnson County were observed downstream from basins with increased construction activity. Sediment yields attributed to the largest (68 acre) active construction site in the study area were 9,300 tons per square mile in 2007 and 12,200 tons per square mile in 2008; 5 to 55 times larger than yields observed at other sampling sites. However, given erodible soils and steep slopes at this site, sediment yields were relatively small compared to the range in historic values from construction sites without erosion and sediment controls in the United States (2,300 to 140,000 tons per square mile). Downstream from this construction site, a sediment forebay and wetland were constructed in series upstream from Shawnee Mission Lake, a 120-acre reservoir within Shawnee Mission Park. Although the original intent of the sediment forebay and constructed wetland were unrelated to upstream construction, they were nonetheless evaluated in 2008 to characterize sediment removal before stream entry into the lake. The sediment forebay was estimated to reduce 33 percent of sediment transported to the lake, whereas the wetland did not appear to decrease downstream sediment transport. Comparisons of time-series data and relations between turbidity and sediment concentration indicate that larger silt-sized particles were deposited within the sediment forebay, whereas smaller silt and clay-sized sediments were transported through the wetland and into the lake. Data collected at sites up and downstream from the constructed wetland indicated that hydraulic retention alone did not substantially reduce sediment loading to Shawnee Mission Lake. Mean-daily turbidity values at sampling sites downstream from basins with increased construction activity were compared to U.S. Environmental Protection Agency turbidity criteria designed to reduce discharge of pollutants from construction sites. The U.S. Environmental Protection Agency numeric turbidity criteria specifies that effluent from construction sites greater than 20 acres not exceed a mean-daily turbidity value of 280 nephelometric turbidity units beginning in 2011; this criteria will apply to sites greater than 10 acres beginning in 2014. Although numeric criteria would not have been applicable to data from sampling sites in Johnson County because they were not directly downstream from construction sites and because individual states still have to determine additional details as to how this criteria will be enforced, comparisons were made to characterize the potential of construction site effluent in Johnson County to exceed U.S. Environmental Protection Agency Criteria, even under extensive erosion and sediment controls. Numeric criteria were exceeded at sampling sites downstream from basins with increased construction activity for multiple days during the study period, potentially indicating the need for additional erosion and sediment controls and (or) treatment to bring discharges from construction sites into compliance with future numeric turbidity criteria. Among sampling sites in the Mill Creek Basin, sediment yields from the urbanizing Clear Creek Basin were approximately 2 to 3 times those from older, more stable urban or rural basins. Sediments eroded from construction sites adjacent to or surrounding streams appear to be more readily transported downstream, whereas sediments eroded from construction sites in headwater areas are more likely to

Dual-tail approach to discovery of novel carbonic anhydrase IX inhibitors by simultaneously matching the hydrophobic and hydrophilic halves of the active site.

PubMed

Hou, Zhuang; Lin, Bin; Bao, Yu; Yan, Hai-Ning; Zhang, Miao; Chang, Xiao-Wei; Zhang, Xin-Xin; Wang, Zi-Jie; Wei, Gao-Fei; Cheng, Mao-Sheng; Liu, Yang; Guo, Chun

2017-05-26

Dual-tail approach was employed to design novel Carbonic Anhydrase (CA) IX inhibitors by simultaneously matching the hydrophobic and hydrophilic halves of the active site, which also contains a zinc ion as part of the catalytic center. The classic sulfanilamide moiety was used as the zinc binding group. An amino glucosamine fragment was chosen as the hydrophilic part and a cinnamamide fragment as the hydrophobic part in order to draw favorable interactions with the corresponding halves of the active site. In comparison with sulfanilamide which is largely devoid of the hydrophilic and hydrophobic interactions with the two halves of the active site, the compounds so designed and synthesized in this study showed 1000-fold improvement in binding affinity. Most of the compounds inhibited the CA effectively with IC 50 values in the range of 7-152 nM. Compound 14e (IC 50 : 7 nM) was more effective than the reference drug acetazolamide (IC 50 : 30 nM). The results proved that the dual-tail approach to simultaneously matching the hydrophobic and hydrophilic halves of the active site by linking hydrophobic and hydrophilic fragments was useful for designing novel CA inhibitors. The effectiveness of those compounds was elucidated by both the experimental data and molecular docking simulations. This work laid a solid foundation for further development of novel CA IX inhibitors for cancer treatment. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

High-resolution crystal structures of Drosophila melanogaster angiotensin-converting enzyme in complex with novel inhibitors and antihypertensive drugs.

PubMed

Akif, Mohd; Georgiadis, Dimitris; Mahajan, Aman; Dive, Vincent; Sturrock, Edward D; Isaac, R Elwyn; Acharya, K Ravi

2010-07-16

Angiotensin I-converting enzyme (ACE), one of the central components of the renin-angiotensin system, is a key therapeutic target for the treatment of hypertension and cardiovascular disorders. Human somatic ACE (sACE) has two homologous domains (N and C). The N- and C-domain catalytic sites have different activities toward various substrates. Moreover, some of the undesirable side effects of the currently available and widely used ACE inhibitors may arise from their targeting both domains leading to defects in other pathways. In addition, structural studies have shown that although both these domains have much in common at the inhibitor binding site, there are significant differences and these are greater at the peptide binding sites than regions distal to the active site. As a model system, we have used an ACE homologue from Drosophila melanogaster (AnCE, a single domain protein with ACE activity) to study ACE inhibitor binding. In an extensive study, we present high-resolution structures for native AnCE and in complex with six known antihypertensive drugs, a novel C-domain sACE specific inhibitor, lisW-S, and two sACE domain-specific phosphinic peptidyl inhibitors, RXPA380 and RXP407 (i.e., nine structures). These structures show detailed binding features of the inhibitors and highlight subtle changes in the orientation of side chains at different binding pockets in the active site in comparison with the active site of N- and C-domains of sACE. This study provides information about the structure-activity relationships that could be utilized for designing new inhibitors with improved domain selectivity for sACE. 2010 Elsevier Ltd. All rights reserved.

Allosteric Regulation of Mammalian Pantothenate Kinase*

PubMed Central

Subramanian, Chitra; Yun, Mi-Kyung; Yao, Jiangwei; Sharma, Lalit Kumar; Lee, Richard E.; White, Stephen W.; Jackowski, Suzanne; Rock, Charles O.

2016-01-01

Pantothenate kinase is the master regulator of CoA biosynthesis and is feedback-inhibited by acetyl-CoA. Comparison of the human PANK3·acetyl-CoA complex to the structures of PANK3 in four catalytically relevant complexes, 5′-adenylyl-β,γ-imidodiphosphate (AMPPNP)·Mg2+, AMPPNP·Mg2+·pantothenate, ADP·Mg2+·phosphopantothenate, and AMP phosphoramidate (AMPPN)·Mg2+, revealed a large conformational change in the dimeric enzyme. The amino-terminal nucleotide binding domain rotates to close the active site, and this allows the P-loop to engage ATP and facilitates required substrate/product interactions at the active site. Biochemical analyses showed that the transition between the inactive and active conformations, as assessed by the binding of either ATP·Mg2+ or acyl-CoA to PANK3, is highly cooperative indicating that both protomers move in concert. PANK3(G19V) cannot bind ATP, and biochemical analyses of an engineered PANK3/PANK3(G19V) heterodimer confirmed that the two active sites are functionally coupled. The communication between the two protomers is mediated by an α-helix that interacts with the ATP-binding site at its amino terminus and with the substrate/inhibitor-binding site of the opposite protomer at its carboxyl terminus. The two α-helices within the dimer together with the bound ligands create a ring that stabilizes the assembly in either the active closed conformation or the inactive open conformation. Thus, both active sites of the dimeric mammalian pantothenate kinases coordinately switch between the on and off states in response to intracellular concentrations of ATP and its key negative regulators, acetyl(acyl)-CoA. PMID:27555321

Site-Specific RNase A Activity Was Dramatically Reduced in Serum from Multiple Types of Cancer Patients

PubMed Central

Huang, Weiyan; Zhao, Mei; Wei, Na; Wang, Xiaoxia; Cao, Huqing; Du, Quan; Liang, Zicai

2014-01-01

Potent RNase activities were found in the serum of mammals but the physiological function of the RNases was never well illustrated, largely due to the caveats in methods of RNase activity measurement. None of the existing methods can distinguish between RNases with different target specificities. A systematic study was recently carried out in our lab to investigate the site-specificity of serum RNases on double-stranded RNA substrates, and found that serum RNases cleave double-stranded RNAs predominantly at 5′-U/A-3′ and 5′-C/A-3′ dinucleotide sites, in a manner closely resembling RNase A. Based on this finding, a FRET assay was developed in the current study to measure this site-specific serum RNase activity in human samples using a double stranded RNA substrate. We demonstrated that the method has a dynamic range of 10−5 mg/ml- 10−1 mg/ml using serial dilution of RNase A. The sera of 303 cancer patients were subjected to comparison with 128 healthy controls, and it was found that serum RNase activities visualized with this site-specific double stranded probe were found to be significantly reduced in patients with gastric cancer, liver cancer, pancreatic cancer, esophageal cancer, ovary cancer, cervical cancer, bladder cancer, kidney cancer and lung cancer, while only minor changes were found in breast and colon cancer patients. This is the first report using double stranded RNA as probe to quantify site-specific activities of RNase A in a serum. The results illustrated that RNase A might be further evaluated to determine if it can serve as a new class of biomarkers for certain cancer types. PMID:24805924

Salt Effect on the Antioxidant Activity of Red Microalgal Sulfated Polysaccharides in Soy-Bean Formula.

PubMed

Burg, Ariela; Oshrat, Levy-Ontman

2015-10-20

Sulfated polysaccharides produced by microalgae, which are known to exhibit various biological activities, may potentially serve as natural antioxidant sources. To date, only a few studies have examined the antioxidant bioactivity of red microalgal polysaccharides. In this research, the effect of different salts on the antioxidant activities of two red microalgal sulfated polysaccharides derived from Porphyridium sp. and Porphyridium aerugineum were studied in a soy bean-based infant milk formula. Salt composition and concentration were both shown to affect the polysaccharides' antioxidant activity. It can be postulated that the salt ions intefer with the polysaccharide chains' interactions and alter their structure, leading to a new three-dimensional structure that better exposes antiooxidant sites in comparison to the polysaccharide without salt supplement. Among the cations that were studied, Ca(2+) had the strongest enhancement effect on antioxidant activities of both polysaccharides. Understanding the effect of salts on polysaccharides' stucture, in addition to furthering knowledge on polysaccharide bioactivities, may also shed light on the position of the antioxidant active sites.

Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae.

PubMed

Daniel, Bastian; Wallner, Silvia; Steiner, Barbara; Oberdorfer, Gustav; Kumar, Prashant; van der Graaff, Eric; Roitsch, Thomas; Sensen, Christoph W; Gruber, Karl; Macheroux, Peter

2016-01-01

Berberine bridge enzyme-like (BBE-like) proteins form a multigene family (pfam 08031), which is present in plants, fungi and bacteria. They adopt the vanillyl alcohol-oxidase fold and predominantly show bi-covalent tethering of the FAD cofactor to a cysteine and histidine residue, respectively. The Arabidopsis thaliana genome was recently shown to contain genes coding for 28 BBE-like proteins, while featuring four distinct active site compositions. We determined the structure of a member of the AtBBE-like protein family (termed AtBBE-like 28), which has an active site composition that has not been structurally and biochemically characterized thus far. The most salient and distinguishing features of the active site found in AtBBE-like 28 are a mono-covalent linkage of a histidine to the 8α-position of the flavin-isoalloxazine ring and the lack of a second covalent linkage to the 6-position, owing to the replacement of a cysteine with a histidine. In addition, the structure reveals the interaction of a glutamic acid (Glu426) with an aspartic acid (Asp369) at the active site, which appear to share a proton. This arrangement leads to the delocalization of a negative charge at the active site that may be exploited for catalysis. The structure also indicates a shift of the position of the isoalloxazine ring in comparison to other members of the BBE-like family. The dioxygen surrogate chloride was found near the C(4a) position of the isoalloxazine ring in the oxygen pocket, pointing to a rapid reoxidation of reduced enzyme by dioxygen. A T-DNA insertional mutant line for AtBBE-like 28 results in a phenotype, that is characterized by reduced biomass and lower salt stress tolerance. Multiple sequence analysis showed that the active site composition found in AtBBE-like 28 is only present in the Brassicaceae, suggesting that it plays a specific role in the metabolism of this plant family.

Aryl hydrocarbon receptor-mediated activity of particulate organic matter from the Paso del Norte airshed along the U.S.-Mexico border.

PubMed Central

Arrieta, Daniel E; Ontiveros, Cynthia C; Li, Wen-Whai; Garcia, Jose H; Denison, Michael S; McDonald, Jacob D; Burchiel, Scott W; Washburn, Barbara Shayne

2003-01-01

In this study, we determined the biologic activity of dichloromethane-extracted particulate matter < 10 micro m in aerodynamic diameter (PM10) obtained from filters at three sites in the Paso del Norte airshed, which includes El Paso, Texas, USA; Juarez, Chihuahua, Mexico, and Sunland Park, New Mexico, USA. The extracts were rich in polycyclic aromatic hydrocarbons (PAHs) and had significant biologic activity, measured using two in vitro assay systems: ethoxyresorufin-(O-deethylase (EROD) induction and the aryl hydrocarbon-receptor luciferase reporter system. In most cases, both EROD (5.25 pmol/min/mg protein) and luciferase activities (994 relative light units/mg) were highest in extracts from the Advance site located in an industrial neighborhood in Juarez. These values represented 58% and 55%, respectively, of induction associated with 1 micro M ss-naphthoflavone exposures. In contrast, little activity was observed at the Northeast Clinic site in El Paso, the reference site. In most cases, luciferase and EROD activity from extracts collected from the Tillman Health Center site, situated in downtown El Paso, fell between those observed at the other two sites. Overall, a statistically significant correlation existed between PM10 and EROD and luciferase activities. Chemical analysis of extracts collected from the Advance site demonstrated that concentrations of most PAHs were higher than those reported in most other metropolitan areas in the United States. Calculations made with these data suggest a cancer risk of 5-12 cases per 100,000 people. This risk estimate, as well as comparisons with the work of other investigators, raises concern regarding the potential for adverse health effects to the residents of this airshed. Further work is needed to understand the sources, exposure, and effects of PM10 and particulate organic material in the Paso del Norte airshed. PMID:12896850

Comparisons of the NGA ground-motion relations

USGS Publications Warehouse

Abrahamson, N.; Atkinson, G.; Boore, D.; Bozorgnia, Y.; Campbell, K.; Chiou, B.; Idriss, I.M.; Silva, W.; Young, S.R.

2008-01-01

The data sets, model parameterizations, and results from the five NGA models for shallow crustal earthquakes in active tectonic regions are compared. A key difference in the data sets is the inclusion or exclusion of aftershocks. A comparison of the median spectral values for strike-slip earthquakes shows that they are within a factor of 1.5 for magnitudes between 6.0 and 7.0 for distances less than 100 km. The differences increase to a factor of 2 for M5 and M8 earthquakes, for buried ruptures, and for distances greater than 100 km. For soil sites, the differences in the modeling of soil/sediment depth effects increase the range in the median long-period spectral values for M7 strike-slip earthquakes to a factor of 3. The five models have similar standard deviations for M6.5-M7.5 earthquakes for rock sites and for soil sites at distances greater than 50 km. Differences in the standard deviations of up to 0.2 natural log units for moderate magnitudes at all distances and for large magnitudes at short distances result from the treatment of the magnitude dependence and the effects of nonlinear site response on the standard deviation. ?? 2008, Earthquake Engineering Research Institute.

Retrieving atmospheric transmissivity for biologically active daily dose, in various european sites

NASA Astrophysics Data System (ADS)

de La Casinière, A.; Touré, M. L.; Lenoble, J.; Cabot, T.

2003-04-01

In the frame of the European Project EDUCE, global UV irradiance spectra recorded all along the year in several European sites are stored in a common database located in Finland. From the spectra set of some of these stations, are calculated atmospheric transmissivities for daily doses of four biologically active UV radiation, namely: UV-B, erythema, DNA damage, and plant damage. A transmissivity is defined as the ratio of the ground level value of the daily dose of interest to its corresponding extra-atmospheric value. Multiple linear correlation of the various transmissivities with three predictors (daily sunshine fraction, cosine of the daily minimum SZA, and daily total ozone column) assumed to be independent variables, are done for year 2000. The coefficients obtained from year 2000 correlation in a given site are expected to retrieve, from the local predictors, the daily dose for year 2001 in the same site, the average error being lesser than 10% for monthly mean values, and lesser than 5% for three-monthly mean values, depending on the daily dose type. Comparison of yearly mean daily doses retrieved in a given site from coefficients obtained in other sites is also presented.

Comparison of designed and randomly generated catalysts for simple chemical reactions.

PubMed

Kipnis, Yakov; Baker, David

2012-09-01

There has been recent success in designing enzymes for simple chemical reactions using a two-step protocol. In the first step, a geometric matching algorithm is used to identify naturally occurring protein scaffolds at which predefined idealized active sites can be realized. In the second step, the residues surrounding the transition state model are optimized to increase transition state binding affinity and to bolster the primary catalytic side chains. To improve the design methodology, we investigated how the set of solutions identified by the design calculations relate to the overall set of solutions for two different chemical reactions. Using a TIM barrel scaffold in which catalytically active Kemp eliminase and retroaldolase designs were obtained previously, we carried out activity screens of random libraries made to be compositionally similar to active designs. A small number of active catalysts were found in screens of 10³ variants for each of the two reactions, which differ from the computational designs in that they reuse charged residues already present in the native scaffold. The results suggest that computational design considerably increases the frequency of catalyst generation for active sites involving newly introduced catalytic residues, highlighting the importance of interaction cooperativity in enzyme active sites. Copyright © 2012 The Protein Society.

Silver-coated nylon dressing plus active DC microcurrent for healing of autogenous skin donor sites.

PubMed

Malin, Edward W; Galin, Chaya M; Lairet, Kimberley F; Huzar, Todd F; Williams, James F; Renz, Evan M; Wolf, Steven E; Cancio, Leopoldo C

2013-11-01

Burn wounds are a significant cause of morbidity and mortality, and improved outcomes are demonstrated with early closure of both primary burn wounds and skin donor sites. Thus, technology that decreases the healing time of burns and donor sites would be potentially lifesaving. We present the results of a single-center, prospective, double-blinded, randomized controlled trial to evaluate the efficacy of silver-coated dressing with active microcurrent in comparison to silver-coated dressing with sham microcurrent on wound-closure time for autogenous skin donor sites. Four hundred five patients were screened for treatment of their donor sites using a silver-coated nylon dressing with either sham or active microcurrent stimulation. Thirty patients were enrolled in the study and then randomized. Of these, 5 patients were removed from analysis due to protocol deviations. Differences in time-to-closure were analyzed using Kaplan-Meier analysis and the proportional hazard regression model. Subjective verbal pain rating scores (0-10; 0, no pain; 10, worst pain) were also recorded. All devices were blinded and programmed at an outside facility, so that every patient had either an active or sham device. The study was unblinded only after the final patient's donor site had healed. All patients achieved donor-site healing before postoperative day 20. The 14 patients in the active microcurrent group [mean, 10.8 (2.9) days; range, 7-15 days] experienced no difference in time to wound healing as compared to the remaining patients in the sham microcurrent group [mean, 11.1 (2.0) days; range, 8-14 days; P = 0.75]. There were no differences in pain from one group compared to the other. None of the donor sites exhibited clinical signs of infection. In a sample size of 25 burn patients, the addition of direct microcurrent to silver-nylon dressings did not decrease time to wound closure of skin donor sites, and it did not show a difference in reported pain levels.

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

Acceleration of Binding Site Comparisons by Graph Partitioning.

PubMed

Krotzky, Timo; Klebe, Gerhard

2015-08-01

The comparison of protein binding sites is a prominent task in computational chemistry and has been studied in many different ways. For the automatic detection and comparison of putative binding cavities the Cavbase system has been developed which uses a coarse-grained set of pseudocenters to represent the physicochemical properties of a binding site and employs a graph-based procedure to calculate similarities between two binding sites. However, the comparison of two graphs is computationally quite demanding which makes large-scale studies such as the rapid screening of entire databases hardly feasible. In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. It employs a clique heuristic to detect the maximum common subgraph of two binding sites and an extended graph model to additionally compare the shape of individual surface patches. In this study, we present an alternative to further accelerate the LC method by partitioning the binding-site graphs into disjoint components prior to their comparisons. The pseudocenter sets are split with regard to their assigned phyiscochemical type, which leads to seven much smaller graphs than the original one. Applying this approach on the same test scenarios as in the former comprehensive way results in a significant speed-up without sacrificing accuracy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stabilization of bacterially expressed erythropoietin by single site-specific introduction of short branched PEG chains at naturally occurring glycosylation sites.

PubMed

Hoffmann, E; Streichert, K; Nischan, N; Seitz, C; Brunner, T; Schwagerus, S; Hackenberger, C P R; Rubini, M

2016-05-24

The covalent attachment of polyethylene glycol (PEG) to therapeutic proteins can improve their physicochemical properties. In this work we utilized the non-natural amino acid p-azidophenylalanine (pAzF) in combination with the chemoselective Staudinger-phosphite reaction to install branched PEG chains to recombinant unglycosylated erythropoietin (EPO) at each single naturally occurring glycosylation site. PEGylation with two short 750 or 2000 Da PEG units at positions 24, 38, or 83 significantly decreased unspecific aggregation and proteolytic degradation while biological activity in vitro was preserved or even increased in comparison to full-glycosylated EPO. This site-specific bioconjugation approach permits to analyse the impact of PEGylation at single positions. These results represent an important step towards the engineering of site-specifically modified EPO variants from bacterial expression with increased therapeutic efficacy.

Disappointment and regret enhance corrugator reactivity in a gambling task

PubMed Central

Wu, Yin; Clark, Luke

2015-01-01

This study investigated how the corrugator and zygomaticus respond to decision outcomes (i.e., gains and losses). We used a gambling task in which participants were presented with obtained followed by non-obtained outcomes. Activity at the corrugator site was sensitive to decision outcomes, such that higher obtained losses (disappointment) and higher non-obtained gains (regret) both heightened corrugator reactivity. Activity at the zygomaticus site was not responsive to obtained or non-obtained outcomes, but did show sensitivity to emotional images in the same participants, in the form of a positive linear relationship with self-reported emotional valence. Corrugator activity was negatively related to emotional valence. The findings indicate the sensitivity of corrugator to objective decision outcomes and also counterfactual comparisons, highlighting the utility of facial electromyography in research on decision making and gambling behavior. PMID:25345723

Water-quality characteristics of streams in forested and rural areas of North Carolina

USGS Publications Warehouse

Simmons, Clyde E.; Heath, Ralph C.

1979-01-01

Data collected in North Carolina during 1973-78 from a statewide network of 39 rural sampling sites were used to define unpolluted or baseline stream quality. The basins were 90 to 100 percent forested and, except for the unknown effects of air pollution, were relatively unaffected by man 's activities. Five distinct geochemical zones were delineated across the State. The chemical characteristics of surface waters in each zone are similar. Mean and other statistical values for major dissolved constituents, nutrients, and minor elements in base runoff and storm runoff were determined. Twenty additional rural sites were located in basins where farming activities ranged from 15 to 55 percent of basins ' land area. Data from these 20 sites were used for comparison with data from the 39 unpolluted sites to determine the increase in constituent levels caused by man. For basins where farming activities accounted for 20 or more percent of total land use, phosphorus levels were 2 to 13 times greater than those from the forested basins and several major constituents were 2 to 3 times greater. Concentrations of minor elements were essentially the same in both developed and undeveloped basins. (Kosco-USGS)

Social media and patient self-management: not all sites are created equal.

PubMed

Ellis, Leonie; Showell, Chris; Turner, Paul

2013-01-01

This paper compares two social media sites that aim to support patients to enhance self-management. The first site, PatientsLikeMe is a well established global site designed to allow peer-to-peer communication between people with similar conditions. The second, HealthShare, is a recently developed site for Australians described as "Australia's Social Health Network". The comparison conducted examines the purpose, ownership, and design of both sites as well as how the data they collect is used. Analysis highlights that PatientsLikeMe actively facilitates patient self-management, while HealthShare is revealed to be a professionally moderated health information portal presented as a social networking site. While the impetus for the development of PatientsLikeMe is clear, the motives underpinning HealthShare are less obvious. With increasing patient interest in connecting with, and sharing information with one another, awareness of the nature and motivations underpinning sites that provide these services is of increasing relevance.

Do recreational activities affect coastal biodiversity?

NASA Astrophysics Data System (ADS)

Riera, Rodrigo; Menci, Cristiano; Sanabria-Fernández, José Antonio; Becerro, Mikel A.

2016-09-01

Human activities are largely affecting coastal communities worldwide. Recreational perturbations have been overlooked in comparison to other perturbations, yet they are potential threats to marine biodiversity. They affect coastal communities in different ways, underpinning consistent shifts in fish and invertebrates assemblages. Several sites were sampled subjected to varying effects by recreational fishermen (low and high pressure) and scuba divers (low and high) in an overpopulated Atlantic island. Non-consistent differences in ecological, trophic and functional diversity were found in coastal communities, considering both factors (;diving; and ;fishing;). Multivariate analyses only showed significant differences in benthic invertebrates between intensively-dived and non-dived sites. The lack of clear trends may be explained by the depletion of coastal resources in the study area, an extensively-affected island by overfishing.

The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: Co-evolution of structure and dynamics with the dehalogenation function

PubMed Central

Kajander, Tommi; Lehtiö, Lari; Schlömann, Michael; Goldman, Adrian

2003-01-01

Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis-muconate as a part of the β-ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl-MLEs). The basis for the Cl-MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl-MLEs, we have solved the structure of Pseudomonas P51 Cl-MLE at 1.95 Å resolution. Comparison of Pseudomonas MLE and Cl-MLE structures reveals the presence of a large cavity in the Cl-MLEs. The cavity may be related to conformational changes on substrate binding in Cl-MLEs, at Gly52. Site-directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl-MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly-Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl-MLEs. The Cl-MLE structure, as a result of the Thr-to-Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl-MLEs. The loose packing and structural motions in Cl-MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl-MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl-MLEs result in lower active site polarity in Cl-MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl-MLEs and make it a better enzyme for dehalogenation of substrate. PMID:12930985

The interaction of trazodone with rat brain muscarinic cholinoceptors.

PubMed

Hyslop, D K; Taylor, D P

1980-01-01

The muscarinic receptor binding of trazodone, a new nontricyclic antidepressant, was compared with established tricyclic antidepressants. The ability to inhibit the binding of [3H]-quinuclidinyl benzilate in vitro was used for comparing atropine-like effects. Trazodone was found to have essentially no activity at the muscarinic acetylcholine binding site in comparison to the tricyclic antidepressants.

The interaction of trazodone with rat brain muscarinic cholinoceptors.

PubMed Central

Hyslop, D. K.; Taylor, D. P.

1980-01-01

The muscarinic receptor binding of trazodone, a new nontricyclic antidepressant, was compared with established tricyclic antidepressants. The ability to inhibit the binding of [3H]-quinuclidinyl benzilate in vitro was used for comparing atropine-like effects. Trazodone was found to have essentially no activity at the muscarinic acetylcholine binding site in comparison to the tricyclic antidepressants. PMID:7470750

National Guard Counterdrug Programs

DTIC Science & Technology

2001-02-14

comparisons to locate indoor Marijuana grows, outdoor infrastructure - Monitor activity at known sites - Meth labs, stash houses, marijuana grows - Real...Identifies key signatures of structures for indoor growth of cannabis - Vehiclelvessel surveillance * Video capabilities for evidence e Global Positioning...System Navigational Equipment - Identify marijuana locations for ground recovery Contact Information Voice (703) 607-5665 DSN Voice 327-5665 FAX (703

Interactions between Uterine EMG at Different Sites Investigated Using Wavelet Analysis: Comparison of Pregnancy and Labor Contractions

NASA Astrophysics Data System (ADS)

Hassan, Mahmoud; Terrien, Jérémy; Karlsson, Brynjar; Marque, Catherine

2010-12-01

This paper describes the use of the Morlet wavelet transform to investigate the difference in the time-frequency plane between uterine EMG signals recorded simultaneously on two different sites on women's abdomen, both during pregnancy and in labor. The methods used are wavelet transform, cross wavelet transform, phase/amplitude correlation, and phase synchronization. We computed the linear relationship and phase synchronization between uterine signals measured during the same contractions at two different sites on data obtained from women during pregnancy and labor. The results show that the Morlet wavelet transform can successfully analyze and quantify the relationship between uterine electrical activities at different sites and could be employed to investigate the evolution of uterine contraction from pregnancy to labor.

Structural and Functional Analyses of a Glycoside Hydrolase Family 5 Enzyme with an Unexpected [beta]-Fucosidase Activity

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

Yoshida, Shosuke; Park, David S.; Bae, Brian

2012-02-15

We present characterization of PbFucA, a family 5 glycoside hydrolase (GH5) from Prevotella bryantii B{sub 1}4. While GH5 members typically are xylanases, PbFucA shows no activity toward xylan polysaccharides. A screen against a panel of p-nitrophenol coupled sugars identifies PbFucA as a {beta}-D-fucosidase. We also present the 2.2 {angstrom} resolution structure of PbFucA and use structure-based mutational analysis to confirm the role of catalytically essential residues. A comparison of the active sites of PbFucA with those of family 5 and 51 glycosidases reveals that while the essential catalytic framework is identical between these enzymes, the steric contours of the respectivemore » active site clefts are distinct and likely account for substrate discrimination. Our results show that members of this cluster of orthologous group (COG) 5520 have {beta}-D-fucosidase activities, despite showing an overall sequence and structural similarity to GH-5 xylanases.« less

Mercury Speciation and Trophic Magnification Slopes in Giant Salamander Larvae from the Pacific Northwest, USA

NASA Astrophysics Data System (ADS)

Bank, M. S.; Crocker, J.; Wachtl, J.; Kleeman, P.; Fellers, G.; Currens, C.; Hothem, R.; Madej, M. A.

2014-12-01

Mercury (Hg) contamination of stream salamanders in the Pacific Northwest region of the United States has received little attention. Here we report total Hg (HgT) and methyl mercury (MeHg) concentrations in larval giant salamanders (Dicamptodon spp.) and surface water from forested and chaparral lotic ecosystems distributed along a latitudinal gradient throughout Northern California and Washington. To test hypotheses related to potential effects from mining land-use activities, salamander larvae were also sampled from a reference site at Whiskeytown National Recreation Area, California, and at a nearby, upstream site (Shasta county) on Bureau of Land Management land where Hg contamination from gold mining activities has been documented. HgT concentrations in whole body larvae ranged from 4.6 to 74.5 ng/g wet wt. and percent MeHg ranged from 67% to 86%. Both HgT and MeHg larval tissue concentrations were significantly higher at the mining site in comparison to measured background levels (P < 0.001). We conclude that salamander larvae in remote stream ecosystems, where Hg sources were dominated by atmospheric deposition, were generally low in HgT and MeHg and, in comparison, watersheds with a legacy of land-use practices (i.e., mining operations) had approximately 4.5 - 5.5 times the level of HgT bioaccumulation. Moreover, trophic magnification slopes were highest in the Shasta county region where mining was present. These findings suggest that mining activities increase HgT and MeHg exposure to salamander larvae in the region and may present a threat to other higher trophically positioned organisms, and their associated food webs.

Comparison of PM10 concentrations and metal content in three different sites of the Venice Lagoon: an analysis of possible aerosol sources.

PubMed

Contini, Daniele; Belosi, Franco; Gambaro, Andrea; Cesari, Daniela; Stortini, Angela Maria; Bove, Maria Chiara

2012-01-01

The Venice Lagoon is exposed to atmospheric pollutants from industrial activities, thermoelectric power plants, petrochemical plants, incinerator, domestic heating, ship traffic, glass factories and vehicular emissions on the mainland. In 2005, construction began on the mobile dams (MOSE), one dam for each channel connecting the lagoon to the Adriatic Sea as a barrier against high tide. These construction works could represent an additional source of pollutants. PM10 samples were taken on random days between 2007 and 2010 at three different sites: Punta Sabbioni, Chioggia and Malamocco, located near the respective dam construction worksites. Chemical analyses of V, Cr, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Sb, Tl and Pb in PM10 samples were performed by Inductively coupled plasma-quadrupole mass spectrometry (ICP-QMS) and results were used to identify the main aerosol sources. The correlation of measured data with meteorology, and source apportionment, failed to highlight a contribution specifically associated to the emissions of the MOSE construction works. The comparison of the measurements at the three sites showed a substantial homogeneity of metal concentrations in the area. Source apportionment with principal component analysis (PCA) and positive matrix factorization (PMF) showed that a four principal factors model could describe the sources of metals in PM10. Three of them were assigned to specific sources in the area and one was characterised as a source of mixed origin (anthropogenic and crustal). A specific anthropogenic source of PM10 rich in Ni and Cr, active at the Chioggia site, was also identified.

Case studies, cross-site comparisons, and the challenge of generalization: comparing agent-based models of land-use change in frontier regions

PubMed Central

Parker, Dawn C.; Entwisle, Barbara; Rindfuss, Ronald R.; Vanwey, Leah K.; Manson, Steven M.; Moran, Emilio; An, Li; Deadman, Peter; Evans, Tom P.; Linderman, Marc; Rizi, S. Mohammad Mussavi; Malanson, George

2009-01-01

Cross-site comparisons of case studies have been identified as an important priority by the land-use science community. From an empirical perspective, such comparisons potentially allow generalizations that may contribute to production of global-scale land-use and land-cover change projections. From a theoretical perspective, such comparisons can inform development of a theory of land-use science by identifying potential hypotheses and supporting or refuting evidence. This paper undertakes a structured comparison of four case studies of land-use change in frontier regions that follow an agent-based modeling approach. Our hypothesis is that each case study represents a particular manifestation of a common process. Given differences in initial conditions among sites and the time at which the process is observed, actual mechanisms and outcomes are anticipated to differ substantially between sites. Our goal is to reveal both commonalities and differences among research sites, model implementations, and ultimately, conclusions derived from the modeling process. PMID:19960107

Case studies, cross-site comparisons, and the challenge of generalization: comparing agent-based models of land-use change in frontier regions.

PubMed

Parker, Dawn C; Entwisle, Barbara; Rindfuss, Ronald R; Vanwey, Leah K; Manson, Steven M; Moran, Emilio; An, Li; Deadman, Peter; Evans, Tom P; Linderman, Marc; Rizi, S Mohammad Mussavi; Malanson, George

2008-01-01

Cross-site comparisons of case studies have been identified as an important priority by the land-use science community. From an empirical perspective, such comparisons potentially allow generalizations that may contribute to production of global-scale land-use and land-cover change projections. From a theoretical perspective, such comparisons can inform development of a theory of land-use science by identifying potential hypotheses and supporting or refuting evidence. This paper undertakes a structured comparison of four case studies of land-use change in frontier regions that follow an agent-based modeling approach. Our hypothesis is that each case study represents a particular manifestation of a common process. Given differences in initial conditions among sites and the time at which the process is observed, actual mechanisms and outcomes are anticipated to differ substantially between sites. Our goal is to reveal both commonalities and differences among research sites, model implementations, and ultimately, conclusions derived from the modeling process.

MULTIMEDIA HUMAN EXPOSURE AND RISK ASSESSMENT MODELING

EPA Science Inventory

Exposures and health risk comparisons from different sites may be used for allocating limited resources available for remedial action. It is important that comparisons between different sites use similar levels of site-specific data and/or screening level data. Risk assessment c...

Multi-Scale Computational Enzymology: Enhancing Our Understanding of Enzymatic Catalysis

PubMed Central

Gherib, Rami; Dokainish, Hisham M.; Gauld, James W.

2014-01-01

Elucidating the origin of enzymatic catalysis stands as one the great challenges of contemporary biochemistry and biophysics. The recent emergence of computational enzymology has enhanced our atomistic-level description of biocatalysis as well the kinetic and thermodynamic properties of their mechanisms. There exists a diversity of computational methods allowing the investigation of specific enzymatic properties. Small or large density functional theory models allow the comparison of a plethora of mechanistic reactive species and divergent catalytic pathways. Molecular docking can model different substrate conformations embedded within enzyme active sites and determine those with optimal binding affinities. Molecular dynamics simulations provide insights into the dynamics and roles of active site components as well as the interactions between substrate and enzymes. Hybrid quantum mechanical/molecular mechanical (QM/MM) can model reactions in active sites while considering steric and electrostatic contributions provided by the surrounding environment. Using previous studies done within our group, on OvoA, EgtB, ThrRS, LuxS and MsrA enzymatic systems, we will review how these methods can be used either independently or cooperatively to get insights into enzymatic catalysis. PMID:24384841

Insights into the Phosphoryl Transfer Catalyzed by cAMP-Dependent Protein Kinase: An X-ray Crystallographic Study of Complexes with Various Metals and Peptide Substrate SP20

PubMed Central

2013-01-01

X-ray structures of several ternary substrate and product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with different bound metal ions. In the PKAc complexes, Mg2+, Ca2+, Sr2+, and Ba2+ metal ions could bind to the active site and facilitate the phosphoryl transfer reaction. ATP and a substrate peptide (SP20) were modified, and the reaction products ADP and the phosphorylated peptide were found trapped in the enzyme active site. Finally, we determined the structure of a pseudo-Michaelis complex containing Mg2+, nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5′-triphosphate) and SP20. The product structures together with the pseudo-Michaelis complex provide snapshots of different stages of the phosphorylation reaction. Comparison of these structures reveals conformational, coordination, and hydrogen bonding changes that might occur during the reaction and shed new light on its mechanism, roles of metals, and active site residues. PMID:23672593

A Retrospective Comparison of Conventional versus Transverse Mini-Incision Technique for Carpal Tunnel Release

PubMed Central

Gülşen, İsmail; Ak, Hakan; Evcılı, Gökhan; Balbaloglu, Özlem; Sösüncü, Enver

2013-01-01

Background. In this retrospective study, we aimed to compare the results of two surgical techniques, conventional and transverse mini-incision. Materials and Methods. 95 patients were operated between 2011 and 2012 in Bitlis State Hospital. 50 patients were operated with conventional technique and 45 of them were operated with minimal transverse incision. Postoperative complications, incision site problems, and the time of starting to use their hands in daily activities were noted. Results. 95 patients were included in the study. The mean age was 48. 87 of them were female and 8 were male. There was no problem of incision site in both of the two surgical techniques. Only in one patient, anesthesia developed in minimal incision technique. The time of starting to use their hands in daily activities was 22,2 days and 17 days in conventional and minimal incision technique, respectively. Conclusion. Two surgical techniques did not show superiority to each other in terms of postoperative complications and incision site problems except the time of starting to use their hands in daily activities. PMID:24396607

Comparisons of shear-wave slowness in the Santa Clara Valley, California using blind interpretations of data from invasive and noninvasive methods

USGS Publications Warehouse

Boore, D.M.; Asten, M.W.

2008-01-01

Many groups contributed to a blind interpretation exercise for the determination of shear-wave slowness beneath the Santa Clara Valley. The methods included invasive methods in deep boreholes as well as noninvasive methods using active and passive sources, at six sites within the valley (with most investigations being conducted at a pair of closely spaced sites near the center of the valley). Although significant variability exists between the models, the slownesses from the various methods are similar enough that linear site amplifications estimated in several ways are generally within 20% of one another. The methods were able to derive slownesses that increase systematically with distance from the valley edge, corresponding to a tendency for the sites to be underlain by finer-grained materials away from the valley edge. This variation is in agreement with measurements made in the boreholes at the sites.

Residual radioactivity in the soil of the Semipalatinsk Nuclear Test Site in the former USSR.

PubMed

Yamamoto, M; Tsukatani, T; Katayama, Y

1996-08-01

This paper deals with our efforts to survey residual radioactivity in the soil sampled at the Semipalatinsk Nuclear Test Site and at off-site areas in Kazakhstan. The soil was sampled at the hypocenter where the first Soviet nuclear explosion was carried out on 29 August 1949, and at the bank of the crater called "Bolapan," which was formed by an underground nuclear detonation on 15 January 1965 along the Shagan River. As a comparison, other soil was also sampled in the cities of Kurchatov and Almaty. These data have allowed a preliminary evaluation of the contemporary radioactive contamination of the land in and around the test site. At the first nuclear explosion site and at Bolapan, higher than background levels of 239,240Pu with weapons-grade plutonium were detected together with fission and activation products such as 137Cs, 60Co, 152Eu, and 154Eu.

Changing subsistence practices at the Dorset Paleoeskimo site of Phillip's Garden, Newfoundland.

PubMed

Hodgetts, Lisa M; Renouf, M A P; Murray, Maribeth S; McCuaig-Balkwill, Darlene; Howse, Lesley

2003-01-01

A comparison of identified faunal assemblages from the Dorset site of Phillip's Garden indicates that harp seal hunting was the main focus of activity throughout the site's occupation. Despite the highly specialized nature of site use, it appears that reliance on harp seal decreased over time while fish and birds became increasingly important. These changes may reflect longer seasonal occupations at the site in later centuries, and/or a decrease in the local availability of harp seal. The observed shift coincides with the onset of a local climatic warming trend, which might have affected harp seal movements in the area. Dorset subsistence and settlement patterns in Newfoundland are still poorly understood due to a lack of preserved faunal assemblages in the region. The temporal trend illustrated here indicates that we cannot assume that these patterns were static throughout the Dorset occupation of the island.

Unit soil loss rate from various construction sites during a storm.

PubMed

Maniquiz, Marla C; Lee, Soyoung; Lee, Eunju; Kong, Dong-Soo; Kim, Lee-Hyung

2009-01-01

The Korean Ministry of Environment (MOE) opts to establish an ordinance having a standard specifying an allowable soil loss rate applicable to construction projects. The predicted amount of soil loss from a construction site exceeding the standard can be used to calculate the percent reduction necessary to comply with the ordinance. This research was conducted to provide a basis to establish a standard by investigating the unit soil loss rates in the three phases of development: pre-construction, active construction and post construction based from 1,036 Environmental Impact Assessment (EIA) reports within the six-year period (2000-2005). Based on the findings, several factors affect the magnitude of soil loss rates particularly storm characteristics, site slope, soil type, location from rivers, as well as the type of construction activity. In general, the unit soil loss rates during the active construction phase are extremely higher in comparison to undisturbed areas; in magnitude of 7 to 80 times larger in urban areas and 18 to 585 times in rural areas. Only between 20 to 40 percent of the soil loss rates was contributed at pre- and post- construction phases indicating that the active construction phase is the most important phase to control.

Activation amplitude and temporal synchrony among back extensor and abdominal muscles during a controlled transfer task: comparison of men and women.

PubMed

Hubley-Kozey, Cheryl L; Butler, Heather L; Kozey, John W

2012-08-01

Muscle synergies are important for spinal stability, but few studies examine temporal responses of spinal muscles to dynamic perturbations. This study examined activation amplitudes and temporal synergies among compartments of the back extensor and among abdominal wall muscles in response to dynamic bidirectional moments of force. We further examined whether responses were different between men and women. 19 women and 18 men performed a controlled transfer task. Surface electromyograms from bilateral sites over 6 back extensor compartments and 6 abdominal wall muscle sites were analyzed using principal component analysis. Key features were extracted from the measured electromyographic waveforms capturing amplitude and temporal variations among muscle sites. Three features explained 97% of the variance. Scores for each feature were computed for each measured waveform and analysis of variance found significant (p<.05) muscle main effects and a sex by muscle interaction. For the back extensors, post hoc analysis revealed that upper and more medial sites were recruited to higher amplitudes, medial sites responded to flexion moments, and the more lateral sites responded to lateral flexion moments. Women had more differences among muscle sites than men for the lateral flexion moment feature. For the abdominal wall muscles the oblique muscles responded with synergies related to fiber orientation, with women having higher amplitudes and more responsiveness to the lateral flexion moment than men. Synergies between the abdominal and back extensor sites as the moment demands change are discussed. These findings illustrate differential activation among erector spinae compartments and abdominal wall muscle sites supporting a highly organized pattern of response to bidirectional external moments with asynchronies more apparent in women. Copyright © 2012 Elsevier B.V. All rights reserved.

Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3'-azido-2'-fluoro-2',3'-dideoxyuridine

NASA Astrophysics Data System (ADS)

Timofeev, V. I.; Abramchik, Yu. A.; Fateev, I. V.; Zhukhlistova, N. E.; Murav'eva, T. I.; Kuranova, I. P.; Esipov, R. S.

2013-11-01

The three-dimensional structures of thymidine phosphorylase from E. coli containing the bound sulfate ion in the phosphate-binding site and of the complex of thymidine phosphorylase with sulfate in the phosphate-binding site and the inhibitor 3'-azido-2'-fluoro-2',3'-dideoxyuridine (N3F-ddU) in the nucleoside-binding site were determined at 1.55 and 1.50 Å resolution, respectively. The amino-acid residues involved in the ligand binding and the hydrogen-bond network in the active site occupied by a large number of bound water molecules are described. A comparison of the structure of thymidine phosphorylase in complex with N3F-ddU with the structure of pyrimidine nucleoside phosphorylase from St. Aureus in complex with the natural substrate thymidine (PDB_ID: 3H5Q) shows that the substrate and the inhibitor in the nucleoside-binding pocket have different orientations. It is suggested that the position of N3F-ddU can be influenced by the presence of the azido group, which prefers a hydrophobic environment. In both structures, the active sites of the subunits are in the open conformation.

Disappointment and regret enhance corrugator reactivity in a gambling task.

PubMed

Wu, Yin; Clark, Luke

2015-04-01

This study investigated how the corrugator and zygomaticus respond to decision outcomes (i.e., gains and losses). We used a gambling task in which participants were presented with obtained followed by non-obtained outcomes. Activity at the corrugator site was sensitive to decision outcomes, such that higher obtained losses (disappointment) and higher non-obtained gains (regret) both heightened corrugator reactivity. Activity at the zygomaticus site was not responsive to obtained or non-obtained outcomes, but did show sensitivity to emotional images in the same participants, in the form of a positive linear relationship with self-reported emotional valence. Corrugator activity was negatively related to emotional valence. The findings indicate the sensitivity of corrugator to objective decision outcomes and also counterfactual comparisons, highlighting the utility of facial electromyography in research on decision making and gambling behavior. © 2014 The Authors. Psychophysiology published by Wiley Periodicals, Inc. on behalf of Society for Psychophysiological Research.

Comparison of the historical record of earthquake hazard with seismic-hazard models for New Zealand and the continental United States

USGS Publications Warehouse

Stirling, M.; Petersen, M.

2006-01-01

We compare the historical record of earthquake hazard experienced at 78 towns and cities (sites) distributed across New Zealand and the continental United States with the hazard estimated from the national probabilistic seismic-hazard (PSH) models for the two countries. The two PSH models are constructed with similar methodologies and data. Our comparisons show a tendency for the PSH models to slightly exceed the historical hazard in New Zealand and westernmost continental United States interplate regions, but show lower hazard than that of the historical record in the continental United States intraplate region. Factors such as non-Poissonian behavior, parameterization of active fault data in the PSH calculations, and uncertainties in estimation of ground-motion levels from historical felt intensity data for the interplate regions may have led to the higher-than-historical levels of hazard at the interplate sites. In contrast, the less-than-historical hazard for the remaining continental United States (intraplate) sites may be largely due to site conditions not having been considered at the intraplate sites, and uncertainties in correlating ground-motion levels to historical felt intensities. The study also highlights the importance of evaluating PSH models at more than one region, because the conclusions reached on the basis of a solely interplate or intraplate study would be very different.

Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic

NASA Astrophysics Data System (ADS)

Eardly, D. F.; Carton, M. W.; Gallagher, J. M.; Patching, J. W.

Results are presented from four cruises to the Porcupine Abyssal Plain (PAP site) that took place during the BENGAL project from September 1996 to March 1998, and two cruises to the PAP and an oligotrophic site (EUMELI) that took place during the DEEPSEAS project between September 1993 and March 1994. Bacterial abundances in sediment and sediment contact water were measured by epifluorescence microscopy. Bacterial activity was determined by 3H-thymidine incorporation as a measure of DNA synthesis, and by 3H-leucine incorporation as a measure of protein synthesis. Activities were measured under atmospheric and in situ pressures and temperatures. Bacterial activity was usually higher in samples incubated at in situ pressure than those incubated at atmospheric pressure indicating that a barophilic community was dominant. Inter-cruise comparisons of abundance and activity during the BENGAL project showed no firm evidence of there being a seasonal response in the benthic microbial community to any episodic phytodetritus event. This was probably because of inter-annual variations in the quality and quantity of phytodetritus deposition at the PAP site, the rapid remineralization of fresh organic material by the microbial communities and the timing of cruises to the study area. 3H-thymidine and 3H-leucine incorporation in sediments was higher during the BENGAL period than the DEEPSEAS programme. A methodological change in the 3H-thymidine incorporation technique for sediments may explain the differences in DNA synthesis observed between the two projects, whereas the lower levels of protein synthesis observed during the DEEPSEAS programme probably reflected both inter-annual variations in activity at the PAP site and the lower productivity that prevailed at surface at the EUMELI oligotrophic site. Rates of 3H-thymidine incorporation in sediment contact water were similar during both projects.

Structure of ATP-Bound Human ATP:Cobalamin Adenosyltransferase

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

Schubert,H.; Hill, C.

Mutations in the gene encoding human ATP:cobalamin adenosyltransferase (hATR) can result in the metabolic disorder known as methylmalonic aciduria (MMA). This enzyme catalyzes the final step in the conversion of cyanocobalamin (vitamin B{sub 12}) to the essential human cofactor adenosylcobalamin. Here we present the 2.5 {angstrom} crystal structure of ATP bound to hATR refined to an R{sub free} value of 25.2%. The enzyme forms a tightly associated trimer, where the monomer comprises a five-helix bundle and the active sites lie on the subunit interfaces. Only two of the three active sites within the trimer contain the bound ATP substrate, therebymore » providing examples of apo- and substrate-bound-active sites within the same crystal structure. Comparison of the empty and occupied sites indicates that twenty residues at the enzyme's N-terminus become ordered upon binding of ATP to form a novel ATP-binding site and an extended cleft that likely binds cobalamin. The structure explains the role of 20 invariant residues; six are involved in ATP binding, including Arg190, which hydrogen bonds to ATP atoms on both sides of the scissile bond. Ten of the hydrogen bonds are required for structural stability, and four are in positions to interact with cobalamin. The structure also reveals how the point mutations that cause MMA are deficient in these functions.« less

Bacterial biomass and activity in the deep waters of the eastern Atlantic—evidence of a barophilic community

NASA Astrophysics Data System (ADS)

Patching, J. W.; Eardly, D.

1997-09-01

Bacterial biomass and activity were investigated in deep waters at two sites in the eastern Atlantic, of similar depth (4560-4800 m), but varying in their nutritional status. The Northern (N) site was eutrophic and subject to a strong seasonal input of surface derived organic matter (phytodetritus) to the sediment. The Southern (S) site was oligotrophic. Deep water at this site does not appear to receive any strong seasonal input. Bacterial numbers in the deep water column at the N site showed no significant seasonal variation but were greater than those at the S site. Deep water bacteria were typically small and free-living. From biovolume determinations, it was estimated that mean concentrations of bacterial organic carbon at depths greater than 500 m were 0.12 (0.03-0.29) μg C 1 -1 and 0.02 (0.01-0.04) μg C 1 -1 at the N and S sites, respectively. Rates of thymidine and leucine incorporation were used as indicators of bacterial activity. Bacterial communities in water in contact with the sediment (SCW; sediment contact water) at both sites (but especially at the S site) were strongly barophilic at in situ temperatures (2.5-4.1°C). The barophilic response of thymidine incorporation was enhanced when SCW samples from the N site were incubated at 11.5°C. It is proposed that this result indicated an elevating effect of pressure on cardinal temperatures and that the SCW community was obligately psychrophilic when unpressurised. Comparison of cell-specific incorporation rates determined under in situ conditions showed bacteria in the SCW to have levels of activity comparable with bacteria from a depth of 150 m. Thymidine incorporation rates were highest in SCW samples taken at the N site in May 1988 and September 1989. Thymidine incorporation by SCW samples taken immediately before (10 April 1994) the main spring-bloom-associated deposition of phytodetritus was significantly lower and comparable with that determined for the oligotrophic S site. The attributes exhibited by the SCW community appeared to be highly localised. We conclude that the bacterial communities of the SCW are active and adapted to their environment. Activity is influenced by the trophic nature of the site and may show temporal changes linked with episodic food supply. We postulate that the existence of such communities is linked to the role of the sediment-water interface as the initial site of deposition of sea-surface derived labile organic material.

Selective Self-Presentation and Social Comparison Through Photographs on Social Networking Sites.

PubMed

Fox, Jesse; Vendemia, Megan A

2016-10-01

Through social media and camera phones, users enact selective self-presentation as they choose, edit, and post photographs of themselves (such as selfies) to social networking sites for an imagined audience. Photos typically focus on users' physical appearance, which may compound existing sociocultural pressures about body image. We identified users of social networking sites among a nationally representative U.S. sample (N = 1,686) and examined women's and men's photo-related behavior, including posting photos, editing photos, and feelings after engaging in upward and downward social comparison with others' photos on social networking sites. We identified some sex differences: women edited photos more frequently and felt worse after upward social comparison than men. Body image and body comparison tendency mediated these effects.

Role of the conserved amino acids of the 'SDN' loop (Ser130, Asp131 and Asn132) in a class A beta-lactamase studied by site-directed mutagenesis.

PubMed

Jacob, F; Joris, B; Lepage, S; Dusart, J; Frère, J M

1990-10-15

Ser130, Asp131 and Asn132 ('SDN') are highly conserved residues in class A beta-lactamases forming one wall of the active-site cavity. All three residues of the SDN loop in Streptomyces albus G beta-lactamase were modified by site-directed mutagenesis. The mutant proteins were expressed in Streptomyces lividans, purified from culture supernatants and their kinetic parameters were determined for several substrates. Ser130 was substituted by Asn, Ala and Gly. The first modification yielded an almost totally inactive protein, whereas the smaller-side-chain mutants (A and G) retained some activity, but were less stable than the wild-type enzyme. Ser130 might thus be involved in maintaining the structure of the active-site cavity. Mutations of Asp131 into Glu and Gly proved to be highly detrimental to enzyme stability, reflecting significant structural perturbations. Mutation of Asn132 into Ala resulted in a dramatically decreased enzymic activity (more than 100-fold) especially toward cephalosporin substrates, kcat. being the most affected parameter, which would indicate a role of Asn132 in transition-state stabilization rather than in ground-state binding. Comparison of the N132A and the previously described N132S mutant enzymes underline the importance of an H-bond-forming residue at position 132 for the catalytic process.

Salt Effect on the Antioxidant Activity of Red Microalgal Sulfated Polysaccharides in Soy-Bean Formula

PubMed Central

Burg, Ariela; Oshrat, Levy-Ontman

2015-01-01

Sulfated polysaccharides produced by microalgae, which are known to exhibit various biological activities, may potentially serve as natural antioxidant sources. To date, only a few studies have examined the antioxidant bioactivity of red microalgal polysaccharides. In this research, the effect of different salts on the antioxidant activities of two red microalgal sulfated polysaccharides derived from Porphyridium sp. and Porphyridium aerugineum were studied in a soy bean-based infant milk formula. Salt composition and concentration were both shown to affect the polysaccharides’ antioxidant activity. It can be postulated that the salt ions intefer with the polysaccharide chains’ interactions and alter their structure, leading to a new three-dimensional structure that better exposes antiooxidant sites in comparison to the polysaccharide without salt supplement. Among the cations that were studied, Ca2+ had the strongest enhancement effect on antioxidant activities of both polysaccharides. Understanding the effect of salts on polysaccharides’ stucture, in addition to furthering knowledge on polysaccharide bioactivities, may also shed light on the position of the antioxidant active sites. PMID:26492255

Arylhydrazone derivatives of naproxen as new analgesic and anti-inflammatory agents: Design, synthesis and molecular docking studies.

PubMed

Azizian, Homa; Mousavi, Zahra; Faraji, Hamidreza; Tajik, Mohammad; Bagherzadeh, Kowsar; Bayat, Peyman; Shafiee, Abbas; Almasirad, Ali

2016-06-01

A series of new arylidenehydrazone derivatives of naproxen were synthesized and evaluated for their analgesic and anti-inflammatory activities. Some of the synthesized analogues showed comparable activities when compared against naproxen for their analgesic and anti-inflammatory properties. 2-(6-methoxy-2-naphthyl)-N'-[(pyridine-4-yl)methylene]propanoic acid hydrazide 4j was found to be the most active analgesic agent. 2-(6-methoxy-2-naphthyl)-N'-[4-nitrobenzylidene]propanoic acid hydrazide 4g showed highest anti-inflammatory activity in comparison to the naproxen. Molecular modeling study of the synthesized compounds suggested that the designed molecules were well located and bound to the COX-1 and COX-2 active sites. Compound 4g showed the highest selectivity for COX-2 (RCOX-2/COX-1=1.94) and higher affinity rather than naproxen in COX-2 active site (RCOX-2/naproxen=1.28). Moreover, the structural analyses confirmed that the E-ap rotamer is the preferred structure for the arylidenehydrazone derivatives. Copyright © 2016 Elsevier Inc. All rights reserved.

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

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

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP

2012-05-09

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexiblemore » in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.« less

Two variants of the major serine protease inhibitor from the sea anemone Stichodactyla helianthus, expressed in Pichia pastoris.

PubMed

García-Fernández, Rossana; Ziegelmüller, Patrick; González, Lidice; Mansur, Manuel; Machado, Yoan; Redecke, Lars; Hahn, Ulrich; Betzel, Christian; Chávez, María de Los Ángeles

2016-07-01

The major protease inhibitor from the sea anemone Stichodactyla helianthus (ShPI-1) is a non-specific inhibitor that binds trypsin and other trypsin-like enzymes, as well as chymotrypsin, and human neutrophil elastase. We performed site-directed mutagenesis of ShPI-1 to produce two variants (rShPI-1/K13L and rShPI/Y15S) that were expressed in Pichia pastoris, purified, and characterized. After a single purification step, 65 mg and 15 mg of protein per liter of culture supernatant were obtained for rShPI-1/K13L and rShPI/Y15S, respectively. Functional studies demonstrated a 100-fold decreased trypsin inhibitory activity as result of the K13L substitution at the reactive (P1) site. This protein variant has a novel tight-binding inhibitor activity of pancreatic elastase and increased activity toward neutrophil elastase in comparison to rShPI-1A. In contrast, the substitution Y15S at P2' site did not affect the Ki value against trypsin, but did reduce activity 10-fold against chymotrypsin and neutrophil elastase. Our results provide two new ShPI-1 variants with modified inhibitory activities, one of them with increased biomedical potential. This study also offers new insight into the functional impact of the P1 and P2' sites on ShPI-1 specificity. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysis of biomolecular solvation sites by 3D-RISM theory.

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

Structural and biochemical insights into 7β-hydroxysteroid dehydrogenase stereoselectivity.

PubMed

Savino, Simone; Ferrandi, Erica Elisa; Forneris, Federico; Rovida, Stefano; Riva, Sergio; Monti, Daniela; Mattevi, Andrea

2016-06-01

Hydroxysteroid dehydrogenases are of great interest as biocatalysts for transformations involving steroid substrates. They feature a high degree of stereo- and regio-selectivity, acting on a defined atom with a specific configuration of the steroid nucleus. The crystal structure of 7β-hydroxysteroid dehydrogenase from Collinsella aerofaciens reveals a loop gating active-site accessibility, the bases of the specificity for NADP(+) , and the general architecture of the steroid binding site. Comparison with 7α-hydroxysteroid dehydrogenase provides a rationale for the opposite stereoselectivity. The presence of a C-terminal extension reshapes the substrate site of the β-selective enzyme, possibly leading to an inverted orientation of the bound substrate. Proteins 2016; 84:859-865. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.

PubMed

Yamashita, A; Kato, H; Wakatsuki, S; Tomizaki, T; Nakatsu, T; Nakajima, K; Hashimoto, T; Yamada, Y; Oda, J

1999-06-15

Tropinone reductase-II (TR-II) catalyzes the NADPH-dependent reduction of the carbonyl group of tropinone to a beta-hydroxyl group. The crystal structure of TR-II complexed with NADP+ and pseudotropine (psi-tropine) has been determined at 1.9 A resolution. A seven-residue peptide near the active site, disordered in the unliganded structure, is fixed in the ternary complex by participation of the cofactor and substrate binding. The psi-tropine molecule is bound in an orientation which satisfies the product configuration and the stereochemical arrangement toward the cofactor. The substrate binding site displays a complementarity to the bound substrate (psi-tropine) in its correct orientation. In addition, electrostatic interactions between the substrate and Glu156 seem to specify the binding position and orientation of the substrate. A comparison between the active sites in TR-II and TR-I shows that they provide different van der Waals surfaces and electrostatic features. These differences likely contribute to the correct binding mode of the substrates, which are in opposite orientations in TR-II and TR-I, and to different reaction stereospecificities. The active site structure in the TR-II ternary complex also suggests that the arrangement of the substrate, cofactor, and catalytic residues is stereoelectronically favorable for the reaction.

Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.

PubMed

Cao, Nan; Tan, Kemin; Annamalai, Thirunavukkarasu; Joachimiak, Andrzej; Tse-Dinh, Yuk-Ching

2018-06-14

We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.

The 24-hour skin hydration and barrier function effects of a hyaluronic 1%, glycerin 5%, and Centella asiatica stem cells extract moisturizing fluid: an intra-subject, randomized, assessor-blinded study.

PubMed

Milani, Massimo; Sparavigna, Adele

2017-01-01

Moisturizing products are commonly used to improve hydration in skin dryness conditions. However, some topical hydrating products could have negative effects on skin barrier function. In addition, hydrating effects of moisturizers are not commonly evaluated up to 24 hours after a single application. Hyaluronic acid (HA) and glycerin are very well-known substances able to improve skin hydration. Centella asiatica extract (CAE) could exert lenitive, anti-inflammatory and reepithelialization actions. Furthermore, CAE could inhibit hyaluronidase enzyme activity, therefore prolonging the effect of HA. A fluid containing HA 1%, glycerin 5% and stem cells CAE has been recently developed (Jaluronius CS [JCS] fluid). To evaluate and compare the 24-hour effects of JCS fluid on skin hydration and on transepidermal water loss (TEWL) in healthy subjects in comparison with the control site. Twenty healthy women, mean age 40 years, were enrolled in an intra-subject (right vs left), randomized, assessor-blinded, controlled, 1-day trial. The primary end points were the skin hydration and TEWL, evaluated at the volar surface of the forearm and in standardized conditions (temperature- and humidity-controlled room: 23°C and 30% of humidity) using a corneometer and a vapometer device at baseline, 1, 8 and 24 hours after JCS fluid application. Measurements were performed by an operator blinded for the treatments. Skin hydration after 24 hours was significantly higher ( P =0.001; Mann-Whitney U test) in the JCS-treated area in comparison with the control site. JCS induced a significant ( P =0.0001) increase in skin hydration at each evaluation time (+59% after 1 hour, +48% after 8 hours and +29% after 24 hours) in comparison with both baseline ( P =0.0001) and non-treated control site ( P =0.001). TEWL after 24 hours was significantly lower ( P =0.049; Mann-Whitney U test) in the JCS-treated area in comparison with the control site (13±4 arbitrary units [AU] vs 16±6 AU). JCS fluid significantly reduced post-stripping TEWL in comparison with baseline after 1, 8 and 24 hours (-52%, -32% and -48%, respectively). In the control site, TEWL was not reduced in comparison with baseline values at each time point's evaluation. A single application of JCS significantly improves skin hydration for up to 24 hours at the same time as improving skin barrier function.

A European-wide 222radon and 222radon progeny comparison study

NASA Astrophysics Data System (ADS)

Schmithüsen, Dominik; Chambers, Scott; Fischer, Bernd; Gilge, Stefan; Hatakka, Juha; Kazan, Victor; Neubert, Rolf; Paatero, Jussi; Ramonet, Michel; Schlosser, Clemens; Schmid, Sabine; Vermeulen, Alex; Levin, Ingeborg

2017-04-01

Although atmospheric 222radon (222Rn) activity concentration measurements are currently performed worldwide, they are being made by many different laboratories and with fundamentally different measurement principles, so compatibility issues can limit their utility for regional-to-global applications. Consequently, we conducted a European-wide 222Rn / 222Rn progeny comparison study in order to evaluate the different measurement systems in use, determine potential systematic biases between them, and estimate correction factors that could be applied to harmonize data for their use as a tracer in atmospheric applications. Two compact portable Heidelberg radon monitors (HRM) were moved around to run for at least 1 month at each of the nine European measurement stations included in this comparison. Linear regressions between parallel data sets were calculated, yielding correction factors relative to the HRM ranging from 0.68 to 1.45. A calibration bias between ANSTO (Australian Nuclear Science and Technology Organisation) two-filter radon monitors and the HRM of ANSTO / HRM = 1.11 ± 0.05 was found. Moreover, for the continental stations using one-filter systems that derive atmospheric 222Rn activity concentrations from measured atmospheric progeny activity concentrations, preliminary 214Po / 222Rn disequilibrium values were also estimated. Mean station-specific disequilibrium values between 0.8 at mountain sites (e.g. Schauinsland) and 0.9 at non-mountain sites for sampling heights around 20 to 30 m above ground level were determined. The respective corrections for calibration biases and disequilibrium derived in this study need to be applied to obtain a compatible European atmospheric 222Rn data set for use in quantitative applications, such as regional model intercomparison and validation or trace gas flux estimates with the radon tracer method.

Quantitative assessment of groundwater quality using a biological indicator: some preliminary observations.

PubMed

Pfeil, R M; Venkat, J A; Plimmer, J R; Sham, S; Davis, K; Nair, P P

1994-02-01

The genotoxicity of groundwater was evaluated, using a novel application of the SOS microplate assay (SOSMA). Organic residues were extracted from groundwater samples from Maryland, Pennsylvania, and Delaware by using C-18 bonded silica solid phase extraction tubes. Total organic carbon content (TOC) of water samples was also determined. The genotoxicity of the extracts was determined by the SOSMA. Relative activity (RA) as determined by the SOSMA is a quantitative measure of genotoxicity based on a comparison to the activity of the mutagen, 4-nitroquinoline oxide. Low levels of RA (about 2x background) were detected in waters from sites within these states. There was considerable temporal and spatial variation in the observed RA, but no definite patterns were observed in the variation. Between sampling sites there was a positive correlation between RA and TOC; however, this relationship appeared to be reversed occasionally within a sampling site. The extraction and bioassay methods provide an easy and relatively inexpensive means of determining water quality.

Active site-directed double mutants of dihydrofolate reductase.

PubMed

Ercikan-Abali, E A; Mineishi, S; Tong, Y; Nakahara, S; Waltham, M C; Banerjee, D; Chen, W; Sadelain, M; Bertino, J R

1996-09-15

Variants of dihydrofolate reductase (DHFR), which confer resistance to antifolates, are used as dominant selectable markers in vitro and in vivo and may be useful in the context of gene therapy. To identify improved mutant human DHFRs with increased catalytic efficiency and decreased binding to methotrexate, we constructed by site-directed mutagenesis four variants with substitutions at both Leu22 and Phe31 (i.e., Phe22-Ser31, Tyr22-Ser31, Phe22-Gly31, and Tyr22-Gly31). Antifolate resistance has been observed previously when individual changes are made at these active-site residues. Substrate and antifolate binding properties of these "double" mutants revealed that each have greatly diminished affinity for antifolates (> 10,000-fold) yet only slightly reduced substrate affinity. Comparison of in vitro measured properties with those of single-residue variants indicates that double mutants are indeed significantly superior. This was verified for one of the double mutants that provided high-level methotrexate resistance following retrovirus-mediated gene transfer in NIH3T3 cells.

Characterization and localization of arginine vasotocin receptors in the brain and kidney of an amphibian

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

Boyd, S.K.

1987-01-01

Because arginine vasotocin (AVT) activates male sexual behaviors in the rough-skinned newt (Taricha granulosa), quantitative autoradiography with radiolabeled arginine vasopressin (/sup 3/H-AVP) was used to localize and characterize putative AVT receptors in the brain of this amphibian. Binding of /sup 3/H-AVP to sites within the medial pallium was saturable, specific, reversible, of high affinity and low capacity. These binding sites appear to represent authentic central nervous system receptors for AVT. Furthermore, ligand specificity for the binding sites in this amphibian differs from that reported for AVP binding sites in rat brains. Dense concentrations of specific binding sites were located inmore » the olfactory nerve as it entered the olfactory bulb within the medial pallium, dorsal pallium, and amygdala pars lateralis of the telencephalon, and in the tegmental region of the medulla. Concentrations of binding sites differed significantly among various brain regions. A comparison of male and female newts collected during the breeding season revealed no sexual dimorphism. These areas may represent site(s) of action where AVT elicits sexual behaviors in male T. granulosa.« less

Comparison of nitrogen monoxide emissions from several African tropical ecosystems and influence of season and fire

NASA Astrophysics Data System (ADS)

SerçA, D.; Delmas, R.; Le Roux, X.; Parsons, D. A. B.; Scholes, M. C.; Abbadie, L.; Lensi, R.; Ronce, O.; Labroue, L.

1998-12-01

NO emission rates from soils were measured for twelve major African ecosystems in four countries (Congo, Niger, Ivory Coast, and South Africa) and within four major phytogeographic domains: the Guineo-Congolese, Guinean, Sahelian, and Zambezian domains. Measurements were performed during wet and/or dry seasons. All the measurements were made with the same dynamic chamber device, which allowed true comparisons to be made. This study showed that emission rates strongly differed between ecosystems and exhibited a marked temporal variability. Ecosystem effect was highly significant during both the dry and wet seasons. Emission rates were low (<0.6 ng NO-N m-2 s-1) in Hyparrhenia and Loudetia savannas of the Guinean or Guineo-Congolese domains. Intermediate NO fluxes were obtained in rain forest and gallery forest ecosystems, in a broad-leafed savanna and in a seasonally wetted grassland (sandy soil) of the Zambezian domain, and in a dry fallow savanna of the Sahelian domain. Emission rates were maximum (>7 ng NO-N m-2 s-1) in a seasonally wetted grassland (site 2) and in particular sites subjected to various disturbances, for example soil fauna activity (termite mounds) or past human disturbance (Acacia patches-settlement site). Microbial activity potentials (i.e., carbon mineralization, nitrification, denitrification, and total net N mineralization) were determined for most of the soils where NO fluxes were measured. In some sites, these potential activities were useful to identify the major processes controlling NO emission rates. Denitrification potential was very low and could not explain substantial NO fluxes from broad- and fine-leafed savannas and Hyperihelia savannas of the Zambezian domain. Very low potentials of both nitrification and denitrification could be related to the low NO fluxes for the three Guinean savanna sites studied. NO fluxes were significantly higher during the wet season than the dry season in both savanna and forest ecosystems. Emission rates in savanna ecosystems were significantly increased within a few hours after fire. The measurements presented here provide a unique, consistent database which can be used to further analyze the processes involved in the spatial and temporal variations of NO emissions.

Radiology and social media: are private practice radiology groups more social than academic radiology departments?

PubMed

Glover, McKinley; Choy, Garry; Boland, Giles W; Saini, Sanjay; Prabhakar, Anand M

2015-05-01

This study assesses the prevalence of use of the most commonly used social media sites among private radiology groups (PRGs) and academic radiology departments (ARDs). The 50 largest PRGs and the 50 ARDs with the highest level of funding from the National Institutes of Health were assessed for presence of a radiology-specific social media account on Facebook, Twitter, Instagram, Pinterest, YouTube, and LinkedIn. Measures of organizational activity and end-user activity were collected, including the number of posts and followers, as appropriate; between-group comparisons were performed. PRGs adopted Facebook 12 months earlier (P = .02) and Twitter 18 months earlier (P = .02) than did ARDs. A total of 76% of PRGs maintained ≥1 account on the social media sites included in the study, compared with 28% of ARDs (P < .0001). The prevalence of having an account on the social media sites for PRGs was: Facebook, 66%; LinkedIn, 56%; Twitter, 42%; YouTube, 20%; Pinterest, 4%; and Instagram, 2%. The prevalence of radiology-specific social media accounts for ARDs was: Facebook, 18%; LinkedIn, 0%; Twitter, 24%; YouTube, 6%; Pinterest, 0%; and Instagram, 0%. There was no significant difference between ARDs and PRGs in measures of end-user or organizational activity on Facebook or Twitter. Use of social media in health care is emerging as mainstream, with PRGs being early adopters of Facebook and Twitter in comparison with ARDs. Competitive environments and institutional policies may be strong factors that influence how social media is used by radiologists at the group and department levels. Copyright © 2015 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Methane Oxidation on Pd-Ceria. A DFT Study of the Combustion Mechanism over Pd, PdO and Pd-ceria Sites

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

Mayernick, Adam D.; Janik, Michael J.

2010-12-24

Palladium/ceria exhibits unique catalytic activity for hydrocarbon oxidation; however, the chemical and structural properties of active sites on the palladium–ceria surface are difficult to characterize. Strong interactions between palladium and the ceria support stabilize oxidized Pd δ+ species, which may contribute to the significant activity of Pd/ceria for methane oxidation. We present a density functional theory (DFT + U) investigation into methane oxidation over Pd/ceria and quantify the activity of the Pd xCe 1-xO 2(1 1 1) mixed oxide surface in comparison with the PdO(1 0 0) and Pd(1 1 1) surfaces. The methane activation barrier is lowest over themore » Pd xCe 1-xO 2(1 1 1) surface, even lower than over the Pd(1 1 1) surface or low coordinated stepped or kinked Pd sites. Subsequent reaction steps in complete oxidation, including product desorption and vacancy refilling, are considered to substantiate that methane activation remains the rate-limiting step despite the low barrier over Pd xCe 1-xO 2(1 1 1). The low barrier over the Pd xCe 1-xO 2(1 1 1) surface demonstrates that mixed ceria-noble metal oxides offer the potential for improved hydrocarbon oxidation performance with respect to dispersed noble metal particles on ceria.« less

Comparison of radionuclide levels in soil, sagebrush, plant litter, cryptogams, and small mammals

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

Landeen, D.S.

1994-09-01

Soil, sagebrush, plant litter, cryptogam, and small mammal samples were collected and analyzed for cesium-137, strontium-90, plutonium-238, plutonium 239/240, technetium-99, and iodine-129 from 1981 to 1986 at the US Department of Energy Hanford Site in southeastern Washington State as part of site characterization and environmental monitoring activities. Samples were collected on the 200 Areas Plateau, downwind from ongoing waste management activities. Plant litter, cryptogams, and small mammals are media that are not routinely utilized in monitoring or characterization efforts for determination of radionuclide concentrations. Studies at Hanford, other US Department of Energy sites, and in eastern Europe have indicated thatmore » plant litter and cryptogams may serve as effective ``natural`` monitors of air quality. Plant litter in this study consists of fallen leaves from sagebrush and ``cryptogams`` describes that portion of the soil crust composed of mosses, lichens, algae, and fungi. Comparisons of cesium-137 and strontium-90 concentrations in the soil, sagebrush, litter, and cryptogams revealed significantly higher (p<0.05) levels in plant litter and cryptogams. Technetium-99 values were the highest in sagebrush and litter. Plutonium-238 and 239/40 and iodine-129 concentrations never exceeded 0.8 pCi/gm in all media. No evidence of any significant amounts of any radionuclides being incorporated into the small mammal community was discovered. The data indicate that plant litter and cryptogams may be better, indicators of environmental quality than soil or vegetation samples. Augmenting a monitoring program with samples of litter and cryptogams may provide a more accurate representation of radionuclide environmental uptake and/or contamination levels in surrounding ecosystems. The results of this study may be applied directly to other radioecological monitoring conducted at other nuclear sites and to the monitoring of other pollutants.« less

Increasing the structural coverage of tuberculosis drug targets.

PubMed

Baugh, Loren; Phan, Isabelle; Begley, Darren W; Clifton, Matthew C; Armour, Brianna; Dranow, David M; Taylor, Brandy M; Muruthi, Marvin M; Abendroth, Jan; Fairman, James W; Fox, David; Dieterich, Shellie H; Staker, Bart L; Gardberg, Anna S; Choi, Ryan; Hewitt, Stephen N; Napuli, Alberto J; Myers, Janette; Barrett, Lynn K; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W; Stacy, Robin; Stewart, Lance J; Edwards, Thomas E; Van Voorhis, Wesley C; Myler, Peter J

2015-03-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increasing the structural coverage of tuberculosis drug targets

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

Baugh, Loren; Phan, Isabelle; Begley, Darren W.

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

Increasing the structural coverage of tuberculosis drug targets

DOE PAGES

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; ...

2014-12-19

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

Increasing the Structural Coverage of Tuberculosis Drug Targets

PubMed Central

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

2015-01-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

Baseline and premining geochemical characterization of mined sites

USGS Publications Warehouse

Nordstrom, D. Kirk

2015-01-01

A rational goal for environmental restoration of new, active, or inactive mine sites would be ‘natural background’ or the environmental conditions that existed before any mining activities or other related anthropogenic activities. In a strictly technical sense, there is no such thing as natural background (or entirely non-anthropogenic) existing today because there is no part of the planet earth that has not had at least some chemical disturbance from anthropogenic activities. Hence, the terms ‘baseline’ and ‘pre-mining’ are preferred to describe these conditions. Baseline conditions are those that existed at the time of the characterization which could be pre-mining, during mining, or post-mining. Protocols for geochemically characterizing pre-mining conditions are not well-documented for sites already mined but there are two approaches that seem most direct and least ambiguous. One is characterization of analog sites along with judicious application of geochemical modeling. The other is reactive-transport modeling (based on careful synoptic sampling with tracer-injection) and subtracting inputs from known mining and mineral processing. Several examples of acidic drainage are described from around the world documenting the range of water compositions produced from pyrite oxidation in the absence of mining. These analog sites provide insight to the processes forming mineralized waters in areas untouched by mining. Natural analog water-chemistry data is compared with the higher metal concentrations, metal fluxes, and weathering rates found in mined areas in the few places where comparisons are possible. The differences are generally 1–3 orders of magnitude higher for acid mine drainage.

Exposure of nonbreeding migratory shorebirds to cholinesterase-inhibiting contaminants in the western hemisphere

USGS Publications Warehouse

Strum, K.M.; Hooper, M.J.; Johnson, K.A.; Lanctot, Richard B.; Zaccagnini, M.E.; Sandercock, B.K.

2010-01-01

Migratory shorebirds frequently forage and roost in agricultural habitats, where they may be exposed to cholinesterase-inhibiting pesticides. Exposure to organophosphorus and carbamate compounds, common anti-cholinesterases, can cause sublethal effects, even death. To evaluate exposure of migratory shorebirds to organophosphorus and carbamates, we sampled birds stopping over during migration in North America and wintering in South America. We compared plasma cholinesterase activities and body masses of individuals captured at sites with no known sources of organophosphorus or carbamates to those captured in agricultural areas where agrochemicals were recommended for control of crop pests. In South America, plasma acetylcholinesterase and butyrylcholinesterase activity in Buff-breasted Sandpipers was lower at agricultural sites than at reference sites, indicating exposure to organophosphorus and carbamates. Results of plasma cholinesterase reactivation assays and foot-wash analyses were inconclusive. A meta-analysis of six species revealed no widespread effect of agricultural chemicals on cholinesterase activity. however, four of six species were negative for acetylcholinesterase and one of six for butyrylcholinesterase, indicating negative effects of pesticides on cholinesterase activity in a subset of shorebirds. Exposure to cholinesterase inhibitors can decrease body mass, but comparisons between treatments and hemispheres suggest that agrochemicals did not affect migratory shorebirds' body mass. Our study, one of the first to estimate of shorebirds' exposure to cholinesterase-inhibiting pesticides, suggests that shorebirds are being exposed to cholinesterase- inhibiting pesticides at specific sites in the winter range but not at migratory stopover sites. future research should examine potential behavioral effects of exposure and identify other potential sitesand levels of exposure. ?? The Cooper Ornithological Society 2010.

Prompt and delayed NAA techniques for the characterization of specimen bank materials.

PubMed

Rossbach, M; Stoeppler, M; Byrne, A R

1993-11-01

The combined application of instrumental-, radiochemical- and prompt gamma neutron activation analysis to two spruce shoot materials from the German Environmental Specimen Bank (ESB) resulted in information on 50 elements, covering more than 50% of the total mass. Comparison of the element concentrations in the 'fingerprint' mode clearly indicated a different status of heavy metal pollution at the two distinct collecting sites.

Comparison of Alternative Hydrogen Donors for Anaerobic Reductive Dechlorination of Tetrachloroethene

DTIC Science & Technology

1998-01-01

feature two - stage anaerobic reductive dechlorination of highly chlorinated compounds coupled with aerobic (sometimes co- metabolic) treatment of the...activity at some naturally attenuated sites. Fathepure and Vogel [76] used a two - stage anaerobic-aerobic reactor system to treat hexachlorobenzene, PCE...Complete removal of the chloroethenes by the two - stage system was observed using pyruvate, formate, or lactose as electron donor for the dechlorinating

Comparison of erosion and channel characteristics

USGS Publications Warehouse

Parker, Gene W.

1998-01-01

Erosion was observed at 33 percent of 22,495 bridge sites in nine States. Among sites with erosion, 56 percent were associated with skewed flows, curved channels, or a combination of these two conditions, and at 18 percent of the sites, channels were straight with steep bank angles. The remaining 26 percent are sites with observable erosion at piers or abutments on straight channels. Comparison of the sites with erosion to channel bed-material indicate that 44 percent of the single-span sites had gravel-size or smaller bed material and 70 percent of the multiple-span sites had gravel-size or smaller bed material.

Unprecedented access of phenolic substrates to the heme active site of a catalase: substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray crystallography and EPR spectroscopy.

PubMed

Loewen, Peter C; Villanueva, Jacylyn; Switala, Jacek; Donald, Lynda J; Ivancich, Anabella

2015-05-01

Heme-containing catalases and catalase-peroxidases catalyze the dismutation of hydrogen peroxide as their predominant catalytic activity, but in addition, individual enzymes support low levels of peroxidase and oxidase activities, produce superoxide, and activate isoniazid as an antitubercular drug. The recent report of a heme enzyme with catalase, peroxidase and penicillin oxidase activities in Bacillus pumilus and its categorization as an unusual catalase-peroxidase led us to investigate the enzyme for comparison with other catalase-peroxidases, catalases, and peroxidases. Characterization revealed a typical homotetrameric catalase with one pentacoordinated heme b per subunit (Tyr340 being the axial ligand), albeit in two orientations, and a very fast catalatic turnover rate (kcat  = 339,000 s(-1) ). In addition, the enzyme supported a much slower (kcat  = 20 s(-1) ) peroxidatic activity utilizing substrates as diverse as ABTS and polyphenols, but no oxidase activity. Two binding sites, one in the main access channel and the other on the protein surface, accommodating pyrogallol, catechol, resorcinol, guaiacol, hydroquinone, and 2-chlorophenol were identified in crystal structures at 1.65-1.95 Å. A third site, in the heme distal side, accommodating only pyrogallol and catechol, interacting with the heme iron and the catalytic His and Arg residues, was also identified. This site was confirmed in solution by EPR spectroscopy characterization, which also showed that the phenolic oxygen was not directly coordinated to the heme iron (no low-spin conversion of the Fe(III) high-spin EPR signal upon substrate binding). This is the first demonstration of phenolic substrates directly accessing the heme distal side of a catalase. © 2015 Wiley Periodicals, Inc.

76 FR 2442 - Reports, Forms, and Record Keeping Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-13

... interviews over a period of approximately 26 months. The survey will ask questions about drinking behavior... wave of telephone interviews with residents in 3 program sites and 2 comparison sites not carrying out... will be 1,200 while sample size for the comparisons sites will be 500, totaling 23,000 interviews...

Comparison of Two Preparation Methods on Catalytic Activity and Selectivity of Ru-Mo/HZSM5 for Methane Dehydroaromatization

DOE PAGES

Petkovic, Lucia M.; Ginosar, Daniel M.

2014-01-01

Catalytic performance of Mo/HZSM5 and Ru-Mo/HZSM5 catalysts prepared by vaporization-deposition of molybdenum trioxide and impregnation with ammonium heptamolybdate was analyzed in terms of catalyst activity and selectivity, nitrogen physisorption analyses, temperature-programmed oxidation of carbonaceous residues, and temperature-programmed reduction. Vaporization-deposition rendered the catalyst more selective to ethylene and coke than the catalyst prepared by impregnation. This result was assigned to lower interaction of molybdenum carbide with the zeolite acidic sites.

Are participant characteristics from ISCOLE study sites comparable to the rest of their country?

PubMed Central

LeBlanc, A G; Katzmarzyk, P T; Barreira, T V; Broyles, S T; Chaput, J-P; Church, T S; Fogelholm, M; Harrington, D M; Hu, G; Kuriyan, R; Kurpad, A; Lambert, E V; Maher, C; Maia, J; Matsudo, V; Olds, T; Onywera, V; Sarmiento, O L; Standage, M; Tudor-Locke, C; Zhao, P; Tremblay, M S

2015-01-01

OBJECTIVES: The International Study of Childhood Obesity, Lifestyle and the Environment (ISCOLE) provides robust, multi-national information on physical activity, diet and weight status in 9–11-year-old children around the world. The purpose of this analysis was to examine the similarities and differences between participant characteristics from ISCOLE sites and data from nationally representative surveys from ISCOLE countries (Australia, Brazil, Canada, China, Colombia, Finland, Kenya, India, Portugal, South Africa, the United Kingdom and the United States). METHODS: Distributions of characteristics were assessed within each ISCOLE country-level database, and compared with published data from national or regional surveys, where available. Variables of comparison were identified a priori and included body mass index (BMI), physical activity (accelerometer-determined steps per day) and screen time (child-report). RESULTS: Of 12 countries, data on weight status (BMI) were available in 8 countries, data on measured physical activity (steps per day) were available in 5 countries and data on self-reported screen time were available in 9 countries. The five ISCOLE countries that were part of the Health Behaviour in School-aged Children Survey (that is, Canada, Finland, Portugal, the United Kingdom (England) and the United States) also provided comparable data on self-reported physical activity. Available country-specific data often used different measurement tools or cut-points, making direct comparisons difficult. Where possible, ISCOLE data were re-analyzed to match country-level data, but this step limited between-country comparisons. CONCLUSIONS: From the analyses performed, the ISCOLE data do not seem to be systematically biased; however, owing to limitations in data availability, data from ISCOLE should be used with appropriate caution when planning country-level population health interventions. This work highlights the need for harmonized measurement tools around the world while accounting for culturally specific characteristics, and the need for collaboration across study centers and research groups. PMID:27152192

Analytic hierarchy process helps select site for limestone quarry expansion in Barbados.

PubMed

Dey, Prasanta Kumar; Ramcharan, Eugene K

2008-09-01

Site selection is a key activity for quarry expansion to support cement production, and is governed by factors such as resource availability, logistics, costs, and socio-economic-environmental factors. Adequate consideration of all the factors facilitates both industrial productivity and sustainable economic growth. This study illustrates the site selection process that was undertaken for the expansion of limestone quarry operations to support cement production in Barbados. First, alternate sites with adequate resources to support a 25-year development horizon were identified. Second, technical and socio-economic-environmental factors were then identified. Third, a database was developed for each site with respect to each factor. Fourth, a hierarchical model in analytic hierarchy process (AHP) framework was then developed. Fifth, the relative ranking of the alternate sites was then derived through pair wise comparison in all the levels and through subsequent synthesizing of the results across the hierarchy through computer software (Expert Choice). The study reveals that an integrated framework using the AHP can help select a site for the quarry expansion project in Barbados.

A comparison in Colorado of three methods to monitor breeding amphibians

USGS Publications Warehouse

Corn, P.S.; Muths, E.; Iko, W.M.

2000-01-01

We surveyed amphibians at 4 montane and 2 plains lentic sites in northern Colorado using 3 techniques: standardized call surveys, automated recording devices (frog-loggers), and intensive surveys including capture-recapture techniques. Amphibians were observed at 5 sites. Species richness varied from 0 to 4 species at each site. Richness scores, the sums of species richness among sites, were similar among methods: 8 for call surveys, 10 for frog-loggers, and 11 for intensive surveys (9 if the non-vocal salamander Ambystoma tigrinum is excluded). The frog-logger at 1 site recorded Spea bombifrons which was not active during the times when call and intensive surveys were conducted. Relative abundance scores from call surveys failed to reflect a relatively large population of Bufo woodhousii at 1 site and only weakly differentiated among different-sized populations of Pseudacris maculata at 3 other sites. For extensive applications, call surveys have the lowest costs and fewest requirements for highly trained personnel. However, for a variety of reasons, call surveys cannot be used with equal effectiveness in all parts of North America.

Regional comparisons of Vs30 and Spectral Ratio Methods

NASA Astrophysics Data System (ADS)

McNamara, D. E.; Gee, L. S.; Stephenson, W. J.; Odum, J. K.; Williams, R. A.; Hartzell, S.

2013-12-01

Earthquake damage is often increased due to local ground-motion amplification in soft soils and thick basin sediments with factors such as topographic effects and water saturation. Seismic hazard assessments depend on detailed information on local site response and many different methods have been developed to estimate site response. Based on numerous empirical studies, the average shear-wave velocity in the upper 30 m (Vs30) has become the most common means of classifying site conditions and has been adopted in the NEHRP design provisions for new buildings. In general, higher Vs30 values are associated with firm, dense rock and lower levels of ground shaking while lower Vs30 values are associated with softer soils and high site amplification. Vs30 is commonly computed by measuring the time it takes for shear-waves to travel from 30m depth to the surface using either active sources such as explosions or passive ambient noise microtremor sources. Since this approach is limited to locations where active measurements are undertaken, recent methods have sought to approximate Vs30 regionally, such as using topographic slope as a proxy. In this presentation, we compute a standard site response, horizontal-to-vertical spectral ratio (HVSR) using long-term power spectral density statistics of both ambient noise and earthquake signals at permanent and temporary seismic stations. We compare the HVSR results to surface observations of Vs30 and approximations using topographic slope in several different regions including the Eastern United States, St. Louis and the Los Angeles basin. In our comparison of the HVSR results to Vs30, we find that HVSR peak frequency can be used as a proxy for Vs30. Relationships between surface measured Vs30 and HVSR are less scattered than with Vs30 estimated using topographic approximations. In general, higher Vs30 is associated with higher HVSR peak frequency with variations in slope for different regions. We use these regional relationships to estimate NEHRP soil class at over 200 seismic stations in the US.

Comparison of ground and satellite based measurements of the fraction of photosynthetically active radiation intercepted by tall-grass prairie

NASA Technical Reports Server (NTRS)

Demetriades-Shah, T. H.; Kanemasu, E. T.; Flitcroft, I.; Su, H.

1990-01-01

The fraction, of photosynthetically active radiation absorbed by vegetation, F sub ipar, is an important requirement for estimating vegetation biomass productivity and related quantities. This was an integral part of a large international effort; the First ISLSCP Field Experiment (FIFE). The main objective of FIFE was to study the effects of vegetation on the land atmosphere interactions and to determine if these interactions can be assessed from satellite spectral measurements. The specific purpose of this experiment was to find out how well measurements of F sub ipar relate to ground, helicopter, and satellite based spectral reflectance measurements. Concurrent measurements of F sub ipar and ground, helicopter, and satellite based measurements were taken at 13 tall grass prairie sites in Kansas. The sites were subjected to various combinations of burning and grazing managements.

Sequencing of the amylopullulanase (apu) gene of Thermoanaerobacter ethanolicus 39E, and identification of the active site by site-directed mutagenesis.

PubMed

Mathupala, S P; Lowe, S E; Podkovyrov, S M; Zeikus, J G

1993-08-05

The complete nucleotide sequence of the gene encoding the dual active amylopullulanase of Thermoanaerobacter ethanolicus 39E (formerly Clostridium thermohydrosulfuricum) was determined. The structural gene (apu) contained a single open reading frame 4443 base pairs in length, corresponding to 1481 amino acids, with an estimated molecular weight of 162,780. Analysis of the deduced sequence of apu with sequences of alpha-amylases and alpha-1,6 debranching enzymes enabled the identification of four conserved regions putatively involved in substrate binding and in catalysis. The conserved regions were localized within a 2.9-kilobase pair gene fragment, which encoded a M(r) 100,000 protein that maintained the dual activities and thermostability of the native enzyme. The catalytic residues of amylopullulanase were tentatively identified by using hydrophobic cluster analysis for comparison of amino acid sequences of amylopullulanase and other amylolytic enzymes. Asp597, Glu626, and Asp703 were individually modified to their respective amide form, or the alternate acid form, and in all cases both alpha-amylase and pullulanase activities were lost, suggesting the possible involvement of 3 residues in a catalytic triad, and the presence of a putative single catalytic site within the enzyme. These findings substantiate amylopullulanase as a new type of amylosaccharidase.

Qzone use and depression among Chinese adolescents: A moderated mediation model.

PubMed

Niu, Geng-Feng; Luo, Yi-Jun; Sun, Xiao-Jun; Zhou, Zong-Kui; Yu, Feng; Yang, Shen-Long; Zhao, Liang

2018-04-15

Social networking sites (SNSs), which provide abundant social comparison opportunities, are ubiquitous around the world, especially among adolescents. In China, Qzone stands out as the most popular SNS. Due to the opportunity it provides for meticulous self-presentation, SNS may give the impression that others are doing better, which is detrimental to individuals' well-being. Based on social comparison theory, the current study aimed to investigate the association between Chinese adolescents' SNS (Qzone) use and depression, as well as the mediating role of negative social comparison and the moderating role of self-esteem. A total of 764 adolescents (aged 12-18 years, M = 14.23, SD = 1.75), who had an active Qzone account, were recruited voluntarily to complete questionnaires on Qzone use intensity, negative social comparison on Qzone, self-esteem, and depression. More intense Qzone use was associated with higher level of negative social comparison on Qzone, which fully mediated the association between Qzone use and depression. Moreover, the mediating effect of negative social comparison on Qzone was moderated by self-esteem. The specific link between Qzone use and negative social comparison was weaker among adolescents with high self-esteem than those with low self-esteem. As all the data in this study were self-reported and cross-sectional, causal associations cannot be identified. Additionally, the specific activities on SNS were not identified. Negative social comparison may be a key factor and mechanism accounting for the positive association between SNS use and depression, while self-esteem could protect adolescents from the adverse outcome of SNS use. Copyright © 2018 Elsevier B.V. All rights reserved.

Assessing the Deepwater Horizon oil spill impact on marine mammal population through acoustics: endangered sperm whales.

PubMed

Ackleh, Azmy S; Ioup, George E; Ioup, Juliette W; Ma, Baoling; Newcomb, Joal J; Pal, Nabendu; Sidorovskaia, Natalia A; Tiemann, Christopher

2012-03-01

Long-term monitoring of endangered species abundance based on acoustic recordings has not yet been pursued. This paper reports the first attempt to use multi-year passive acoustic data to study the impact of the Deepwater Horizon oil spill on the population of endangered sperm whales. Prior to the spill the Littoral Acoustic Demonstration Center (LADC) collected acoustic recordings near the spill site in 2007. These baseline data now provide a unique opportunity to better understand how the oil spill affected marine mammals in the Gulf of Mexico. In September 2010, LADC redeployed recording buoys at previously used locations 9, 25, and 50 miles away from the incident site. A statistical methodology that provides point and interval estimates of the abundance of the sperm whale population at the two nearest sites is presented. A comparison of the 2007 and the 2010 recordings shows a decrease in acoustic activity and abundance of sperm whales at the 9-mile site by a factor of 2, whereas acoustic activity and abundance at the 25-mile site has clearly increased. This indicates that some sperm whales may have relocated farther away from the spill. Follow-up experiments will be important for understanding long-term impact. © 2012 Acoustical Society of America

The dynamics of camphor in the cytochrome P450 CYP101D2

PubMed Central

Vohra, Shabana; Musgaard, Maria; Bell, Stephen G; Wong, Luet-Lok; Zhou, Weihong; Biggin, Philip C

2013-01-01

The recent crystal structures of CYP101D2, a cytochrome P450 protein from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 revealed that both the native (substrate-free) and camphor-soaked forms have open conformations. Furthermore, two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure, one being located in the access channel and the other in a cavity on the surface near the F-helix side of the F-G loop termed the substrate recognition site. These latter sites may be key intermediate positions on the pathway for substrate access to or product egress from the active site. Here, we show via the use of unbiased atomistic molecular dynamics simulations that despite the open conformation of the native and camphor-bound crystal structures, the underlying dynamics of CYP101D2 appear to be very similar to other CYP proteins. Simulations of the native structure demonstrated that the protein is capable of sampling many different conformational substates. At the same time, simulations with the camphor positioned at various locations within the access channel or recognition site show that movement towards the active site or towards bulk solvent can readily occur on a short timescale, thus confirming many previously reported in silico studies using steered molecular dynamics. The simulations also demonstrate how the fluctuations of an aromatic gate appear to control access to the active site. Finally, comparison of camphor-bound simulations with the native simulations suggests that the fluctuations can be of similar level and thus are more representative of the conformational selection model rather than induced fit. PMID:23832606

HTLV-1 Integration into Transcriptionally Active Genomic Regions Is Associated with Proviral Expression and with HAM/TSP

PubMed Central

Meekings, Kiran N.; Leipzig, Jeremy; Bushman, Frederic D.; Taylor, Graham P.; Bangham, Charles R. M.

2008-01-01

Human T-lymphotropic virus type 1 (HTLV-1) causes leukaemia or chronic inflammatory disease in ∼5% of infected hosts. The level of proviral expression of HTLV-1 differs significantly among infected people, even at the same proviral load (proportion of infected mononuclear cells in the circulation). A high level of expression of the HTLV-1 provirus is associated with a high proviral load and a high risk of the inflammatory disease of the central nervous system known as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). But the factors that control the rate of HTLV-1 proviral expression remain unknown. Here we show that proviral integration sites of HTLV-1 in vivo are not randomly distributed within the human genome but are associated with transcriptionally active regions. Comparison of proviral integration sites between individuals with high and low levels of proviral expression, and between provirus-expressing and provirus non-expressing cells from within an individual, demonstrated that frequent integration into transcription units was associated with an increased rate of proviral expression. An increased frequency of integration sites in transcription units in individuals with high proviral expression was also associated with the inflammatory disease HAM/TSP. By comparing the distribution of integration sites in human lymphocytes infected in short-term cell culture with those from persistent infection in vivo, we infer the action of two selective forces that shape the distribution of integration sites in vivo: positive selection for cells containing proviral integration sites in transcriptionally active regions of the genome, and negative selection against cells with proviral integration sites within transcription units. PMID:18369476

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.

PubMed Central

Jeruzalmi, D; Steitz, T A

1998-01-01

The T7 RNA polymerase-T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 A crystal structure of the complex reveals that lysozyme binds at a site remote from the polymerase active site, suggesting an indirect mechanism of inhibition. Comparison of the T7 RNA polymerase structure with that of the homologous pol I family of DNA polymerases reveals identities in the catalytic site but also differences specific to RNA polymerase function. The structure of T7 RNA polymerase presented here differs significantly from a previously published structure. Sequence similarities between phage RNA polymerases and those from mitochondria and chloroplasts, when interpreted in the context of our revised model of T7 RNA polymerase, suggest a conserved fold. PMID:9670025

Rapid assessment of environmental health risks posed by mining operations in low- and middle-income countries: selected case studies.

PubMed

Caravanos, Jack; Ericson, Bret; Ponce-Canchihuamán, Johny; Hanrahan, David; Block, Meredith; Susilorini, Budi; Fuller, Richard

2013-11-01

Previous studies have evaluated associated health risks and human exposure pathways at mining sites. Others have provided estimates of the scale of the issue based in part on surveys. However, a global census of mining-related hazardous waste sites has been lacking. The Toxic Sites Identification Program (TSIP) implemented by Blacksmith Institute (New York, NY, USA) since 2009 is an ongoing effort to catalogue a wide range of chemically contaminated sites with a potential human health risk (Ericson et al., Environ Monit Assess doi:10.1007/s 10661-012-2665-2, 2012). The TSIP utilizes a rapid assessment instrument, the Initial Site Screening (ISS), to quickly and affordably identify key site criteria including human exposure pathways, estimated populations at risk, and sampling information. The resulting ISS allows for comparison between sites exhibiting different contaminants and pollution sources. This paper explores the results of a subset of ISSs completed at 131 artisanal and small-scale gold mining areas and 275 industrial mining and ore processing sites in 45 countries. The authors show that the ISS captures key data points, allowing for prioritization of sites for further investigation or remedial activity.

A method for estimating the incident PAR on inclined surfaces

NASA Astrophysics Data System (ADS)

Xie, Xiaoping; Gao, Wei; Gao, Zhiqiang

2008-08-01

A new simple model has been developed that incorporates Digital Elevation Model (DEM) and Moderate Resolution Imaging Spectroradiometer (MODIS) products to produce incident photosynthetically active radiation (PAR) for tilted surface. The method is based on a simplification of the general radiative transfer equation, which considers five major processes of attenuation of solar radiation: 1) Rayleigh scattering, 2) absorption by ozone and water vapor, 3) aerosol scattering, 4) multiple reflectance between surface and atmosphere, and 5) three terrain factors: slope and aspect, isotropic sky view factor, and additional radiation by neighbor reflectance. A comparison of the model results with observational data from the Yucheng and Changbai Mountain sites of the Chinese Ecosystem Research Network (CERN) shows the correlation coefficient as 0.929 and 0.904, respectively. A comparison of the model results with the 2006 filed measured PAR in the Yucheng and Changbai sites shows the correlation coefficient as 0.929 and 0.904, respectively, and the average percent error as 10% and 15%, respectively.

Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals

PubMed Central

Kim, Chae Un; Song, HyoJin; Avvaru, Balendu Sankara; Gruner, Sol M.; Park, SangYoun; McKenna, Robert

2016-01-01

Carbonic anhydrases are mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO2/HCO3−. Previously, the X-ray crystal structures of CO2-bound holo (zinc-bound) and apo (zinc-free) human carbonic anhydrase IIs (hCA IIs) were captured at high resolution. Here, we present sequential timeframe structures of holo- [T = 0 s (CO2-bound), 50 s, 3 min, 10 min, 25 min, and 1 h] and apo-hCA IIs [T = 0 s, 50 s, 3 min, and 10 min] during the “slow” release of CO2. Two active site waters, WDW (deep water) and WDW′ (this study), replace the vacated space created on CO2 release, and another water, WI (intermediate water), is seen to translocate to the proton wire position W1. In addition, on the rim of the active site pocket, a water W2′ (this study), in close proximity to residue His64 and W2, gradually exits the active site, whereas His64 concurrently rotates from pointing away (“out”) to pointing toward (“in”) active site rotameric conformation. This study provides for the first time, to our knowledge, structural “snapshots” of hCA II intermediate states during the formation of the His64-mediated proton wire that is induced as CO2 is released. Comparison of the holo- and apo-hCA II structures shows that the solvent network rearrangements require the presence of the zinc ion. PMID:27114542

Site occupation of indium and jump frequencies of cadmium in FeGa 3

NASA Astrophysics Data System (ADS)

Newhouse, Randal; Collins, Gary S.; Zacate, Matthew O.

2016-12-01

Perturbed angular correlation (PAC) measurements using the In-111 probe were carried out on FeGa3 as part of a broader investigation of indium site occupation and cadmium diffusion in intermetallic compounds. One PAC signal was observed with hyperfine parameters ω 1= 513.8(1) Mrad/s and η= 0.939(2) at room temperature. By comparison with quadrupole frequencies observed in PAC measurements on isostructural RuIn3, it was determined that indium occupies only the 8j site in the FeGa3 structure, denoted Ga(2) below because two out of the three Ga sites have this point symmetry. PAC spectra at elevated temperature exhibited damping characteristic of electric field gradients (EFGs) that fluctuate as Cd probes jump among Ga(2) sites within the lifetime of the excited PAC level. A stochastic model for the EFG fluctuations based on four conceivable, single-step jump-pathways connecting one Ga(2) site to neighboring Ga(2) sites was developed and used to fit PAC spectra. The four pathways lead to two observable EFG reorientation rates, and these reorientation rates were found to be strongly dependent on EFG orientation. Calculations using density functional theory were used to reduce the number of unknowns in the model with respect to EFG orientation. This made it possible to determine with reasonable precision the total jump rate of Cd among Ga(2) sites that correspond to a change in mirror plane orientation of site-symmetry. This total jump rate was found to be thermally activated with an activation enthalpy of 1.8 ±0.1 eV.

Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.

PubMed

Vetting, Matthew W; Wackett, Lawrence P; Que, Lawrence; Lipscomb, John D; Ohlendorf, Douglas H

2004-04-01

The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.

Preparation of activated carbon monolith by application of phenolic resins as carbon precursors

NASA Astrophysics Data System (ADS)

Sajad, Mehran; Kazemzad, Mahmood; Hosseinnia, Azarmidokht

2014-04-01

In the current work, activated carbon monoliths have been prepared by application of different phenolic hydrocarbons namely catechol and resorcinol as carbon precursors. For synthesis of carbon monolith, the precursors have been mixed with Genapol PF-10 as template and then polymerized in the presence of lysine as catalyst. Then the polymerized monolith carbonized in inert atmosphere at 700°C and activated by water steam at 550°C. It was found that resorcinol polymerization is easier than catechol and occurred at 90°C while for polymerization of catechol elevated temperature of 120°C at hydrothermal condition is necessary. The prepared activated carbon samples have been characterized by various analysis methods including scanning electron microscopy (SEM), surface area measurement, and transmission electron microscopy (TEM). The adsorptions of three different aromatic hydrocarbons by the prepared activated carbon samples have also been investigated by high performance liquid chromatography (HPLC) and UV-Vis spectroscopy. It was found that carbon monolith prepared by catechol as carbon precursor has higher adsorpability and strength in comparison with the other sample. The higher performance of carbon monolith prepared by catechol can be associated with its higher active sites in comparison with resorcinol.

Structural Investigation of a Novel N-Acetyl Glucosamine Binding Chi-Lectin Which Reveals Evolutionary Relationship with Class III Chitinases

PubMed Central

Patil, Dipak N.; Datta, Manali; Dev, Aditya; Dhindwal, Sonali; Singh, Nirpendra; Dasauni, Pushpanjali; Kundu, Suman; Sharma, Ashwani K.; Tomar, Shailly; Kumar, Pravindra

2013-01-01

The glycosyl hydrolase 18 (GH18) family consists of active chitinases as well as chitinase like lectins/proteins (CLPs). The CLPs share significant sequence and structural similarities with active chitinases, however, do not display chitinase activity. Some of these proteins are reported to have specific functions and carbohydrate binding property. In the present study, we report a novel chitinase like lectin (TCLL) from Tamarindus indica. The crystal structures of native TCLL and its complex with N-acetyl glucosamine were determined. Similar to the other CLPs of the GH18 members, TCLL lacks chitinase activity due to mutations of key active site residues. Comparison of TCLL with chitinases and other chitin binding CLPs shows that TCLL has substitution of some chitin binding site residues and more open binding cleft due to major differences in the loop region. Interestingly, the biochemical studies suggest that TCLL is an N-acetyl glucosamine specific chi-lectin, which is further confirmed by the complex structure of TCLL with N-acetyl glucosamine complex. TCLL has two distinct N-acetyl glucosamine binding sites S1 and S2 that contain similar polar residues, although interaction pattern with N-acetyl glucosamine varies extensively among them. Moreover, TCLL structure depicts that how plants utilize existing structural scaffolds ingenuously to attain new functions. To date, this is the first structural investigation of a chi-lectin from plants that explore novel carbohydrate binding sites other than chitin binding groove observed in GH18 family members. Consequently, TCLL structure confers evidence for evolutionary link of lectins with chitinases. PMID:23717482

Proviruses with Long-Term Stable Expression Accumulate in Transcriptionally Active Chromatin Close to the Gene Regulatory Elements: Comparison of ASLV-, HIV- and MLV-Derived Vectors

PubMed Central

Miklík, Dalibor; Šenigl, Filip; Hejnar, Jiří

2018-01-01

Individual groups of retroviruses and retroviral vectors differ in their integration site preference and interaction with the host genome. Hence, immediately after infection genome-wide distribution of integrated proviruses is non-random. During long-term in vitro or persistent in vivo infection, the genomic position and chromatin environment of the provirus affects its transcriptional activity. Thus, a selection of long-term stably expressed proviruses and elimination of proviruses, which have been gradually silenced by epigenetic mechanisms, helps in the identification of genomic compartments permissive for proviral transcription. We compare here the extent and time course of provirus silencing in single cell clones of the K562 human myeloid lymphoblastoma cell line that have been infected with retroviral reporter vectors derived from avian sarcoma/leukosis virus (ASLV), human immunodeficiency virus type 1 (HIV) and murine leukaemia virus (MLV). While MLV proviruses remain transcriptionally active, ASLV proviruses are prone to rapid silencing. The HIV provirus displays gradual silencing only after an extended time period in culture. The analysis of integration sites of long-term stably expressed proviruses shows a strong bias for some genomic features—especially integration close to the transcription start sites of active transcription units. Furthermore, complex analysis of histone modifications enriched at the site of integration points to the accumulation of proviruses of all three groups in gene regulatory segments, particularly close to the enhancer loci. We conclude that the proximity to active regulatory chromatin segments correlates with stable provirus expression in various retroviral species. PMID:29517993

Torpor and basking after a severe wildfire: mammalian survival strategies in a scorched landscape.

PubMed

Matthews, Jaya K; Stawski, Clare; Körtner, Gerhard; Parker, Cassandra A; Geiser, Fritz

2017-02-01

Wildfires can completely obliterate above-ground vegetation, yet some small terrestrial mammals survive during and after fires. As knowledge about the physiological and behavioural adaptations that are crucial for post-wildfire survival is scant, we investigated the thermal biology of a small insectivorous marsupial (Antechinus flavipes) after a severe forest fire. Some populations of antechinus survived the fire in situ probably by hiding deep in rocky crevices, the only fire-proof sites near where they were trapped. We hypothesised that survival in the post-fire landscape was achieved by decreasing daytime activity and using torpor frequently to save energy. Indeed, daytime activity was less common and torpor expression was substantially higher (≥2-fold) at the post-fire site than observed in an unburnt control site and also in comparison to a laboratory study, both when food was provided ad libitum and withheld. Basking in the post-fire site was also recorded, which was likely used to further reduce energy expenditure. Our data suggest that torpor and basking are used by this terrestrial mammal to reduce energy and foraging requirements, which is important in a landscape where food and shelter are limited and predation pressure typically is increased.

Total dissolved gas and water temperature in the lower Columbia River, Oregon and Washington, 2003: Quality-assurance data and comparison to water-quality standards

USGS Publications Warehouse

Tanner, Dwight Q.; Bragg, Heather M.; Johnston, Matthew W.

2003-01-01

The variances to the States of Oregon and Washington water-quality standards for total dissolved gas were exceeded at six of the seven monitoring sites. The sites at Camas and Bonneville forebay had the most days exceeding the variance of 115% saturation. The forebay exceedances may have been the result of the cumulative effects of supersaturated water moving downstream through the lower Columbia River. Apparently, the levels of total dissolved gas did not decrease rapidly enough downstream from the dams before reaching the next site. From mid-July to mid-September, water temperatures were usually above 20 degrees Celsius at each of the seven lower Columbia River sites. According to the Oregon water-quality standard, when the temperature of the lower Columbia River exceeds 20 degrees Celsius, no measurable temperature increase resulting from anthropogenic activities is allowed. Transient increases of about 1 degree Celsius were noted at the John Day forebay site, due to localized solar heating.

Sediment sorting along tidal sand waves: A comparison between field observations and theoretical predictions

NASA Astrophysics Data System (ADS)

Van Oyen, Tomas; Blondeaux, Paolo; Van den Eynde, Dries

2013-07-01

A site-by-site comparison between field observations and theoretical predictions of sediment sorting patterns along tidal sand waves is performed for ten locations in the North Sea. At each site, the observed grain size distribution along the bottom topography and the geometry of the bed forms is described in detail and the procedure used to obtain the model parameters is summarized. The model appears to accurately describe the wavelength of the observed sand waves for the majority of the locations; still providing a reliable estimate for the other sites. In addition, it is found that for seven out of the ten locations, the qualitative sorting process provided by the model agrees with the observed grain size distribution. A discussion of the site-by-site comparison is provided which, taking into account uncertainties in the field data, indicates that the model grasps the major part of the key processes controlling the phenomenon.

Silver nanoparticles anchored reduced graphene oxide for enhanced electrocatalytic activity towards methanol oxidation

NASA Astrophysics Data System (ADS)

Kumar, Sanjeev; Mahajan, Mani; Singh, Rajinder; Mahajan, Aman

2018-02-01

In this report, silver nanoparticles (Ag NPs) anchored reduced graphene oxide (rGO) sheets (rGO/Ag) nanohybrid has been explored as anode material in direct methanol fuel cells (DMFCs). The synthesized rGO/Ag nanohybrid is characterized by XRD, XPS, FTIR spectroscopy and HRTEM techniques. Cyclic voltammograms demonstrate that the rGO/Ag nanohybrid exhibits higher electrocatalytic activity in comparison to rGO sheets for methanol oxidation reaction (MOR). This enhancement is attributed to the synergetic effect produced by the presence of more active sites provided by Ag NPs anchored on a conducting network of large surface area rGO sheets.

Thick-foils activation technique for neutron spectrum unfolding with the MINUIT routine-Comparison with GEANT4 simulations

NASA Astrophysics Data System (ADS)

Vagena, E.; Theodorou, K.; Stoulos, S.

2018-04-01

Neutron activation technique has been applied using a proposed set of twelve thick metal foils (Au, As, Cd, In, Ir, Er, Mn, Ni, Se, Sm, W, Zn) for off-site measurements to obtain the neutron spectrum over a wide energy range (from thermal up to a few MeV) in intense neutron-gamma mixed fields such as around medical Linacs. The unfolding procedure takes into account the activation rates measured using thirteen (n , γ) and two (n , p) reactions without imposing a guess solution-spectrum. The MINUIT minimization routine unfolds a neutron spectrum that is dominated by fast neutrons (70%) peaking at 0.3 MeV, while the thermal peak corresponds to the 15% of the total neutron fluence equal to the epithermal-resonances area. The comparison of the unfolded neutron spectrum against the simulated one with the GEANT4 Monte-Carlo code shows a reasonable agreement within the measurement uncertainties. Therefore, the proposed set of activation thick-foils could be a useful tool in order to determine low flux neutrons spectrum in intense mixed field.

Progress report. Task 1 - quaternary tectonics, 1 October 1991--30 September 1992

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

NONE

1992-09-30

Progress is reported on a study concerned with the quaternary tectonics of Yucca Mountain, the proposed site for an underground disposal facility for high-level radioactive wastes. Refinement and revision of crater Flat Quaternary stratigraphy continued and consisted of several activities: revision of rock varnish cation leaching curve; sample comparison of RV manganese;,iron microlaminations;and correlation of Crater Flat allostratigraphic units with regional chronologies.

Total dissolved gas and water temperature in the lower Columbia River, Oregon and Washington, 2002: Quality-assurance data and comparison to water-quality standards

USGS Publications Warehouse

Tanner, Dwight Q.; Johnston, Matthew W.; Bragg, Heather M.

2002-12-10

From mid-July to mid-September, water temperatures were usually above 20 degrees Celsius at each of the seven lower Columbia River sites in operation. According to the Oregon water-quality standard, when the temperature of the lower Columbia River exceeds 20 degrees Celsius, no measurable temperature increase resulting from anthropogenic activities is allowed.

Crystal structure of KPC-2

PubMed Central

Ke, Wei; Bethel, Christopher R.; Thomson, Jodi M.; Bonomo, Robert A.; van den Akker, Focco

2008-01-01

β-lactamases inactivate β-lactam antibiotics and are a major cause of antibiotic resistance. The recent outbreaks of Klebsiella pneumoniae carbapenem-resistant (KPC) infections mediated by KPC type β-lactamases are creating a serious threat to our “last resort” antibiotics, the carbapenems. KPC β-lactamases are thus carbapenemases and are a subclass of Class A β-lactamases that have evolved to efficiently hydrolyze carbapenems and cephamycins which contain substitutions at the α position proximal to the carbonyl group that normally render these β-lactams resistant to hydrolysis. To investigate the molecular basis of this carbapenemase activity, we have determined the structure of KPC-2 at 1.85Å resolution. The active site of KPC-2 reveals the presence of a bicine buffer molecule which interacts via its carboxyl group with conserved active site residues S130, K234, T235, and T237; this likely resembles the interactions the β-lactam carboxyl moiety makes in the Michaelis-Menten complex. Comparison of the KPC-2 structure with non-carbapenemases and previously determined NMC-A and SME-1 carbapenemase structures shows several active site alterations that are unique among carbapenemases. An outward shift of the catalytic S70 residue renders the active sites of the carbapenemases more shallow likely allowing easier access of the bulkier substrates. Further space for the α-substituents is likely provided by shifts in N132 and N170 in addition to concerted movements in the postulated carboxyl binding pocket that might allow the substrates to bind in a slightly different angle to accommodate these α-substituents. The structure of KPC-2 thus provides key insights into the carbapenemase activity of emerging Class A β-lactamases. PMID:17441734

Direct comparison of the performance of a bio-inspired synthetic nickel catalyst and a [NiFe]-hydrogenase, both covalently attached to electrodes.

PubMed

Rodriguez-Maciá, Patricia; Dutta, Arnab; Lubitz, Wolfgang; Shaw, Wendy J; Rüdiger, Olaf

2015-10-12

The active site of hydrogenases has been a source of inspiration for the development of molecular catalysts. However, direct comparisons between molecular catalysts and enzymes have not been possible because different techniques are used to evaluate both types of catalysts, minimizing our ability to determine how far we have come in mimicking the enzymatic performance. The catalytic properties of the [Ni(P(Cy) 2 N(Gly) 2 )2 ](2+) complex with the [NiFe]-hydrogenase from Desulfovibrio vulgaris immobilized on a functionalized electrode were compared under identical conditions. At pH 7, the enzyme shows higher activity and lower overpotential with better stability, while at low pH, the molecular catalyst outperforms the enzyme in all respects. This is the first direct comparison of enzymes and molecular complexes, enabling a unique understanding of the benefits and detriments of both systems, and advancing our understanding of the utilization of these bio-inspired complexes in fuel cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lateralisation effect in comprehension of emotional facial expression: a comparison between EEG alpha band power and behavioural inhibition (BIS) and activation (BAS) systems.

PubMed

Balconi, Michela; Mazza, Guido

2010-05-01

Asymmetry in comprehension of facial expression of emotions was explored in the present study by analysing alpha band variation within the right and left cortical sides. Second, the behavioural activation system (BAS) and behavioural inhibition system (BIS) were considered as an explicative factor to verify the effect of a motivational/emotional variable on alpha activity. A total of 19 participants looked at an ample range of facial expressions of emotions (anger, fear, surprise, disgust, happiness, sadness, and neutral) in random order. The results demonstrated that anterior frontal sites were more active than central and parietal sites in response to facial stimuli. Moreover, right and left side responses varied as a function of emotional types, with an increased right frontal activity for negative, aversive emotions vs an increased left response for positive emotion. Finally, whereas higher BIS participants generated more right hemisphere activation for some negative emotions (such as fear, anger, surprise, and disgust), BAS participants were more responsive to positive emotion (happiness) within the left hemisphere. Motivational significance of facial expressions was considered to elucidate cortical differences in participants' responses to emotional types.

Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

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

Chang, Soo-Ik; Hammes, G.G.

1989-11-01

Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chickenmore » and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the {beta}-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution.« less

Evolutionary Analysis of Functional Divergence among Chemokine Receptors, Decoy Receptors, and Viral Receptors

PubMed Central

Daiyasu, Hiromi; Nemoto, Wataru; Toh, Hiroyuki

2012-01-01

Chemokine receptors (CKRs) function in the inflammatory response and in vertebrate homeostasis. Decoy and viral receptors are two types of CKR homologs with modified functions from those of the typical CKRs. The decoy receptors are able to bind ligands without signaling. On the other hand, the viral receptors show constitutive signaling without ligands. We examined the sites related to the functional difference. At first, the decoy and viral receptors were each classified into five groups, based on the molecular phylogenetic analysis. A multiple amino acid sequence alignment between each group and the CKRs was then constructed. The difference in the amino acid composition between the group and the CKRs was evaluated as the Kullback–Leibler (KL) information value at each alignment site. The KL information value is considered to reflect the difference in the functional constraints at the site. The sites with the top 5% of KL information values were selected and mapped on the structure of a CKR. The comparisons with decoy receptor groups revealed that the detected sites were biased on the intracellular side. In contrast, the sites detected from the comparisons with viral receptor groups were found on both the extracellular and intracellular sides. More sites were found in the ligand binding pocket in the analyses of the viral receptor groups, as compared to the decoy receptor groups. Some of the detected sites were located in the GPCR motifs. For example, the DRY motif of the decoy receptors was often degraded, although the motif of the viral receptors was basically conserved. The observations for the viral receptor groups suggested that the constraints in the pocket region are loose and that the sites on the intracellular side are different from those for the decoy receptors, which may be related to the constitutive signaling activity of the viral receptors. PMID:22855685

Evolutionary Analysis of Functional Divergence among Chemokine Receptors, Decoy Receptors, and Viral Receptors.

PubMed

Daiyasu, Hiromi; Nemoto, Wataru; Toh, Hiroyuki

2012-01-01

Chemokine receptors (CKRs) function in the inflammatory response and in vertebrate homeostasis. Decoy and viral receptors are two types of CKR homologs with modified functions from those of the typical CKRs. The decoy receptors are able to bind ligands without signaling. On the other hand, the viral receptors show constitutive signaling without ligands. We examined the sites related to the functional difference. At first, the decoy and viral receptors were each classified into five groups, based on the molecular phylogenetic analysis. A multiple amino acid sequence alignment between each group and the CKRs was then constructed. The difference in the amino acid composition between the group and the CKRs was evaluated as the Kullback-Leibler (KL) information value at each alignment site. The KL information value is considered to reflect the difference in the functional constraints at the site. The sites with the top 5% of KL information values were selected and mapped on the structure of a CKR. The comparisons with decoy receptor groups revealed that the detected sites were biased on the intracellular side. In contrast, the sites detected from the comparisons with viral receptor groups were found on both the extracellular and intracellular sides. More sites were found in the ligand binding pocket in the analyses of the viral receptor groups, as compared to the decoy receptor groups. Some of the detected sites were located in the GPCR motifs. For example, the DRY motif of the decoy receptors was often degraded, although the motif of the viral receptors was basically conserved. The observations for the viral receptor groups suggested that the constraints in the pocket region are loose and that the sites on the intracellular side are different from those for the decoy receptors, which may be related to the constitutive signaling activity of the viral receptors.

Mercury transfer from soil to olive trees. A comparison of three different contaminated sites.

PubMed

Higueras, Pablo L; Amorós, José Á; Esbrí, José Maria; Pérez-de-los-Reyes, Caridad; López-Berdonces, Miguel A; García-Navarro, Francisco J

2016-04-01

Mercury contents in soil and olive tree leaves have been studied in 69 plots around three different source areas of this element in Spain: Almadén (Ciudad Real), Flix (Tarragona) and Jódar (Jaén). Almadén was the world's largest cinnabar (HgS) mining district and was active until 2003, Flix is the oldest Spanish chlor-alkali plant (CAP) and has been active from 1898 to the present day and Jódar is a decommissioned CAP that was active for 14 years (1977-1991). Total mercury contents have been measured by high-frequency modulation atomic absorption spectrometry with Zeeman effect (ZAAS-HFM) in the soils and olive tree leaves from the three studied areas. The average soil contents range from 182 μg kg(-1) in Flix to 23,488 μg kg(-1) in Almadén, while the average leaf content ranges from 161 μg kg(-1) in Jódar to 1213 μg kg(-1) in Almadén. Despite the wide range of data, a relationship between soil-leaf contents has been identified: in Almadén and Jódar, multiplicative (bilogarithmic) models show significant correlations (R = 0.769 and R = 0.484, respectively). Significant correlations were not identified between soil and leaf contents in Flix. The continuous activity of the Flix CAP, which remains open today, can explain the different uptake patterns for mercury, which is mainly atmospheric in origin, in comparison to the other two sites, where activity ceased more than 10 years ago and only soil uptake patterns based on the Michaelis-Menten enzymatic model curve are observed.

Benchmarking in pathology: development of an activity-based costing model.

PubMed

Burnett, Leslie; Wilson, Roger; Pfeffer, Sally; Lowry, John

2012-12-01

Benchmarking in Pathology (BiP) allows pathology laboratories to determine the unit cost of all laboratory tests and procedures, and also provides organisational productivity indices allowing comparisons of performance with other BiP participants. We describe 14 years of progressive enhancement to a BiP program, including the implementation of 'avoidable costs' as the accounting basis for allocation of costs rather than previous approaches using 'total costs'. A hierarchical tree-structured activity-based costing model distributes 'avoidable costs' attributable to the pathology activities component of a pathology laboratory operation. The hierarchical tree model permits costs to be allocated across multiple laboratory sites and organisational structures. This has enabled benchmarking on a number of levels, including test profiles and non-testing related workload activities. The development of methods for dealing with variable cost inputs, allocation of indirect costs using imputation techniques, panels of tests, and blood-bank record keeping, have been successfully integrated into the costing model. A variety of laboratory management reports are produced, including the 'cost per test' of each pathology 'test' output. Benchmarking comparisons may be undertaken at any and all of the 'cost per test' and 'cost per Benchmarking Complexity Unit' level, 'discipline/department' (sub-specialty) level, or overall laboratory/site and organisational levels. We have completed development of a national BiP program. An activity-based costing methodology based on avoidable costs overcomes many problems of previous benchmarking studies based on total costs. The use of benchmarking complexity adjustment permits correction for varying test-mix and diagnostic complexity between laboratories. Use of iterative communication strategies with program participants can overcome many obstacles and lead to innovations.

Inter-comparison of source apportionment of PM10 using PMF and CMB in three sites nearby an industrial area in central Italy

NASA Astrophysics Data System (ADS)

Cesari, Daniela; Donateo, Antonio; Conte, Marianna; Contini, Daniele

2016-12-01

Receptor models (RMs), based on chemical composition of particulate matter (PM), such as Chemical Mass Balance (CMB) and Positive Matrix Factorization (PMF), represent useful tools for determining the impact of PM sources to air quality. This information is useful, especially in areas influenced by anthropogenic activities, to plan mitigation strategies for environmental management. Recent inter-comparison of source apportionment (SA) results showed that one of the difficulties in the comparison of estimated source contributions is the compatibility of the sources, i.e. the chemical profiles of factor/sources used in receptor models. This suggests that SA based on integration of several RMs could give more stable and reliable solutions with respect to a single model. The aim of this work was to perform inter-comparison of PMF (using PMF3.0 and PMF5.0 codes) and CMB outputs, focusing on both source chemical profiles and estimates of source contributions. The dataset included 347 daily PM10 samples collected in three sites in central Italy located near industrial emissions. Samples were chemically analysed for the concentrations of 21 chemical species (NH4+, Ca2 +, Mg2 +, Na+, K+, Mg2 +, SO42 -, NO3-, Cl-, Si, Al, Ti, V, Mn, Fe, Ni, Cu, Zn, Br, EC, and OC) used as input of RMs. The approach identified 9 factor/sources: marine, traffic, resuspended dust, biomass burning, secondary sulphate, secondary nitrate, crustal, coal combustion power plant and harbour-industrial. Results showed that the application of constraints in PMF5.0 improved interpretability of profiles and comparability of estimated source contributions with stoichiometric calculations. The inter-comparison of PMF and CMB gave significant differences for secondary nitrate, biomass burning, and harbour-industrial sources, due to non-compatibility of these source profiles that have local specificities. When these site-dependent specificities were taken into account, optimising the input source profiles of CMB, a significant improvement in the comparison of the estimated source contributions with PMF was obtained.

Comparison of essential oil components and in vitro anticancer activity in wild and cultivated Salvia verbenaca.

PubMed

Russo, Alessandra; Cardile, Venera; Graziano, Adriana C E; Formisano, Carmen; Rigano, Daniela; Canzoneri, Marisa; Bruno, Maurizio; Senatore, Felice

2015-01-01

The objectives of our research were to study the chemical composition and the in vitro anticancer effect of the essential oil of Salvia verbenaca growing in natural sites in comparison with those of cultivated (Sc) plants. The oil from wild (Sw) S. verbenaca presented hexadecanoic acid (23.1%) as the main constituent, while the oil from Sc plants contained high quantities of hexahydrofarnesyl acetone (9.7%), scarce in the natural oil (0.7%). The growth-inhibitory and proapoptotic effects of the essential oils from Sw and Sc S. verbenaca were evaluated in the human melanoma cell line M14, testing cell vitality, cell membrane integrity, genomic DNA fragmentation and caspase-3 activity. Both the essential oils were able to inhibit the growth of the cancer cells examined inducing also apoptotic cell death, but the essential oil from cultivated samples exhibited the major effects.

Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs.

PubMed

Pavkov-Keller, Tea; Bakhuis, Janny; Steinkellner, Georg; Jolink, Fenneke; Keijmel, Esther; Birner-Gruenberger, Ruth; Gruber, Karl

2016-10-10

Hydroxynitrile lyases (HNLs) catalyze the asymmetric addition of HCN to aldehydes producing enantiomerically pure cyanohydrins. These enzymes can be heterologously expressed in large quantities making them interesting candidates for industrial applications. The HNLs from Rosaceae evolved from flavin dependent dehydrogenase/oxidase structures. Here we report the high resolution X-ray structure of the highly glycosylated Prunus amygdalus HNL isoenzyme5 (PaHNL5 V317A) expressed in Aspergillus niger and its complex with benzyl alcohol. A comparison with the structure of isoenzyme PaHNL1 indicates a higher accessibility to the active site and a larger cavity for PaHNL5. Additionally, the PaHNL5 complex structure with benzyl alcohol was compared with the structurally related aryl-alcohol oxidase (AAO). Even though both enzymes contain an FAD-cofactor and histidine residues at crucial positions in the active site, PaHNL5 lacks the oxidoreductase activity. The structures indicate that in PaHNLs benzyl alcohol is bound too far away from the FAD cofactor in order to be oxidized. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases

PubMed Central

Turk, Dušan; Janjić, Vojko; Štern, Igor; Podobnik, Marjetka; Lamba, Doriano; Weis Dahl, Søren; Lauritzen, Connie; Pedersen, John; Turk, Vito; Turk, Boris

2001-01-01

Dipeptidyl peptidase I (DPPI) or cathepsin C is the physiological activator of groups of serine proteases from immune and inflammatory cells vital for defense of an organism. The structure presented shows how an additional domain transforms the framework of a papain-like endopeptidase into a robust oligomeric protease-processing enzyme. The tetrahedral arrangement of the active sites exposed to solvent allows approach of proteins in their native state; the massive body of the exclusion domain fastened within the tetrahedral framework excludes approach of a polypeptide chain apart from its termini; and the carboxylic group of Asp1 positions the N-terminal amino group of the substrate. Based on a structural comparison and interactions within the active site cleft, it is suggested that the exclusion domain originates from a metallo-protease inhibitor. The location of missense mutations, characterized in people suffering from Haim–Munk and Papillon–Lefevre syndromes, suggests how they disrupt the fold and function of the enzyme. PMID:11726493

An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

PubMed Central

Knutson, Stacy T.; Westwood, Brian M.; Leuthaeuser, Janelle B.; Turner, Brandon E.; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D.; Harper, Angela F.; Brown, Shoshana D.; Morris, John H.; Ferrin, Thomas E.; Babbitt, Patricia C.

2017-01-01

Abstract Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. PMID:28054422

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

PubMed

Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

2017-04-01

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Field Measurements Indicate Unexpected, Serious Underestimation of Mussel Heart Rates and Thermal Tolerance by Laboratory Studies

PubMed Central

Tagliarolo, Morgana; McQuaid, Christopher D.

2016-01-01

Attempts to predict the response of species to long-term environmental change are generally based on extrapolations from laboratory experiments that inevitably simplify the complex interacting effects that occur in the field. We recorded heart rates of two genetic lineages of the brown mussel Perna perna over a full tidal cycle in-situ at two different sites in order to evaluate the cardiac responses of the two genetic lineages present on the South African coast to temperature and the immersion/emersion cycle. “Robomussel” temperature loggers were used to monitor thermal conditions at the two sites over one year. Comparison with live animals showed that robomussels provided a good estimate of mussel body temperatures. A significant difference in estimated body temperatures was observed between the sites and the results showed that, under natural conditions, temperatures regularly approach or exceed the thermal limits of P. perna identified in the laboratory. The two P. perna lineages showed similar tidal and diel patterns of heart rate, with higher cardiac activity during daytime immersion and minimal values during daytime emersion. Comparison of the heart rates measured in the field with data previously measured in the laboratory indicates that laboratory results seriously underestimate heart rate activity, by as much as 75%, especially during immersion. Unexpectedly, field estimates of body temperatures indicated an ability to tolerate temperatures considered lethal on the basis of laboratory measurements. This suggests that the interaction of abiotic conditions in the field does not necessarily raise vulnerability to high temperatures. PMID:26840775

Evaluation of permeable fractures in rock aquifers

NASA Astrophysics Data System (ADS)

Bok Lee, Hang

2015-04-01

In this study, the practical usefulness and fundamental applicability of a self-potential (SP) method for identifying the permeable fractures were evaluated by a comparison of SP methods with other geophysical logging methods and hydraulic tests. At a 10 m-shallow borehole in the study site, the candidates of permeable fractures crossing the borehole were first determined by conventional geophysical methods such as an acoustic borehole televiwer, temperature, electrical conductivity and gamma-gamma loggings, which was compared to the analysis by the SP method. Constant pressure injection and recovery tests were conducted for verification of the hydraulic properties of the fractures identified by various logging methods. The acoustic borehole televiwer and gamma-gamma loggings detected the open space or weathering zone within the borehole, but they cannot prove the possibility of a groundwater flow through the detected fractures. The temperature and electrical conductivity loggings had limitations to detect the fractured zones where groundwater in the borehole flows out to the surrounding rock aquifers. Comparison of results from different methods showed that there is a best correlation between the distribution of hydraulic conductivity and the variation of the SP signals, and the SP logging can estimate accurately the hydraulic activity as well as the location of permeable fractures. Based on the results, the SP method is recommended for determining the hydraulically-active fractures rather than other conventional geophysical loggings. This self-potential method can be effectively applied in the initial stage of a site investigation which selects the optimal location and evaluates the hydrogeological property of fractures in target sites for the underground structure including the geothermal reservoir and radioactive waste disposal.

Calcium-stimulated autophosphorylation site of plant chimeric calcium/calmodulin-dependent protein kinase

NASA Technical Reports Server (NTRS)

Sathyanarayanan, P. V.; Siems, W. F.; Jones, J. P.; Poovaiah, B. W.

2001-01-01

The existence of two molecular switches regulating plant chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK), namely the C-terminal visinin-like domain acting as Ca(2+)-sensitive molecular switch and calmodulin binding domain acting as Ca(2+)-stimulated autophosphorylation-sensitive molecular switch, has been described (Sathyanarayanan, P. V., Cremo, C. R., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 30417-30422). Here we report the identification of Ca(2+)-stimulated autophosphorylation site of CCaMK by matrix-assisted laser desorption ionization time of flight-mass spectrometry. Thr(267) was confirmed as the Ca(2+)-stimulated autophosphorylation site by post-source decay experiments and by site-directed mutagenesis. The purified T267A mutant form of CCaMK did not show Ca(2+)-stimulated autophosphorylation, autophosphorylation-dependent variable calmodulin affinity, or Ca(2+)/calmodulin stimulation of kinase activity. Sequence comparison of CCaMK from monocotyledonous plant (lily) and dicotyledonous plant (tobacco) suggests that the autophosphorylation site is conserved. This is the first identification of a phosphorylation site specifically responding to activation by second messenger system (Ca(2+) messenger system) in plants. Homology modeling of the kinase and calmodulin binding domain of CCaMK with the crystal structure of calcium/calmodulin-dependent protein kinase 1 suggests that the Ca(2+)-stimulated autophosphorylation site is located on the surface of the kinase and far from the catalytic site. Analysis of Ca(2+)-stimulated autophosphorylation with increasing concentration of CCaMK indicates the possibility that the Ca(2+)-stimulated phosphorylation occurs by an intermolecular mechanism.

Price comparisons on the internet based on computational intelligence.

PubMed

Kim, Jun Woo; Ha, Sung Ho

2014-01-01

Information-intensive Web services such as price comparison sites have recently been gaining popularity. However, most users including novice shoppers have difficulty in browsing such sites because of the massive amount of information gathered and the uncertainty surrounding Web environments. Even conventional price comparison sites face various problems, which suggests the necessity of a new approach to address these problems. Therefore, for this study, an intelligent product search system was developed that enables price comparisons for online shoppers in a more effective manner. In particular, the developed system adopts linguistic price ratings based on fuzzy logic to accommodate user-defined price ranges, and personalizes product recommendations based on linguistic product clusters, which help online shoppers find desired items in a convenient manner.

Price Comparisons on the Internet Based on Computational Intelligence

PubMed Central

Kim, Jun Woo; Ha, Sung Ho

2014-01-01

Information-intensive Web services such as price comparison sites have recently been gaining popularity. However, most users including novice shoppers have difficulty in browsing such sites because of the massive amount of information gathered and the uncertainty surrounding Web environments. Even conventional price comparison sites face various problems, which suggests the necessity of a new approach to address these problems. Therefore, for this study, an intelligent product search system was developed that enables price comparisons for online shoppers in a more effective manner. In particular, the developed system adopts linguistic price ratings based on fuzzy logic to accommodate user-defined price ranges, and personalizes product recommendations based on linguistic product clusters, which help online shoppers find desired items in a convenient manner. PMID:25268901

Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

2015-04-01

On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC bacteria. Therefore the applicability of on-site enzymatic activity determination as a direct surrogate or proxy parameter for microbiological standard assays and quantification of fecal indicator bacteria (FIB) concentration could not be approved and further research in this field is necessary. Presently we conclude that rapid on-site detection of enzymatic activity is applicable for surface water monitoring and that it constitutes a complementary on-site monitoring parameter with high potential. Selection of the type of measured enzymatic activities has to be done on a catchment-specific basis and further work is needed to learn more about its detailed information characteristics in different habitats. The accomplishment of this method detecting continuous data of enzymatic activity in high temporal resolution caused by a target bacterial member is on the way of becoming a powerful tool for water quality monitoring, health related water quality- and early warning requirements.

The value of redundant measurements - highlights from AmeriFlux site visits using a portable eddy covariance system

NASA Astrophysics Data System (ADS)

Chan, S.; Billesbach, D. P.; Hanson, C. V.; Dengel, S.; Polonik, P.; Biraud, S.

2016-12-01

The AmeriFlux network conducts independent site visits using a portable eddy covariance system (PECS). Short-term (<2 weeks), side-by-side comparisons enable the network to evaluate inter-comparability between sites, improve data quality, and assess measurement uncertainty across the network. The PECS includes commonly used sensors for turbulent flux, radiation, and meteorological measurements which are maintained and calibrated using established best practices at levels at or above the manufacturer's recommendations. The importance of site visits was realized at the inception of the AmeriFlux network with the first site visit in 1997. Since that time, more than 180 site visits at over 120 different sites have been conducted. Site visit reports over the years have led to many key findings and important advances within the flux community which are highlighted in the presentation. Furthermore, we summarize and synthesize results from recent site comparisons that were conducted with the latest generation of the PECS (2013-present). The presentation quantifies observed differences between the PECS and network sites for key flux, radiation, and meteorological metrics. The aggregated comparisons provide insight into comparability amongst network sites as well as areas for improvement. We identify common errors and issues and discuss some best practices.

Ultrastructural studies of synthetic apatite crystals.

PubMed

Arends, J; Jongebloed, W L

1979-03-01

In this paper a survey is given of some ultrastructural properties of synthetic hydroxyapatite. The preparation method by which single crystals with a length in the range of 0.1-3.0mm and a defined purity and stoïchiometry can be produced is given. Two groups of materials are considered in detail: carbonate-rich (greater than 0.1% CO3) and low-carbonate hydroxyapatites. The experiments on carbonate-rich material, being the most interesting from a biological point of view, show that acids attack at an active site in the hexagonal basal-plane of the crystals. Later on the crystals dissolve in the center of the crystal parallel to the c-axis forming tube-like structures. The active site can be protected from dissolution if the crystals are pretreated by EHDP or MFP. A comparison with lattice defect theory shows that most likely dislocations of the "hollow-core" type are responsible for the preferential dissolution.

Adaptive biochemical and physiological responses of Eriobotrya japonica to fluoride air pollution.

PubMed

Elloumi, Nada; Zouari, Mohamed; Mezghani, Imed; Ben Abdallah, Ferjani; Woodward, Steve; Kallel, Monem

2017-09-01

The biochemical and physiological effects of fluoride were investigated in loquat trees (Eriobotrya japonica) grown in the vicinity of a phosphate fertilizer plant in Tunisia. Photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (E), superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) activities were assessed; along with photosynthetic pigments, lipid peroxidation, electrolytic leakage (EL) and total phenolic contents in foliage and roots of trees at different distances from the phosphate fertilizer plant. All assessed parameters showed significant discrepancies in comparison with unpolluted sites. Obtained results showed high oxidative stress indices including H 2 O 2 , lipid peroxidation, and EL, SOD, CAT and GPx activities and proline contents in leaves and roots at the polluted sites as compared to control. In contrast, leaf Pn, Gs, E and photosynthetic pigment contents were low as compared to the control. These results indicate that even though antioxidant responses increased near the factory, adverse effects on physiology were pronounced.

Understanding the conformation transition in the activation pathway of β2 adrenergic receptor via a targeted molecular dynamics simulation.

PubMed

Xiao, Xiuchan; Zeng, Xiaojun; Yuan, Yuan; Gao, Nan; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

2015-01-28

G protein coupled receptors (GPCRs) play a crucial role in regulating signal recognition and transduction through their activation. The conformation transition in the activation pathway is of particular importance for their function. However, it has been poorly elucidated due to experimental difficulties in determining the conformations and the time limitation of conventional molecular dynamics (CMD) simulation. Thus, in this work, we employed a targeted molecular dynamic (TMD) simulation to study the activation process from an inactive structure to a fully active one for β2 adrenergic receptor (β2AR). As a reference, 110 ns CMD simulations on wild β2AR and its D130N mutant were also carried out. TMD results show that there is at least an intermediate conformation cluster in the activation process, evidenced by the principal component analysis and the structural and dynamic differences of some important motifs. It is noteworthy that the activation of the ligand binding site lags the G-protein binding site, displaying uncoupled correlation. Comparisons between the CMD and TMD results show that the D130N mutation significantly speeds up ICL2 and key ionic lock to enter into the intermediate state, which to some extent facilitates the activation involved in the NPxxY, DRY region and the separation between TM3 and TM6. However, the contribution from the D130N mutation to the activation of the ligand binding site could not be observed within the scale of 110 ns time. These observations could provide novel insights into previous studies for better understanding of the activation mechanism for β2AR.

Ground-motion site effects from multimethod shear-wave velocity characterization at 16 seismograph stations deployed for aftershocks of the August 2011 Mineral, Virginia earthquake

USGS Publications Warehouse

Stephenson, William J.; Odum, Jackson K.; McNamara, Daniel E.; Williams, Robert A.; Angster, Stephen J

2014-01-01

We characterize shear-wave velocity versus depth (Vs profile) at 16 portable seismograph sites through the epicentral region of the 2011 Mw 5.8 Mineral (Virginia, USA) earthquake to investigate ground-motion site effects in the area. We used a multimethod acquisition and analysis approach, where active-source horizontal shear (SH) wave reflection and refraction as well as active-source multichannel analysis of surface waves (MASW) and passive-source refraction microtremor (ReMi) Rayleigh wave dispersion were interpreted separately. The time-averaged shear-wave velocity to a depth of 30 m (Vs30), interpreted bedrock depth, and site resonant frequency were estimated from the best-fit Vs profile of each method at each location for analysis. Using the median Vs30 value (270–715 m/s) as representative of a given site, we estimate that all 16 sites are National Earthquake Hazards Reduction Program (NEHRP) site class C or D. Based on a comparison of simplified mapped surface geology to median Vs30 at our sites, we do not see clear evidence for using surface geologic units as a proxy for Vs30 in the epicentral region, although this may primarily be because the units are similar in age (Paleozoic) and may have similar bulk seismic properties. We compare resonant frequencies calculated from ambient noise horizontal:vertical spectral ratios (HVSR) at available sites to predicted site frequencies (generally between 1.9 and 7.6 Hz) derived from the median bedrock depth and average Vs to bedrock. Robust linear regression of HVSR to both site frequency and Vs30 demonstrate moderate correlation to each, and thus both appear to be generally representative of site response in this region. Based on Kendall tau rank correlation testing, we find that Vs30 and the site frequency calculated from average Vs to median interpreted bedrock depth can both be considered reliable predictors of weak-motion site effects in the epicentral region.

Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1†,‡

PubMed Central

McCormick, Michael S.; Lippard, Stephen J.

2011-01-01

In all structurally characterized bacterial multicomponent monooxygenase (BMM) hydroxylase proteins, a series of hydrophobic cavities in the α-subunit trace a conserved path from the protein exterior to the carboxylate-bridged diiron active site. The present study examines these cavities as a potential route for dioxygen transport to the active site by crystallographic characterization of a xenon-pressurized sample of the hydroxylase component of phenol hydroxylase from Pseudomonas sp. OX1. Computational analyses of the hydrophobic cavities in the hydroxylase α-subunits of phenol hydroxylase (PHH), toluene/o-xylene monooxygenase (ToMOH), and soluble methane monooxygenase (sMMOH) are also presented. The results, together with previous findings from crystallographic studies of xenon-pressurized sMMO hydroxylase, clearly identify the propensity for these cavities to bind hydrophobic gas molecules in the protein interior. This proposed functional role is supported by recent stopped flow kinetic studies of ToMOH variants (Song, et al., 2011). In addition to information about the Xe sites, the structure determination revealed significantly reduced regulatory protein binding to the hydroxylase in comparison to the previously reported structure of PHH, as well as the presence of a newly identified metal binding site in the α-subunit that adopts a linear coordination environment consistent with Cu(I), and a glycerol molecule bound to Fe1 in a fashion that is unique among hydrocarbon-diiron site adducts reported to date in BMM hydroxylase structures. Finally, a comparative analysis of the α-subunit structures of MMOH, ToMOH, and PHH details proposed routes for the other three BMM substrates, the hydrocarbon, electrons, and protons, comprising cavities, channels, hydrogen-bonding networks, and pores in the structures of their α-subunits. PMID:22136180

Environmental studies conducted at the Fenton Hill Hot Dry Rock geothermal development site

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

Miera, F.R. Jr.; Langhorst, G.; McEllin, S.

1984-05-01

An environmental investigation of Hot Dry Rock (HDR) geothermal development was conducted at Fenton Hill, New Mexico, during 1976-1979. Activities at the Fenton Hill Site included an evaluation of baseline data for biotic and abiotic ecosystem components. Identification of contaminants produced by HDR processes that had the potential for reaching the surrounding environment is also discussed. Three dominant vegetative communities were identified in the vicinity of the site. These included grass-forb, aspen, and mixed conifer communities. The grass-forb area was identified as having the highest number of species encountered, with Phleum pratense and Dactylis glomerata being the dominant grass species.more » Frequency of occurrence and mean coverage values are also given for other species in the three main vegetative complexes. Live trapping of small mammals was conducted to determine species composition, densities, population, and diversity estimates for this component of the ecosystem. The data indicate that Peromyscus maniculatus was the dominant species across all trapping sites during the study. Comparisons of relative density of small mammals among the various trapping sites show the grass-forb vegetative community to have had the highest overall density. Comparisons of small mammal diversity for the three main vegetative complexes indicate that the aspen habitat had the highest diversity and the grass-forb habitat had the lowest. Analyses of waste waters from the closed circulation loop indicate that several trace contaminants (e.g., arsenic, cadmium, fluoride, boron, and lithium) were present at concentrations greater than those reported for surface waters of the region.« less

Comparison of shear-wave slowness profiles at 10 strong-motion sites from noninvasive SASW measurements and measurements made in boreholes

USGS Publications Warehouse

Brown, L.T.; Boore, D.M.; Stokoe, K.H.

2002-01-01

The spectral-analysis-of-surface-waves (SASW) method is a relatively new in situ method for determining shear-wave slownesses. All measurements are made on the ground surface, making it much less costly than methods that require boreholes. The SASW method uses a number of active sources (ranging from a commercial Vibroseis truck to a small handheld hammer for the study conducted here) and different receiver spacings to map a curve of apparent phase velocity versus frequency. With the simplifying assumption that the phase velocities correspond to fundamental mode surface waves, forward modeling yields an estimate of the sub-surface shear-wave slownesses. To establish the reliability of this indirect technique, we conducted a blind evaluation of the SASW method. SASW testing was performed at 10 strong-motion stations at which borehole seismic measurements were previously or subsequently made; if previously made, the borehole results were not used for the interpretation of the SASW data, and vice-versa. Comparisons of the shear-wave slownesses from the SASW and borehole measurements are generally very good. The differences in predicted ground-motion amplifications are less than about 15% for most frequencies. In addition, both methods gave the same NEHRP site classification for seven of the sites. For the other three sites the average velocities from the downhole measurements were only 5-13 m/sec larger than the velocity defining the class C/D boundary. This study demonstrates that in many situations the SASW method can provide subsurface information suitable for site response predictions.

Site-specific surveillance project at the Koppers Company, Inc. , National Priorities List Site, Texarkana, Texas. Final report, March 1994

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

Not Available

A site-specific surveillance project was conducted at the Koppers Company, a National Priorities List site. The findings indicated that living in the Koppers area was associated with a higher prevalance of reported rashes than among residents of a similar neighborhood in Texarkana not located near this site. Koppers residents did not appear to have higher rates of either adverse pregnancy outcomes or cancer than comparison residents. They did have many more concerns about their soil, water, and chemical odors in their neighborhood than did residents of the comparison neighborhood.

Preparation and Characterization of Mesoporous Nickel derived from Liquid crystalline Template and Evaluation of its Electro catalytic activity towards Methanol Oxidation

NASA Astrophysics Data System (ADS)

Mohanapriya, S.; Renuka devi, R.; Raj, V.

2018-02-01

Mesoporous Nickel has been prepared by electrodeposition using non-ionic surfactant based liquid crystalline template under optimized processing conditions. Physico-chemical properties of mesoporous nickel is systematically characterized through XRD, SEM and AFM analyses. Comparison of electrocatalytic activity of mesoporous nickel with smooth nickel was interrogated using cyclic voltammetry (CV), chronoamperometry (CA) and electrochemical impedance spectroscopy (EIS) analyses. Distinctly enhanced electrocatalytic activity with improved surface poisoning resistance related to mesoporous nickel electrode towards methanol oxidation stems from unique mesoporous morphology. This mesoporous morphology with high surface to volume ratio is highly beneficial to promote active catalytic centers to offer readily accessible Pt catalytic sites for MOR, through facilitating mass and electron transports.

Exploring the interaction of patient activation and message design variables: message frame and presentation mode influence on the walking behavior of patients with type 2 diabetes.

PubMed

Ledford, Christy J W

2012-10-01

Examining interpersonal (physician-patient) communication strategies for promoting walking exercise to patients with type 2 diabetes assigned to primary care clinics, the study evaluated two message design variables--frame and presentation mode--as influencers of communication and adoption success. The single-site, four-week, prospective intervention study followed a 2×3 factorial, non-equivalent comparison group quasi-experimental design. Results showed frame was significantly related to steps walked; however, when including patient activation as an interaction, frame was non-significant. The model including patient activation interactions, however, detected significant mode effects on behavior. Results provide evidence that statistics are most effectively used with activated patients.

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid–base catalysis

PubMed Central

Schultz, Eric P.; Vasquez, Ernesto E.; Scott, William G.

2014-01-01

The hammerhead ribozyme catalyzes RNA cleavage via acid–base catalysis. Whether it does so by general acid–base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid–base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK a of the substituted purine; in both cases inosine, which is similar to G in pK a and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data. PMID:25195740

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

PubMed

Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

2014-09-01

The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.

A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase.

PubMed

Jimenez-Sandoval, Pedro; Vique-Sanchez, Jose Luis; Hidalgo, Marisol López; Velazquez-Juarez, Gilberto; Diaz-Quezada, Corina; Arroyo-Navarro, Luis Fernando; Moran, Gabriela Montero; Fattori, Juliana; Jessica Diaz-Salazar, A; Rudiño-Pinera, Enrique; Sotelo-Mundo, Rogerio; Figueira, Ana Carolina Migliorini; Lara-Gonzalez, Samuel; Benítez-Cardoza, Claudia G; Brieba, Luis G

2017-11-01

The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer. Copyright © 2017 Elsevier B.V. All rights reserved.

A mixed ecologic-cohort comparison of physical activity & weight among young adults from five populations of African origin.

PubMed

Luke, Amy; Bovet, Pascal; Plange-Rhule, Jacob; Forrester, Terrence E; Lambert, Estelle V; Schoeller, Dale A; Dugas, Lara R; Durazo-Arvizu, Ramon A; Shoham, David A; Cao, Guichan; Brage, Soren; Ekelund, Ulf; Cooper, Richard S

2014-04-24

Examination of patterns and intensity of physical activity (PA) across cultures where obesity prevalence varies widely provides insight into one aspect of the ongoing epidemiologic transition. The primary hypothesis being addressed is whether low levels of PA are associated with excess weight and adiposity. We recruited young adults from five countries (500 per country, 2500 total, ages 25-45 years), spanning the range of obesity prevalence. Men and women were recruited from a suburb of Chicago, Illinois, USA; urban Jamaica; rural Ghana; peri-urban South Africa; and the Seychelles. PA was measured using accelerometry and expressed as minutes per day of moderate-to-vigorous activity or sedentary behavior. Obesity (BMI ≥ 30) prevalence ranged from 1.4% (Ghanaian men) to 63.8% (US women). South African men were the most active, followed by Ghanaian men. Relatively small differences were observed across sites among women; however, women in Ghana accumulated the most activity. Within site-gender sub-groups, the correlation of activity with BMI and other measures of adiposity was inconsistent; the combined correlation across sites was -0.17 for men and -0.11 for women. In the ecological analysis time spent in moderate-to-vigorous activity was inversely associated with BMI (r = -0.71). These analyses suggest that persons with greater adiposity tend to engage in less PA, although the associations are weak and the direction of causality cannot be inferred because measurements are cross-sectional. Longitudinal data will be required to elucidate direction of association.

Helix A Stabilization Precedes Amino-terminal Lobe Activation upon Calcium Binding to Calmodulin

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

Chen, Baowei; Lowry, David; Mayer, M. Uljana

2008-08-09

The structural coupling between opposing domains of CaM was investigated using the conformationally sensitive biarsenical probe 4,5-bis(1,3,2-dithioarsolan-2-yl)-resorufin (ReAsH), which upon binding to an engineered tetracysteine binding motif near the end of helix A (Thr-5 to Phe-19) becomes highly fluorescent. Changes in conformation and dynamics are reflective of the native CaM structure, as there is no change in the 1H- 15N HSQC NMR spectrum in comparison to wild-type CaM. We find evidence of a conformational intermediate associated with CaM activation, where calcium occupancy of sites in the amino-terminal and carboxyl-terminal lobes of CaM differentially affect the fluorescence intensity of bound ReAsH.more » Insight into the structure of the conformational intermediate is possible from a consideration of calcium-dependent changes in rates of ReAsH binding and helix A mobility, which respectively distinguish secondary structural changes associated with helix A stabilization from the tertiary structural reorganization of the amino-terminal lobe of CaM necessary for high-affinity binding to target proteins. Helix A stabilization is associated with calcium occupancy of sites in the carboxyl-terminal lobe (Kd = 0.36 ± 0.04 μM), which results in a reduction in the rate of ReAsH binding from 4900 M -1 sec -1 to 370 M -1 sec -1. In comparison, tertiary structural changes involving helix A and other structural elements in the amino-terminal lobe requires calcium-occupancy of amino-terminal sites (Kd = 18 ± 3 μM). Observed secondary and tertiary structural changes involving helix A in response to the sequential calcium occupancy of carboxyl- and amino-terminal lobe calcium binding sites suggest an important involvement of helix A in mediating the structural coupling between the opposing domains of CaM. These results are discussed in terms of a model in which carboxyl-terminal lobe calcium activation induces secondary structural changes within the interdomain linker that release helix A, thereby facilitating the formation of calcium binding sites in the amino-terminal lobe and linked tertiary structural rearrangements to form a high-affinity binding cleft that can associate with target proteins.« less

Comparison of three pesticide fate models based on lysimeter data of chloridazon and s-metolachlor from the Wagna test site, Austria

NASA Astrophysics Data System (ADS)

Brückner, Lisa; Klammler, Gernot; Schuhmann, Andrea; Kupfersberger, Hans; Fank, Johann

2017-04-01

A lysimeter experiment was conducted at the agricultural test site in Wagna, Austria, where clayey-sandy cambisol are predominant. The pesticides chloridazon and s-metolachlor were applied between 2010 and 2014 and the concentration of the active ingredients and their metabolites were measured regularly in the soil and the leachate in different depths (Schuhmann et al. 2016). During the lysimeter experiment maize, pumpkin and triticale were cultivated, which are the main field crops in that region. Beside this data, precise measurements of the soil hydrology parameters as well as meteorological data are available. Average annual precipitation at this site is 972 mm, mean annual groundwater recharge is 358 mm (2005-2014). Based on this data and the different breakthrough curves a comparison of the three different pesticide fate models PEARL, PELMO and MACRO is carried out for the pesticides s-metolachlor and chloridazon and their metabolites metolachlor oxanilic acid, metolachlor ethane sulfonic acid, desphenyl-chloridazon and methyl-desphenyl-chloridazon. The results of the modeling of the water movement and pesticide fate are evaluated and discussed. This work will contribute to a better understanding of the performance of this pesticide fate models for the above mentioned soil and hydrologic conditions. Schuhmann, A; Gans, O; Weiss, S; Fank, J; Klammler, G; Haberhauer, G; Gerzabek, MH (2016): A long-term lysimeter experiment to investigate the environmental dispersion of the herbicide chloridazon and its metabolites - comparison of lysimeter types. J SOIL SEDIMENT. 2016; 16(3): 1032-1045

Abundance of Ixodes ricinus and prevalence of Borrelia burgdorferi s.l. in the nature reserve Siebengebirge, Germany, in comparison to three former studies from 1978 onwards

PubMed Central

2012-01-01

Background During the last decades, population densities of Ixodes ricinus and prevalences of Borrelia burgdorferi s.l. have increased in different regions in Europe. In the present study, we determined tick abundance and the prevalence of different Borrelia genospecies in ticks from three sites in the Siebengebirge, Germany, which were already examined in the years 1987, 1989, 2001 and 2003. Data from all investigations were compared. Methods In 2007 and 2008, host-seeking I. ricinus were collected by monthly blanket dragging at three distinct vegetation sites in the Siebengebirge, a nature reserve and a well visited local recreation area near Bonn, Germany. In both years, 702 ticks were tested for B. burgdorferi s.l. DNA by nested PCR, and 249 tick samples positive for Borrelia were further genotyped by reverse line blotting. Results A total of 1046 and 1591 I. ricinus were collected in 2007 and 2008, respectively. In comparison to previous studies at these sites, the densities at all sites increased from 1987/89 and/or from 2003 until 2008. Tick densities and Borrelia prevalences in 2007 and 2008, respectively, were not correlated for all sites and both years. Overall, Borrelia prevalence of all ticks decreased significantly from 2007 (19.5%) to 2008 (16.5%), thus reaching the same level as in 2001 two times higher than in 1987/89 (7.6%). Since 2001, single infections with a Borrelia genospecies predominated in all collections, but the number of multiple infections increased, and in 2007, for the first time, triple Borrelia infections occurred. Prevalences of Borrelia genospecies differed considerably between the three sites, but B. garinii or B. afzelii were always the most dominant genospecies. B. lusitaniae was detected for the first time in the Siebengebirge, also in co-infections with B. garinii or B. valaisiana. Conclusions Over the last two centuries tick densities have changed in the Siebengebirge at sites that remained unchanged by human activity since they belong to a nature reserve. Abiotic and biotic conditions most likely favored the host-seeking activity of I. ricinus and the increase of multiple Borrelia infections in ticks. These changes have led to a potential higher risk of humans and animals to be infected with Lyme borreliosis. PMID:23171708

Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics.

PubMed

Chek, Min Fey; Kim, Sun-Yong; Mori, Tomoyuki; Arsad, Hasni; Samian, Mohammed Razip; Sudesh, Kumar; Hakoshima, Toshio

2017-07-13

Polyhydroxyalkanoate (PHA) is a promising candidate for use as an alternative bioplastic to replace petroleum-based plastics. Our understanding of PHA synthase PhaC is poor due to the paucity of available three-dimensional structural information. Here we present a high-resolution crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, PhaC Cs -CAT. The structure shows that PhaC Cs -CAT forms an α/β hydrolase fold comprising α/β core and CAP subdomains. The active site containing Cys291, Asp447 and His477 is located at the bottom of the cavity, which is filled with water molecules and is covered by the partly disordered CAP subdomain. We designated our structure as the closed form, which is distinct from the recently reported catalytic domain from Cupriavidus necator (PhaC Cn -CAT). Structural comparison showed PhaC Cn -CAT adopting a partially open form maintaining a narrow substrate access channel to the active site, but no product egress. PhaC Cs -CAT forms a face-to-face dimer mediated by the CAP subdomains. This arrangement of the dimer is also distinct from that of the PhaC Cn -CAT dimer. These findings suggest that the CAP subdomain should undergo a conformational change during catalytic activity that involves rearrangement of the dimer to facilitate substrate entry and product formation and egress from the active site.

Biomimicry enhances sequential reactions of tethered glycolytic enzymes, TPI and GAPDHS.

PubMed

Mukai, Chinatsu; Gao, Lizeng; Bergkvist, Magnus; Nelson, Jacquelyn L; Hinchman, Meleana M; Travis, Alexander J

2013-01-01

Maintaining activity of enzymes tethered to solid interfaces remains a major challenge in developing hybrid organic-inorganic devices. In nature, mammalian spermatozoa have overcome this design challenge by having glycolytic enzymes with specialized targeting domains that enable them to function while tethered to a cytoskeletal element. As a step toward designing a hybrid organic-inorganic ATP-generating system, we implemented a biomimetic site-specific immobilization strategy to tether two glycolytic enzymes representing different functional enzyme families: triose phosphoisomerase (TPI; an isomerase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDHS; an oxidoreductase). We then evaluated the activities of these enzymes in comparison to when they were tethered via classical carboxyl-amine crosslinking. Both enzymes show similar surface binding regardless of immobilization method. Remarkably, specific activities for both enzymes were significantly higher when tethered using the biomimetic, site-specific immobilization approach. Using this biomimetic approach, we tethered both enzymes to a single surface and demonstrated their function in series in both forward and reverse directions. Again, the activities in series were significantly higher in both directions when the enzymes were coupled using this biomimetic approach versus carboxyl-amine binding. Our results suggest that biomimetic, site-specific immobilization can provide important functional advantages over chemically specific, but non-oriented attachment, an important strategic insight given the growing interest in recapitulating entire biological pathways on hybrid organic-inorganic devices.

Biomimicry Enhances Sequential Reactions of Tethered Glycolytic Enzymes, TPI and GAPDHS

PubMed Central

Mukai, Chinatsu; Gao, Lizeng; Bergkvist, Magnus; Nelson, Jacquelyn L.; Hinchman, Meleana M.; Travis, Alexander J.

2013-01-01

Maintaining activity of enzymes tethered to solid interfaces remains a major challenge in developing hybrid organic-inorganic devices. In nature, mammalian spermatozoa have overcome this design challenge by having glycolytic enzymes with specialized targeting domains that enable them to function while tethered to a cytoskeletal element. As a step toward designing a hybrid organic-inorganic ATP-generating system, we implemented a biomimetic site-specific immobilization strategy to tether two glycolytic enzymes representing different functional enzyme families: triose phosphoisomerase (TPI; an isomerase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDHS; an oxidoreductase). We then evaluated the activities of these enzymes in comparison to when they were tethered via classical carboxyl-amine crosslinking. Both enzymes show similar surface binding regardless of immobilization method. Remarkably, specific activities for both enzymes were significantly higher when tethered using the biomimetic, site-specific immobilization approach. Using this biomimetic approach, we tethered both enzymes to a single surface and demonstrated their function in series in both forward and reverse directions. Again, the activities in series were significantly higher in both directions when the enzymes were coupled using this biomimetic approach versus carboxyl-amine binding. Our results suggest that biomimetic, site-specific immobilization can provide important functional advantages over chemically specific, but non-oriented attachment, an important strategic insight given the growing interest in recapitulating entire biological pathways on hybrid organic-inorganic devices. PMID:23626684

Molecular cloning, characterization and comparison of bile salt hydrolases from Lactobacillus johnsonii PF01.

PubMed

Chae, J P; Valeriano, V D; Kim, G-B; Kang, D-K

2013-01-01

To clone, characterize and compare the bile salt hydrolase (BSH) genes of Lactobacillus johnsonii PF01. The BSH genes were amplified by polymerase chain reaction (PCR) using specific oligonucleotide primers, and the products were inserted into the pET21b expression vector. Escherichia coli BLR (DE3) cells were transformed with pET21b vectors containing the BSH genes and induced using 0·1 mmol l(-1) isopropylthiolgalactopyranoside. The overexpressed BSH enzymes were purified using a nickel-nitrilotriacetic acid (Ni(2+) -NTA) agarose column and their activities characterized. BSH A hydrolysed tauro-conjugated bile salts optimally at pH 5·0 and 55°C, whereas BSH C hydrolysed glyco-conjugated bile salts optimally at pH 5·0 and 70°C. The enzymes had no preferential activities towards a specific cholyl moiety. BSH enzymes vary in their substrate specificities and characteristics to broaden its activity. Despite the lack of conservation in their putative substrate-binding sites, these remain functional through motif conservation. This is to our knowledge the first report of isolation of BSH enzymes from a single strain, showing hydrolase activity towards either glyco-conjugated or tauro-conjugated bile salts. Future structural homology studies and site-directed mutagenesis of sites associated with substrate specificity may elucidate specificities of BSH enzymes. © 2012 The Society for Applied Microbiology.

Controlling electrodeposited ultrathin amorphous Fe hydroxides film on V-doped nickel sulfide nanowires as efficient electrocatalyst for water oxidation

NASA Astrophysics Data System (ADS)

Shang, Xiao; Yan, Kai-Li; Lu, Shan-Shan; Dong, Bin; Gao, Wen-Kun; Chi, Jing-Qi; Liu, Zi-Zhang; Chai, Yong-Ming; Liu, Chen-Guang

2017-09-01

Developing cost-effective electrocatalysts with both high activity and stability remains challenging for oxygen evolution reaction (OER) in water electrolysis. Herein, based on V-doped nickel sulfide nanowire on nickel foam (NiVS/NF), we further conduct controllable electrodeposition of Fe hydroxides film on NiVS/NF (eFe/NiVS/NF) to further improve OER performance and stability. For comparison, ultrafast chemical deposition of Fe hydroxides on NiVS/NF (uFe/NiVS/NF) is also utilized. V-doping of NiVS/NF may introduce more active sites for OER, and nanowire structure can expose abundant active sites and facilitate mass transport. Both of the two depositions generate amorphous Fe hydroxides film covering on the surface of nanowires and lead to enhanced OER activities. Furthermore, electrodeposition strategy realizes uniform Fe hydroxides film on eFe/NiVS/NF confirmed by superior OER activity of eFe/NiVS/NF than uFe/NiVS/NF with relatively enhanced stability. The OER activity of eFe/NiVS/NF depends on various electrodepositon time, and the optimal time (15 s) is obtained with maximum OER activity. Therefore, the controllable electrodeposition of Fe may provide an efficient and simple strategy to enhance the OER properties of electrocatalysts.

Transmutation of human glutathione transferase A2-2 with peroxidase activity into an efficient steroid isomerase.

PubMed

Pettersson, Par L; Johansson, Ann-Sofie; Mannervik, Bengt

2002-08-16

A major goal in protein engineering is the tailor-making of enzymes for specified chemical reactions. Successful attempts have frequently been based on directed molecular evolution involving libraries of random mutants in which variants with desired properties were identified. For the engineering of enzymes with novel functions, it would be of great value if the necessary changes of the active site could be predicted and implemented. Such attempts based on the comparison of similar structures with different substrate selectivities have previously met with limited success. However, the present work shows that the knowledge-based redesign restricted to substrate-binding residues in human glutathione transferase A2-2 can introduce high steroid double-bond isomerase activity into the enzyme originally characterized by glutathione peroxidase activity. Both the catalytic center activity (k(cat)) and catalytic efficiency (k(cat)/K(m)) match the values of the naturally evolved glutathione transferase A3-3, the most active steroid isomerase known in human tissues. The substrate selectivity of the mutated glutathione transferase was changed 7000-fold by five point mutations. This example demonstrates the functional plasticity of the glutathione transferase scaffold as well as the potential of rational active-site directed mutagenesis as a complement to DNA shuffling and other stochastic methods for the redesign of proteins with novel functions.

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

Not Available

The Nuclear Waste Policy Act of 1982 (42 USC sections 10101-10226) requires the environmental assessment of a proposed site to include a statement of the basis for nominating a site as suitable for characterization. Volume 2 provides a detailed statement evaluating the site suitability of the Deaf Smith County Site under DOE siting guidelines, as well as a comparison of the Deaf Smith County Site to the other sites under consideration. The evaluation of the Deaf Smith County Site is based on the impacts associated with the reference repository design, but the evaluation will not change if based on themore » Mission Plan repository concept. The second part of this document compares the Deaf Smith County Site to Davis Canyon, Hanford, Richton Dome and Yucca Mountain. This comparison is required under DOE guidelines and is not intended to directly support subsequent recommendation of three sites for characterization as candidate sites. 259 refs., 29 figs., 66 refs. (MHB)« less

A comparison of single- and multi-site calibration and validation: a case study of SWAT in the Miyun Reservoir watershed, China

NASA Astrophysics Data System (ADS)

Bai, Jianwen; Shen, Zhenyao; Yan, Tiezhu

2017-09-01

An essential task in evaluating global water resource and pollution problems is to obtain the optimum set of parameters in hydrological models through calibration and validation. For a large-scale watershed, single-site calibration and validation may ignore spatial heterogeneity and may not meet the needs of the entire watershed. The goal of this study is to apply a multi-site calibration and validation of the Soil andWater Assessment Tool (SWAT), using the observed flow data at three monitoring sites within the Baihe watershed of the Miyun Reservoir watershed, China. Our results indicate that the multi-site calibration parameter values are more reasonable than those obtained from single-site calibrations. These results are mainly due to significant differences in the topographic factors over the large-scale area, human activities and climate variability. The multi-site method involves the division of the large watershed into smaller watersheds, and applying the calibrated parameters of the multi-site calibration to the entire watershed. It was anticipated that this case study could provide experience of multi-site calibration in a large-scale basin, and provide a good foundation for the simulation of other pollutants in followup work in the Miyun Reservoir watershed and other similar large areas.

Structural Evolution of Differential Amino Acid Effector Regulation in Plant Chorismate Mutases*

PubMed Central

Westfall, Corey S.; Xu, Ang; Jez, Joseph M.

2014-01-01

Chorismate mutase converts chorismate into prephenate for aromatic amino acid biosynthesis. To understand the molecular basis of allosteric regulation in the plant chorismate mutases, we analyzed the three Arabidopsis thaliana chorismate mutase isoforms (AtCM1–3) and determined the x-ray crystal structures of AtCM1 in complex with phenylalanine and tyrosine. Functional analyses show a wider range of effector control in the Arabidopsis chorismate mutases than previously reported. AtCM1 is activated by tryptophan with phenylalanine and tyrosine acting as negative effectors; however, tryptophan, cysteine, and histidine activate AtCM3. AtCM2 is a nonallosteric form. The crystal structure of AtCM1 in complex with tyrosine and phenylalanine identifies differences in the effector sites of the allosterically regulated yeast enzyme and the other two Arabidopsis isoforms. Site-directed mutagenesis of residues in the effector site reveals key features leading to differential effector regulation in these enzymes. In AtCM1, mutations of Gly-213 abolish allosteric regulation, as observed in AtCM2. A second effector site position, Gly-149 in AtCM1 and Asp-132 in AtCM3, controls amino acid effector specificity in AtCM1 and AtCM3. Comparisons of chorismate mutases from multiple plants suggest that subtle differences in the effector site are conserved in different lineages and may lead to specialized regulation of this branch point enzyme. PMID:25160622

Long-term application of winery wastewater - Effect on soil microbial populations and soil chemistry

NASA Astrophysics Data System (ADS)

Mosse, Kim; Patti, Antonio; Smernik, Ron; Cavagnaro, Timothy

2010-05-01

The ability to reuse winery wastewater (WWW) has potential benefits both with respect to treatment of a waste stream, as well as providing a beneficial water resource in water limited regions such as south-eastern Australia, California and South Africa. Over an extended time period, this practice leads to changes in soil chemistry, and potentially, also to soil microbial populations. In this study, we compared the short term effects of WWW (both treated and untreated) application on soil biology and chemistry in two adjacent paired sites with the same soil type, one of which had received WWW for approximately 30 years, and the other which had not. The paired sites were treated with an industrially relevant quantity of WWW, and the soil microbial activity (measured as soil CO2 efflux) and common soil physicochemical properties were monitored over a 16-day period. In addition, Solid State 13C NMR was employed on whole soil samples from the two sites, to measure and compare the chemical nature of the soil organic matter at the paired sites. The acclimatised soil showed a high level of organic matter and a greater spike in microbial activity following WWW addition, in comparison with the non-acclimatised soil, suggesting differences in soil chemistry and soil microbial communities between the two sites. Soil nitrate and phosphorus levels showed significant differences between WWW treatments; these differences likely to be microbially mediated.

Role of hydrogen bonds in the reaction mechanism of chalcone isomerase.

PubMed

Jez, Joseph M; Bowman, Marianne E; Noel, Joseph P

2002-04-23

In flavonoid, isoflavonoid, and anthocyanin biosynthesis, chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into (S)-flavanones with a second-order rate constant that approaches the diffusion-controlled limit. The three-dimensional structures of alfalfa CHI complexed with different flavanones indicate that two sets of hydrogen bonds may possess critical roles in catalysis. The first set of interactions includes two conserved amino acids (Thr48 and Tyr106) that mediate a hydrogen bond network with two active site water molecules. The second set of hydrogen bonds occurs between the flavanone 7-hydroxyl group and two active site residues (Asn113 and Thr190). Comparison of the steady-state kinetic parameters of wild-type and mutant CHIs demonstrates that efficient cyclization of various chalcones into their respective flavanones requires both sets of contacts. For example, the T48A, T48S, Y106F, N113A, and T190A mutants exhibit 1550-, 3-, 30-, 7-, and 6-fold reductions in k(cat) and 2-3-fold changes in K(m) with 4,2',4'-trihydroxychalcone as a substrate. Kinetic comparisons of the pH-dependence of the reactions catalyzed by wild-type and mutant enzymes indicate that the active site hydrogen bonds contributed by these four residues do not significantly alter the pK(a) of the intramolecular cyclization reaction. Determinations of solvent kinetic isotope and solvent viscosity effects for wild-type and mutant enzymes reveal a change from a diffusion-controlled reaction to one limited by chemistry in the T48A and Y106F mutants. The X-ray crystal structures of the T48A and Y106F mutants support the assertion that the observed kinetic effects result from the loss of key hydrogen bonds at the CHI active site. Our results are consistent with a reaction mechanism for CHI in which Thr48 polarizes the ketone of the substrate and Tyr106 stabilizes a key catalytic water molecule. Hydrogen bonds contributed by Asn113 and Thr190 provide additional stabilization in the transition state. Conservation of these residues in CHIs from other plant species implies a common reaction mechanism for enzyme-catalyzed flavanone formation in all plants.

Results from the FIN-2 formal comparison

NASA Astrophysics Data System (ADS)

Connolly, Paul; Hoose, Corinna; Liu, Xiaohong; Moehler, Ottmar; Cziczo, Daniel; DeMott, Paul

2017-04-01

During the Fifth International Ice Nucleation Workshop (FIN-2) at the AIDA Ice Nucleation facility in Karlsruhe, Germany in March 2015, a formal comparison of ice nucleation measurement methods was conducted. During the experiments the samples of ice nucleating particles were not revealed to the instrument scientists, hence this was referred to as a "blind comparison". The two samples used were later revealed to be Arizona Test Dust and an Argentina soil sample. For these two samples seven mobile ice nucleating particle counters sampled directly from the AIDA chamber or from the aerosol preparation chamber at specified temperatures, whereas filter samples were taken for two offline deposition nucleation instruments. Wet suspension methods for determining IN concentrations were also used with 10 different methods employed. For the wet suspension methods experiments were conducted using INPs collected from the air inside the chambers (impinger sampling) and INPs taken from the bulk samples (vial sampling). Direct comparisons of the ice nucleating particle concentrations are reported as well as derived ice nucleation active site densities. The study highlights the difficulties in performing such analyses, but generally indicates that there is reasonable agreement between the wet suspension techniques. It is noted that ice nucleation efficiency derived from the AIDA chamber (quantified using the ice active surface site density approach) is higher than that for the cold stage techniques. This is both true for the Argentina soil sample and, to a lesser extent, for the Arizona Test Dust sample too. Other interesting effects were noted: for the ATD the impinger sampling demonstrated higher INP efficiency at higher temperatures (>255 K) than the vial sampling, but agreed at the lower temperatures (<255K), whereas the opposite was true for the Argentina soil sample. The results are analysed to better understand the performance of the various techniques and to address any size-sorting effects and / or sampling line loses.

Second generation engineering of transketolase for polar aromatic aldehyde substrates.

PubMed

Payongsri, Panwajee; Steadman, David; Hailes, Helen C; Dalby, Paul A

2015-04-01

Transketolase has significant industrial potential for the asymmetric synthesis of carboncarbon bonds with new chiral centres. Variants evolved on propanal were found previously with nascent activity on polar aromatic aldehydes 3-formylbenzoic acid (3-FBA), 4-formylbenzoic acid (4-FBA), and 3-hydroxybenzaldehyde (3-HBA), suggesting a potential novel route to analogues of chloramphenicol. Here we evolved improved transketolase activities towards aromatic aldehydes, by saturation mutagenesis of two active-site residues (R358 and S385), predicted to interact with the aromatic substituents. S385 variants selectively controlled the aromatic substrate preference, with up to 13-fold enhanced activities, and KM values comparable to those of natural substrates with wild-type transketolase. S385E even completely removed the substrate inhibition for 3-FBA, observed in all previous variants. The mechanisms of catalytic improvement were both mutation type and substrate dependent. S385E improved 3-FBA activity via kcat, but reduced 4-FBA activity via KM. Conversely, S385Y/T improved 3-FBA activity via KM and 4-FBA activity via kcat. This suggested that both substrate proximity and active-site orientation are very sensitive to mutation. Comparison of all variant activities on each substrate indicated different binding modes for the three aromatic substrates, supported by computational docking. This highlights a potential divergence in the evolution of different substrate specificities, with implications for enzyme engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Insights into the O-Acetylation Reaction of Hydroxylated Heterocyclic Amines by Human Arylamine N-Acetyltransferases: A Computational Study

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

Lau, E Y; Felton, J S; Lightstone, F C

2006-06-06

A computational study was performed to better understand the differences between human arylamine N-acetyltransferase (NAT) 1 and 2. Homology models were constructed from available crystal structures and comparisons of the active site residues 125, 127, and 129 for these two enzymes provide insight into observed substrate differences. The NAT2 model provided a basis for understanding how some of the common mutations may affect the structure of the protein. Molecular dynamics simulations of the human NAT models and the template structure (NAT from Mycobacterium smegmatis) were performed and showed the models to be stable and reasonable. Docking studies of hydroxylated heterocyclicmore » amines in the models of NAT1 and NAT2 probed the differences exhibited by these two proteins with mutagenic agents. The hydroxylated heterocyclic amines were only able to fit into the NAT2 active site, and an alternative binding site by the P-loop was found using our models and will be discussed. Additionally, quantum mechanical calculations were performed to study the O-acetylation reaction of the hydroxylated heterocyclic amines N-OH MeIQx and N-OH PhIP. This study has given us insight into why there are substrate differences among isoenzymes and explains some of the polymorphic activity differences.« less

On the evolution of diet and landscape during the Upper Paleolithic through Mesolithic at Franchthi Cave (Peloponnese, Greece).

PubMed

Stiner, Mary C; Munro, Natalie D

2011-05-01

Franchthi Cave in southern Greece preserves one of the most remarkable records of socioeconomic change of the Late Pleistocene through early Holocene. Located on the southern end of the Argolid Peninsula, the area around the site was greatly affected by climate variation and marine transgression. This study examines the complex interplay of site formation processes (material deposition rates), climate-driven landscape change, and human hunting systems during the Upper Paleolithic through Mesolithic at Franchthi Cave based on the H1B faunal series. Building on earlier work, we establish the full spectrum of the meat diet using taphonomic evidence, and we analyze these data for trends in socioeconomic reorganization. Foraging patterns during the Aurignacian and "Gravettoid" occupations at Franchthi were terrestrial and already rather diversified in comparison to Middle Paleolithic diets in southern Greece. Hunting shifted abruptly to a mixed marine-terrestrial pattern during the Final Paleolithic, and fishing activities intensified though the Mesolithic. The zooarchaeological data indicate two consecutive trends of increasing dietary breadth, the first within an exclusively terrestrial context, and the second as marine habitats came into use through the end of the Mesolithic. The intensity of the human occupations at this site increased in tandem with intensified use of animal and plants. Comparison to the inland site of Klissoura Cave 1 indicates that the trend toward broader diets was regional as well as local. Copyright © 2010 Elsevier Ltd. All rights reserved.

Prioritizing conservation activities using reserve site selection methods and population viability analysis.

PubMed

Newbold, Stephen C; Siikamäki, Juha

2009-10-01

In recent years a large literature on reserve site selection (RSS) has developed at the interface between ecology, operations research, and environmental economics. Reserve site selection models use numerical optimization techniques to select sites for a network of nature reserves for protecting biodiversity. In this paper, we develop a population viability analysis (PVA) model for salmon and incorporate it into an RSS framework for prioritizing conservation activities in upstream watersheds. We use spawner return data for three closely related salmon stocks in the upper Columbia River basin and estimates of the economic costs of watershed protection from NOAA to illustrate the framework. We compare the relative cost-effectiveness of five alternative watershed prioritization methods, based on various combinations of biological and economic information. Prioritization based on biological benefit-economic cost comparisons and accounting for spatial interdependencies among watersheds substantially outperforms other more heuristic methods. When using this best-performing prioritization method, spending 10% of the cost of protecting all upstream watersheds yields 79% of the biological benefits (increase in stock persistence) from protecting all watersheds, compared to between 20% and 64% for the alternative methods. We also find that prioritization based on either costs or benefits alone can lead to severe reductions in cost-effectiveness.

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status.

PubMed

Richards, Vincent P; Alvarez, Andres J; Luce, Amy R; Bedenbaugh, Molly; Mitchell, Mary Lyn; Burne, Robert A; Nascimento, Marcelle M

2017-08-01

The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMI NGS ) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMI NGS , and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different ( P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis , which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans , Scardovia wiggsiae , Parascardovia denticolens , and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression. Copyright © 2017 American Society for Microbiology.

Microbiomes of Site-Specific Dental Plaques from Children with Different Caries Status

PubMed Central

Alvarez, Andres J.; Luce, Amy R.; Bedenbaugh, Molly; Mitchell, Mary Lyn

2017-01-01

ABSTRACT The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMINGS) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMINGS, and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different (P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis, which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans, Scardovia wiggsiae, Parascardovia denticolens, and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression. PMID:28507066

Spatial resolution of pace mapping of idiopathic ventricular tachycardia/ectopy originating in the right ventricular outflow tract.

PubMed

Bogun, Frank; Taj, Majid; Ting, Michael; Kim, Hyungjin Myra; Reich, Stephen; Good, Eric; Jongnarangsin, Krit; Chugh, Aman; Pelosi, Frank; Oral, Hakan; Morady, Fred

2008-03-01

Pace mapping has been used to identify the site of origin of focal ventricular arrhythmias. The spatial resolution of pace mapping has not been adequately quantified using currently available three-dimensional mapping systems. The purpose of this study was to determine the spatial resolution of pace mapping in patients with idiopathic ventricular tachycardia or premature ventricular contractions originating in the right ventricular outflow tract. In 16 patients with idiopathic ventricular tachycardia/ectopy from the right ventricular outflow tract, comparisons and classifications of pace maps were performed by two observers (good pace map: match >10/12 leads; inadequate pace map: match < or =10/12 leads) and a customized MATLAB 6.0 program (assessing correlation coefficient and normalized root mean square of the difference (nRMSd) between test and template signals). With an electroanatomic mapping system, the correlation coefficient of each pace map was correlated with the distance between the pacing site and the effective ablation site. The endocardial area within the 10-ms activation isochrone was measured. The ablation procedure was effective in all patients. Sites with good pace maps had a higher correlation coefficient and lower nRMSd than sites with inadequate pace maps (correlation coefficient: 0.96 +/- 0.03 vs 0.76 +/- 0.18, P <.0001; nRMSd: 0.41 +/- 0.16 vs 0.89 +/- 0.39, P <.0001). Using receiver operating characteristic curves, appropriate cutoff values were >0.94 for correlation coefficient (sensitivity 81%, specificity 89%) and < or =0.54 for nRMSd (sensitivity 76%, specificity 80%). Good pace maps were located a mean of 7.3 +/- 5.0 mm from the effective ablation site and had a mean activation time of -24 +/- 7 ms. However, in 3 (18%) of 16 patients, the best pace map was inadequate at the effective ablation site, with an endocardial activation time at these sites of -25 +/- 12 ms. Pace maps with correlation coefficient > or =0.94 were confined to an area of 1.8 +/- 0.6 cm2. The 10-ms isochrone measured 1.2 +/- 0.7 cm2. The spatial resolution of a good pace map for targeting ventricular tachycardia/ectopy is 1.8 cm2 in the right ventricular outflow tract and therefore is inferior to the spatial resolution of activation mapping as assessed by isochronal activation. In approximately 20% of patients, pace mapping is unreliable in identifying the site of origin, possibly due a deeper site of origin and preferential conduction via fibers connecting the focus to the endocardial surface.

Factors affecting female space use in ten populations of prairie chickens

USGS Publications Warehouse

Winder, Virginia L.; Carrlson, Kaylan M.; Gregory, Andrew J.; Hagen, Christian A.; Haukos, David A.; Kesler, Dylan C.; Larsson, Lena C.; Matthews, Ty W.; McNew, Lance B.; Patten, Michael; Pitman, Jim C.; Powell, Larkin A.; Smith, Jennifer A.; Thompson, Tom; Wolfe, Donald H.; Sandercock, Brett K.

2015-01-01

Conservation of wildlife depends on an understanding of the interactions between animal movements and key landscape factors. Habitat requirements of wide-ranging species often vary spatially, but quantitative assessment of variation among replicated studies at multiple sites is rare. We investigated patterns of space use for 10 populations of two closely related species of prairie grouse: Greater Prairie-Chickens (Tympanuchus cupido) and Lesser Prairie-Chickens (T. pallidicinctus). Prairie chickens require large, intact tracts of native grasslands, and are umbrella species for conservation of prairie ecosystems in North America. We used resource utilization functions to investigate space use by female prairie chickens during the 6-month breeding season from March through August in relation to lek sites, habitat conditions, and anthropogenic development. Our analysis included data from 382 radio-marked individuals across a major portion of the extant range. Our project is a unique opportunity to study comparative space use of prairie chickens, and we employed standardized methods that facilitated direct comparisons across an ecological gradient of study sites. Median home range size of females varied ~10-fold across 10 sites (3.6–36.7 km2), and home ranges tended to be larger at sites with higher annual precipitation. Proximity to lek sites was a strong and consistent predictor of space use for female prairie chickens at all 10 sites. The relative importance of other predictors of space use varied among sites, indicating that generalized habitat management guidelines may not be appropriate for these two species. Prairie chickens actively selected for prairie habitats, even at sites where ~90% of the land cover within the study area was prairie. A majority of the females monitored in our study (>95%) had activity centers within 5 km of leks, suggesting that conservation efforts can be effectively concentrated near active lek sites. Our data on female space use suggest that lek surveys of male prairie chickens can indirectly assess habitat suitability for females during the breeding season. Lek monitoring and surveys for new leks provide information on population trends, but can also guide management actions aimed at improving nesting and brood-rearing habitats.

Methods to Identify Changes in Background Water-Quality Conditions Using Dissolved-Solids Concentrations and Loads as Indicators, Arkansas River and Fountain Creek, in the Vicinity of Pueblo, Colorado

USGS Publications Warehouse

Ortiz, Roderick F.

2004-01-01

Effective management of existing water-storage capacity in the Arkansas River Basin is anticipated to help satisfy the need for water in southeastern Colorado. A strategy to meet these needs has been developed, but implementation could affect the water quality of the Arkansas River and Fountain Creek in the vicinity of Pueblo, Colorado. Because no known methods are available to determine what effects future changes in operations will have on water quality, the U.S. Geological Survey, in cooperation with the Southeastern Colorado Water Activity Enterprise, began a study in 2002 to develop methods that could identify if future water-quality conditions have changed significantly from background (preexisting) water-quality conditions. A method was developed to identify when significant departures from background (preexisting) water-quality conditions occur in the lower Arkansas River and Fountain Creek in the vicinity of Pueblo, Colorado. Additionally, the methods described in this report provide information that can be used by various water-resource agencies for an internet-based decision-support tool. Estimated dissolved-solids concentrations at five sites in the study area were evaluated to designate historical background conditions and to calculate tolerance limits used to identify statistical departures from background conditions. This method provided a tool that could be applied with defined statistical probabilities associated with specific tolerance limits. Drought data from 2002 were used to test the method. Dissolved-solids concentrations exceeded the tolerance limits at all four sites on the Arkansas River at some point during 2002. The number of exceedances was particularly evident when streamflow from Pueblo Reservoir was reduced, and return flows and ground-water influences to the river were more prevalent. No exceedances were observed at the site on Fountain Creek. These comparisons illustrated the need to adjust the concentration data to account for varying streamflow. As such, similar comparisons between flow-adjusted data were done. At the site Arkansas River near Avondale, nearly all the 2002 flow-adjusted concentration data were less than the flow-adjusted tolerance limit which illustrated the effects of using flow-adjusted concentrations. Numerous exceedances of the flow-adjusted tolerance limits, however, were observed at the sites Arkansas River above Pueblo and Arkansas River at Pueblo. These results indicated that the method was able to identify a change in the ratio of source waters under drought conditions. Additionally, tolerance limits were calculated for daily dissolved-solids load and evaluated in a similar manner. Several other mass-load approaches were presented to help identify long-term changes in water quality. These included comparisons of cumulative mass load at selected sites and comparisons of mass load contributed at the Arkansas River near Avondale site by measured and unmeasured sources.

Effect of Siloxane Ring Strain and Cation Charge Density on the Formation of Coordinately Unsaturated Metal Sites on Silica: Insights from Density Functional Theory (DFT) Studies

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

Das, Ujjal; Zhang, Guanghui; Hu, Bo

2015-10-28

Amorphous silica (SiO 2) is commonly used as a support in heterogeneous catalysis. However, due to the structural disorder and temperature induced change of surface morphology, the structures of silica supported metal catalysts are difficult to determine. Most studies are primarily focused on understanding the interactions of different types of surface hydroxyl groups with metal ions. In comparison, the effect of siloxane ring size on the structure of silica supported metal catalysts and how it affects catalytic activity is poorly understood. Here, we have used density functional theory calculations to understand the effect of siloxane ring strain on structure andmore » activity of different monomeric Lewis acid metal sites on silica. In particular, we have found that large siloxane rings favor strong dative bonding interaction between metal ion and surface hydroxyls, leading to the formation of high-coordinate metal sites. In comparison, metal-silanol interaction is weak in small siloxane rings, resulting in low-coordinate metal sites. The physical origin of this size dependence is associated with siloxane ring strain, and, a correlation between metal-silanol interaction energy and ring strain energy has been observed. In addition to ring strain, the strength of the metal-silanol interaction also depends on the positive charge density of the cations. In fact, a correlation also exists between metal-silanol interaction energy and charge density of several first-row transition and post-transition metals. The theoretical results are compared with the EXAFS data of monomeric Zn(II) and Ga(III) ions grafted on silica. In conclusion, the molecular level insights of how metal ion coordination on silica depends on siloxane ring strain and cation charge density will be useful in the synthesis of new catalysts.« less

Effect of conformational mobility and hydrogen-bonding interactions on the selectivity of some guanidinoaryl-substituted mechanism-based inhibitors of trypsin-like serine proteases.

PubMed

Rai, R; Katzenellenbogen, J A

1992-11-13

Previously, we have reported that some guanidino-substituted alpha- and beta-aryl enol lactones I and II behaved as selective, mechanism-based inhibitors of some trypsin-like proteases (Rai, R.; Katzenellenbogen, J.A. J. Med. Chem., submitted). In this study, we describe the synthesis and kinetic evaluation of some related, guanidino-substituted enol lactones having greater conformational mobility and affording additional hydrogen-bonding sites at the active site. The alpha-aryl-substituted lactones 1 and 2, which have greater conformational mobility in the guanidinoaryl linkage than I, selectively inhibited the trypsin-like enzymes, and they were relatively poor inactivators of alpha-chymotrypsin and human neutrophil elastase (HNE). The iodo enol lactone 2 permanently inactivated trypsin, urokinase, tissue plasminogen activator, and plasmin, showing exceptionally high specificity in its interaction with trypsin and urokinase. The selectivity pattern exhibited by the closely related, conformationally less mobile alpha-aryl-substituted iodo lactone Ib, which was previously shown to be a selective suicide substrate of urokinase and plasmin, provides an interesting comparison. The alpha-benzamido-substituted lactones 3 and 4, which afford an additional site for active-site hydrogen bonding, were found to be very potent alternate substrate inhibitors of trypsin and urokinase. In addition, the iodo lactone 4 permanently inactivated alpha-chymotrypsin. The importance of secondary interactions in increasing the specificities in the case of alpha-chymotrypsin is discussed.

Mapping the Substrate Binding Site of Phenylacetone Monooxygenase from Thermobifida fusca by Mutational Analysis▿†

PubMed Central

Dudek, Hanna M.; de Gonzalo, Gonzalo; Torres Pazmiño, Daniel E.; Stępniak, Piotr; Wyrwicz, Lucjan S.; Rychlewski, Leszek; Fraaije, Marco W.

2011-01-01

Baeyer-Villiger monooxygenases catalyze oxidations that are of interest for biocatalytic applications. Among these enzymes, phenylacetone monooxygenase (PAMO) from Thermobifida fusca is the only protein showing remarkable stability. While related enzymes often present a broad substrate scope, PAMO accepts only a limited number of substrates. Due to the absence of a substrate in the elucidated crystal structure of PAMO, the substrate binding site of this protein has not yet been defined. In this study, a structural model of cyclopentanone monooxygenase, which acts on a broad range of compounds, has been prepared and compared with the structure of PAMO. This revealed 15 amino acid positions in the active site of PAMO that may account for its relatively narrow substrate specificity. We designed and analyzed 30 single and multiple mutants in order to verify the role of these positions. Extensive substrate screening revealed several mutants that displayed increased activity and altered regio- or enantioselectivity in Baeyer-Villiger reactions and sulfoxidations. Further substrate profiling resulted in the identification of mutants with improved catalytic properties toward synthetically attractive compounds. Moreover, the thermostability of the mutants was not compromised in comparison to that of the wild-type enzyme. Our data demonstrate that the positions identified within the active site of PAMO, namely, V54, I67, Q152, and A435, contribute to the substrate specificity of this enzyme. These findings will aid in more dedicated and effective redesign of PAMO and related monooxygenases toward an expanded substrate scope. PMID:21724896

Site comparison for optical visibility statistics in southern Arizona

NASA Technical Reports Server (NTRS)

Cowles, K. A.

1990-01-01

One of the best locations in the continental United States for astronomical telescopes is southern Arizona. The mountains surrounding Tucson have clear skies 80 percent of the year, with image quality generally better than 2 seconds on peaks. Two of the existing observatory sites in this area are being considered as locations for one of the three Atmospheric Visibility Monitoring (AVM) observatories. These sites are Mount Lemmon and Mount Hopkins. A comparison of the characteristics of each of the sites is made here to identify the more desirable of the two locations. It is recommended that Mount Lemmon be selected as the Arizona site for this project.

The Carbon-Land Model Intercomparison Project (C-LAMP): A Model-Data Comparison System for Evaluation of Coupled Biosphere-Atmosphere Models

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

Hoffman, Forrest M; Randerson, Jim; Thornton, Peter E

2009-01-01

The need to capture important climate feebacks in general circulation models (GCMs) has resulted in new efforts to include atmospheric chemistry and land and ocean biogeochemistry into the next generation of production climate models, now often referred to as Earth System Models (ESMs). While many terrestrial and ocean carbon models have been coupled to GCMs, recent work has shown that such models can yield a wide range of results, suggesting that a more rigorous set of offline and partially coupled experiments, along with detailed analyses of processes and comparisons with measurements, are warranted. The Carbon-Land Model Intercomparison Project (C-LAMP) providesmore » a simulation protocol and model performance metrics based upon comparisons against best-available satellite- and ground-based measurements (Hoffman et al., 2007). C-LAMP provides feedback to the modeling community regarding model improvements and to the measurement community by suggesting new observational campaigns. C-LAMP Experiment 1 consists of a set of uncoupled simulations of terrestrial carbon models specifically designed to examine the ability of the models to reproduce surface carbon and energy fluxes at multiple sites and to exhibit the influence of climate variability, prescribed atmospheric carbon dioxide (CO{sub 2}), nitrogen (N) deposition, and land cover change on projections of terrestrial carbon fluxes during the 20th century. Experiment 2 consists of partially coupled simulations of the terrestrial carbon model with an active atmosphere model exchanging energy and moisture fluxes. In all experiments, atmospheric CO{sub 2} follows the prescribed historical trajectory from C{sup 4}MIP. In Experiment 2, the atmosphere model is forced with prescribed sea surface temperatures (SSTs) and corresponding sea ice concentrations from the Hadley Centre; prescribed CO{sub 2} is radiatively active; and land, fossil fuel, and ocean CO{sub 2} fluxes are advected by the model. Both sets of experiments have been performed using two different terrestrial biogeochemistry modules coupled to the Community Land Model version 3 (CLM3) in the Community Climate System Model version 3 (CCSM3): The CASA model of Fung, et al., and the carbon-nitrogen (CN) model of Thornton. Comparisons against Ameriflus site measurements, MODIS satellite observations, NOAA flask records, TRANSCOM inversions, and Free Air CO{sub 2} Enrichment (FACE) site measurements, and other datasets have been performed and are described in Randerson et al. (2009). The C-LAMP diagnostics package was used to validate improvements to CASA and CN for use in the next generation model, CLM4. It is hoped that this effort will serve as a prototype for an international carbon-cycle model benchmarking activity for models being used for the Inter-governmental Panel on Climate Change (IPCC) Fifth Assessment Report. More information about C-LAMP, the experimental protocol, performance metrics, output standards, and model-data comparisons from the CLM3-CASA and CLM3-CN models are available at http://www.climatemodeling.org/c-lamp.« less

Controlling for Landform Age When Determining the Settlement History of the Kuril Islands

PubMed Central

MacInnes, Breanyn; Fitzhugh, Ben; Holman, Darryl

2014-01-01

Archaeological investigations of settlement patterns in dynamic landscapes can be strongly biased by the evolution of the Earth’s surface. The Kuril Island volcanic arc exemplifies such a dynamic landscape, where landscape-modifying geological forces were active during settlement, including sea-level changes, tectonic emergence, volcanic eruptive processes, coastal aggradation, and dune formation. With all these ongoing processes, in this paper we seek to understand how new landscape formation in the Holocene might bias archaeological interpretations of human settlement in the Kurils. Resolving this issue is fundamental to any interpretation of human settlement history derived from the distribution and age of archaeological sites from the region. On the basis of a comparison of landform ages and earliest archaeological occupation ages on those landforms, we conclude that landform creation did not significantly bias our aggregate archaeological evidence for earliest settlement. Some sections of the archipelago have larger proportions of landform creation dates closer to archaeological evidence of settlement and undoubtedly some archaeological sites have been lost to geomorphic processes. However, comparisons between regions reveal comparable archaeological establishment patterns irrespective of geomorphic antiquity. PMID:25684855

A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics.

PubMed

van Hazel, Ilke; Dungan, Sarah Z; Hauser, Frances E; Morrow, James M; Endler, John A; Chang, Belinda S W

2016-07-01

Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates. © 2016 The Protein Society.

Effects of Grazing Pressure on Efficiency of Grazing on North American Great Plains Rangelands

USDA-ARS?s Scientific Manuscript database

Robust prediction models describing vegetation and animal responses to stocking rate in North American Great Plains rangelands are lacking as across site comparisons are limited by different qualitative designations of light, moderate and heavy stocking. Comparisons of stocking rates across sites ca...

Evaluating the Longevity and Hydraulic Performance of Permeable Reactive Barriers at Department of Defense Sites

DTIC Science & Technology

2003-01-01

Army Ammunitions Plant) PRBs have become feasible with trenching. Other construction 5 methods, such as jetting, hydraulic fracturing , and vibratory...where the affected aquifer is deeper, innovative methods, such as jetting and hydraulic fracturing , are available, but there is not as much widespread...such as jetting and hydraulic fracturing ) can be used at relatively higher cost. The cost comparison of a PRB versus an active remedy, such as a

Prototype solar heating and cooling systems, including potable hot water

NASA Technical Reports Server (NTRS)

Bloomquist, D.; Oonk, R. L.

1977-01-01

Progress made in the development, delivery, and support of two prototype solar heating and cooling systems including potable hot water is reported. The system consists of the following subsystems: collector, auxiliary heating, potable hot water, storage, control, transport, and government-furnished site data acquisition. A comparison of the proposed Solaron Heat Pump and Solar Desiccant Heating and Cooling Systems, installation drawings, data on the Akron House at Akron, Ohio, and other program activities are included.

The Structural Basis of Substrate Recognition in an exo-b-d-glucosaminidase Involved in Chitosan Hydrolysis

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

Van Bueren, A.; Ghinet, M; Gregg, K

2009-01-01

Family 2 of the glycoside hydrolase classification is one of the largest families. Structurally characterized members of this family include enzymes with ?-galactosidase activity (Escherichia coli LacZ), ?-glucuronidase activity (Homo sapiens GusB), and ?-mannosidase activity (Bacteroides thetaiotaomicron BtMan2A). Here, we describe the structure of a family 2 glycoside hydrolase, CsxA, from Amycolatopsis orientalis that has exo-?-d-glucosaminidase (exo-chitosanase) activity. Analysis of a product complex (1.85 A resolution) reveals a unique negatively charged pocket that specifically accommodates the nitrogen of nonreducing end glucosamine residues, allowing this enzyme to discriminate between glucose and glucosamine. This also provides structural evidence for the role ofmore » E541 as the catalytic nucleophile and D469 as the catalytic acid/base. The structures of an E541A mutant in complex with a natural ?-1,4-d-glucosamine tetrasaccharide substrate and both E541A and D469A mutants in complex with a pNP-?-d-glucosaminide synthetic substrate provide insight into interactions in the + 1 subsite of this enzyme. Overall, a comparison with the active sites of other GH2 enzymes highlights the unique architecture of the CsxA active site, which imparts specificity for its cationic substrate.« less

The Structural Basis of Substrate Recognition in an exo-beta-d-Glucosaminidase Involved in Chitosan Hydrolysis

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

Lammerts van Bueren, A.; Ghinet, M; Gregg, K

2009-01-01

Family 2 of the glycoside hydrolase classification is one of the largest families. Structurally characterized members of this family include enzymes with beta-galactosidase activity (Escherichia coli LacZ), beta-glucuronidase activity (Homo sapiens GusB), and beta-mannosidase activity (Bacteroides thetaiotaomicron BtMan2A). Here, we describe the structure of a family 2 glycoside hydrolase, CsxA, from Amycolatopsis orientalis that has exo-beta-D-glucosaminidase (exo-chitosanase) activity. Analysis of a product complex (1.85 A resolution) reveals a unique negatively charged pocket that specifically accommodates the nitrogen of nonreducing end glucosamine residues, allowing this enzyme to discriminate between glucose and glucosamine. This also provides structural evidence for the role ofmore » E541 as the catalytic nucleophile and D469 as the catalytic acid/base. The structures of an E541A mutant in complex with a natural beta-1,4-D-glucosamine tetrasaccharide substrate and both E541A and D469A mutants in complex with a pNP-beta-D-glucosaminide synthetic substrate provide insight into interactions in the +1 subsite of this enzyme. Overall, a comparison with the active sites of other GH2 enzymes highlights the unique architecture of the CsxA active site, which imparts specificity for its cationic substrate.« less

Molecular dynamics simulations on the inhibition of cyclin-dependent kinases 2 and 5 in the presence of activators.

PubMed

Zhang, Bing; Tan, Vincent B C; Lim, Kian Meng; Tay, Tong Earn

2006-06-01

Interests in CDK2 and CDK5 have stemmed mainly from their association with cancer and neuronal migration or differentiation related diseases and the need to design selective inhibitors for these kinases. Molecular dynamics (MD) simulations have not only become a viable approach to drug design because of advances in computer technology but are increasingly an integral part of drug discovery processes. It is common in MD simulations of inhibitor/CDK complexes to exclude the activator of the CDKs in the structural models to keep computational time tractable. In this paper, we present simulation results of CDK2 and CDK5 with roscovitine using models with and without their activators (cyclinA and p25). While p25 was found to induce slight changes in CDK5, the calculations support that cyclinA leads to significant conformational changes near the active site of CDK2. This suggests that detailed and structure-based inhibitor design targeted at these CDKs should employ activator-included models of the kinases. Comparisons between P/CDK2/cyclinA/roscovitine and CDK5/p25/roscovitine complexes reveal differences in the conformations of the glutamine around the active sites, which may be exploited to find highly selective inhibitors with respect to CDK2 and CDK5.

Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3.

PubMed

Heaslet, Holly; Lin, Ying-Chuan; Tam, Karen; Torbett, Bruce E; Elder, John H; Stout, C David

2007-01-09

We have obtained the 1.7 A crystal structure of FIV protease (PR) in which 12 critical residues around the active site have been substituted with the structurally equivalent residues of HIV PR (12X FIV PR). The chimeric PR was crystallized in complex with the broad-based inhibitor TL-3, which inhibits wild type FIV and HIV PRs, as well as 12X FIV PR and several drug-resistant HIV mutants 1234. Biochemical analyses have demonstrated that TL-3 inhibits these PRs in the order HIV PR > 12X FIV PR > FIV PR, with Ki values of 1.5 nM, 10 nM, and 41 nM, respectively 234. Comparison of the crystal structures of the TL-3 complexes of 12X FIV and wild-typeFIV PR revealed theformation of additinal van der Waals interactions between the enzyme inhibitor in the mutant PR. The 12X FIV PR retained the hydrogen bonding interactions between residues in the flap regions and active site involving the enzyme and the TL-3 inhibitor in comparison to both FIV PR and HIV PR. However, the flap regions of the 12X FIV PR more closely resemble those of HIV PR, having gained several stabilizing intra-flap interactions not present in wild type FIV PR. These findings offer a structural explanation for the observed inhibitor/substrate binding properties of the chimeric PR.

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

Heaslet, H.; Lin, Y.-C.; Tam, K.

We have obtained the 1.7 angstrom crystal structure of FIV protease (PR) in which 12 critical residues around the active site have been substituted with the structurally equivalent residues of HIV PR (12X FIV PR). The chimeric PR was crystallized in complex with the broad-based inhibitor TL-3, which inhibits wild type FIV and HIV PRs, as well as 12X FIV PR and several drug-resistant HIV mutants [1-4]. Biochemical analyses have demonstrated that TL-3 inhibits these PRs in the order HIV PR > 12X FIV PR > FIV PR, with Ki values of 1.5 nM, 10 nM, and 41 nM, respectivelymore » [2-4]. Comparison of the crystal structures of the TL-3 complexes of 12X FIV and wild-typeFIV PR revealed the formation of additional van der Waals interactions between the enzyme inhibitor in the mutant PR. The 12X FIV PR retained the hydrogen bonding interactions between residues in the flap regions and active site involving the enzyme and the TL-3 inhibitor in comparison to both FIV PR and HIV PR. However, the flap regions of the 12X FIV PR more closely resemble those of HIV PR, having gained several stabilizing intra-flap interactions not present in wild type FIV PR. These findings offer a structural explanation for the observed inhibitor/substrate binding properties of the chimeric PR.« less

Marine molluscs and fish as biomarkers of pollution stress in littoral regions of the Red Sea, Mediterranean Sea and North Sea

NASA Astrophysics Data System (ADS)

Bresler, Vladimir; Bissinger, Vera; Abelson, Avigdor; Dizer, Halim; Sturm, Armin; Kratke, Renate; Fishelson, Lev; Hansen, Peter-Diedrich

1999-12-01

The intensive development of industry and urban structures along the seashores of the world, as well as the immense increase in marine transportation and other activities, has resulted in the deposition of thousands of new chemicals and organic compounds, endangering the existence of organisms and ecosystems. The conventional single biomarker methods used in ecological assessment studies cannot provide an adequate base for environmental health assessment, management and sustainability planning. The present study uses a set of novel biochemical, physiological, cytogenetic and morphological methods to characterize the state of health of selected molluscs and fish along the shores of the German North Sea, as well as the Israeli Mediterranean and Red Sea. The methods include measurement of activity of multixenobiotic resistance-mediated transporter (MXRtr) and the system of active transport of organic anions (SATOA) as indicators of antixenobiotic defence; glutathione S-transferase (GST) activity as an indicator of biotransformation of xenobiotics; DNA unwinding as a marker of genotoxicity; micronucleus test for clastogenicity; levels of phagocytosis for immunotoxicity; cholinesterase (ChE) activity and level of catecholamines as indicators of neurotoxicity; permeability of external epithelia to anionic hydrophilic probe, intralysosomal accumulation of cationic amphiphilic probe and activity of non-specific esterases as indicators of cell/tissue viability. Complete histopathological examination was used for diagnostics of environmental pathology. The obtained data show that the activity of the defensive pumps, MXRtr and SATOA in the studied organisms was significantly higher in the surface epithelia of molluscs from a polluted site than that of the same species from control, unpolluted stations, providing clear evidence of response to stress. Enhanced frequency of DNA lesions (alkaline and acidic DNA unwinding) and micronucleus-containing cells was significantly higher in samples from polluted sites in comparison to those from the clean sites that exhibited genotoxic and clastogenic activity of the pollutants. In all the studied molluscs a negative correlation was found between the MXRtr levels of activity and the frequency of micronucleus-containing hemocytes. The expression of this was in accordance with the level of pollution. The complete histopathological examination demonstrates significantly higher frequencies of pathological alterations in organs of animals from polluted sites. A strong negative correlation was found between the frequency of these alterations and MXRtr activity in the same specimens. In addition to these parameters, a decrease in the viability was noted in molluscs from the polluted sites, but ChE activities remained similar at most sites. The methods applied in our study unmasked numerous early cryptic responses and negative alterations of health in populations of marine biota sampled from the polluted sites. This demonstrates that genotoxic, clastogenic and pathogenic xenobiotics are present and act in the studied sites and this knowledge can provide a reliable base for consideration for sustainable development.

Are the users of social networking sites homogeneous? A cross-cultural study.

PubMed

Alarcón-Del-Amo, María-Del-Carmen; Gómez-Borja, Miguel-Ángel; Lorenzo-Romero, Carlota

2015-01-01

The growing use of Social Networking Sites (SNS) around the world has made it necessary to understand individuals' behaviors within these sites according to different cultures. Based on a comparative study between two different European countries (The Netherlands versus Spain), a comparison of typologies of networked Internet users has been obtained through a latent segmentation approach. These typologies are based on the frequency with which users perform different activities, their socio-demographic variables, and experience in social networking and interaction patterns. The findings show new insights regarding international segmentation in order to analyse SNS user behaviors in both countries. These results are relevant for marketing strategists eager to use the communication potential of networked individuals and for marketers willing to explore the potential of online networking as a low cost and a highly efficient alternative to traditional networking approaches. For most businesses, expert users could be valuable opinion leaders and potential brand influencers.

Are the users of social networking sites homogeneous? A cross-cultural study

PubMed Central

Alarcón-del-Amo, María-del-Carmen; Gómez-Borja, Miguel-Ángel; Lorenzo-Romero, Carlota

2015-01-01

The growing use of Social Networking Sites (SNS) around the world has made it necessary to understand individuals' behaviors within these sites according to different cultures. Based on a comparative study between two different European countries (The Netherlands versus Spain), a comparison of typologies of networked Internet users has been obtained through a latent segmentation approach. These typologies are based on the frequency with which users perform different activities, their socio-demographic variables, and experience in social networking and interaction patterns. The findings show new insights regarding international segmentation in order to analyse SNS user behaviors in both countries. These results are relevant for marketing strategists eager to use the communication potential of networked individuals and for marketers willing to explore the potential of online networking as a low cost and a highly efficient alternative to traditional networking approaches. For most businesses, expert users could be valuable opinion leaders and potential brand influencers. PMID:26321971

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

Seitz, R.R.; Rittmann, P.D.; Wood, M.I.

The US Department of Energy Headquarters established a performance assessment task team (PATT) to integrate the activities of DOE sites that are preparing performance assessments for the disposal of newly generated low-level waste. The PATT chartered a subteam with the task of comparing computer codes and exposure scenarios used for dose calculations in performance assessments. This report documents the efforts of the subteam. Computer codes considered in the comparison include GENII, PATHRAE-EPA, MICROSHIELD, and ISOSHLD. Calculations were also conducted using spreadsheets to provide a comparison at the most fundamental level. Calculations and modeling approaches are compared for unit radionuclide concentrationsmore » in water and soil for the ingestion, inhalation, and external dose pathways. Over 30 tables comparing inputs and results are provided.« less

Hemifield-dependent N1 and event-related theta/delta oscillations: An unbiased comparison of surface Laplacian and common EEG reference choices

PubMed Central

Kayser, Jürgen; Tenke, Craig E.

2015-01-01

Surface Laplacian methodology has been used to reduce the impact of volume conduction and arbitrary choice of EEG recording reference for the analysis of surface potentials. However, the empirical implications of employing these different transformations to the same EEG data remain obscure. This study directly compared the statistical effects of four commonly-used (nose, linked mastoids, average) or recommended (reference electrode standardization technique [REST]) references and their spherical spline current source density (CSD) transformation for a large data set stemming from a well-understood experimental manipulation. ERPs (72 sites) recorded from 130 individuals during a visual half-field paradigm with highly-controlled emotional stimuli were characterized by mid-parietooccipital N1 (125 ms peak latency) and event-related synchronization (ERS) of theta/delta (160 ms), which were most robust over the contralateral hemisphere. All five data transformations were rescaled to the same covariance and submitted to a single temporal or time-frequency PCA (Varimax) to yield simplified estimates of N1 or theta/delta ERS. Unbiased nonparametric permutation tests revealed that these hemifield-dependent asymmetries were by far most focal and prominent for CSD data, despite all transformations showing maximum effects at mid-parietooccipital sites. Employing smaller subsamples (signal-to-noise) or window-based ERP/ERS amplitudes did not affect these comparisons. Furthermore, correlations between N1 and theta/delta ERS at these sites were strongest for CSD and weakest for nose-referenced data. Contrary to the common notion that the spatial high pass filter properties of a surface Laplacian reduce important contributions of neuronal generators to the EEG signal, the present findings demonstrate that instead volume conduction inherent in surface potentials weakens the representation of neuronal activation patterns at scalp that directly reflect regional brain activity. PMID:25562833

Interferometric investigations with the S1 constellation: an application to the Vesuvius/Campi Flegrei volcanic test site

NASA Astrophysics Data System (ADS)

Borgstrom, Sven; Del Gaudio, Carlo; De Martino, Prospero; Siniscalchi, Valeria; Prats-Iraola, Pau; Nannini, Matteo; Yague-Martinez, Nestor; Pinheiro, Muriel; Kim, Jun-Su; Vecchioli, Francesco; Minati, Federico; Costantini, Mario; Foumelis, Michael; Desnos, Yves-Louis

2017-04-01

The contribution focuses on the current status of the ESA study entitled "INSARAP Sentinel-1 Constellation Study" and investigates the interferometric performance of the S1A/S1B units. In particular, we refer to the Vesuvius/Campi Flegrei (Southern Italy) volcanic test site, where the continuous inflation (about 35 cm from 2011 to date) and the huge availability of ground-based geodetic data (continuous GPS - cGPS - leveling, tiltmetric, gravimetric, etc.) from the INGV-Osservatorio Vesuviano monitoring networks have allowed to get a clear deformation signal, besides the comparison between S1A/S1B and geodetic data. In this regard, the integration between InSAR and geodetic measurements is crucial for a continuous and extended monitoring of such an active volcanic area, as InSAR investigations allow to get an information on wide areas, whereas permanent networks (e.g., cGPS), allow to provide a continuous information complementing InSAR, which is limited by its revisiting time. Comparisons between S1 constellation data and geodetic measurements, with a particular focus on cGPS, will be presented, exploiting both LOS and inverted (E-W and vertical inversion) InSAR data starting from October, 2014. In addition, as a next step we are planning to model the deformation source of the area by exploiting the S1 time series results. Ultimately, very encouraging results suggest for a continuation of this activity also for the future, showing the great potential of S1 constellation data for monitoring active volcanic areas and, in general, to retrieve a very high quality deformation signal.

Shear Wave Velocity and Site Amplification Factors for 25 Strong-Motion Instrument Stations Affected by the M5.8 Mineral, Virginia, Earthquake of August 23, 2011

USGS Publications Warehouse

Kayen, Robert E.; Carkin, Brad A.; Corbett, Skye C.; Zangwill, Aliza; Estevez, Ivan; Lai, Lena

2015-01-01

Vertical one-dimensional shear wave velocity (Vs) profiles are presented for 25 strong-motion instrument sites along the Mid-Atlantic eastern seaboard, Piedmont region, and Appalachian region, which surround the epicenter of the M5.8 Mineral, Virginia, Earthquake of August 23, 2011. Testing was performed at sites in Pennsylvania, Maryland, West Virginia, Virginia, the District of Columbia, North Carolina, and Tennessee. The purpose of the study is to determine the detailed site velocity profile, the average velocity in the upper 30 meters of the profile (VS,30), the average velocity for the entire profile (VS,Z), and the National Earthquake Hazards Reduction Program (NEHRP) site classification. The Vs profiles are estimated using a non-invasive continuous-sine-wave method for gathering the dispersion characteristics of surface waves. A large trailer-mounted active source was used to shake the ground during the testing and produce the surface waves. Shear wave velocity profiles were inverted from the averaged dispersion curves using three independent methods for comparison, and the root-mean square combined coefficient of variation (COV) of the dispersion and inversion calculations are estimated for each site.

Site Protection Program and Progress Report of Ali Observatory, Tibet

NASA Astrophysics Data System (ADS)

Yao, Yongqiang; Zhou, Yunhe; Wang, Xiaohua; He, Jun; Zhou, Shu

2015-08-01

The Ali observatory, Tibet, is a promising new site identified through ten year site survey over west China, and it is of significance to establish rules of site protection during site development. The site protection program is described with five aspects: site monitoring, technical support, local government support, specific organization, and public education. The long-term sky brightness monitoring is ready with site testing instruments and basic for light pollution measurement; the monitoring also includes directions of main light sources, providing periodical reports and suggestions for coordinating meetings. The technical supports with institutes and manufacturers help to publish lighting standards and replace light fixtures; the research pays special attention to the blue-rich sources, which impact the important application of high altitude sites. An official leading group towards development and protection of astronomical resources has been established by Ali government; one of its tasks is to issue regulations against light pollution, including special restrictions of airport, mine, and winter heating, and to supervise lighting inspection and rectification. A site protection office under the official group and local astronomical society are organized by Ali observatory; the office can coordinate in government levels and promote related activities. A specific website operated by the protection office releases activity propaganda, evaluation results, and technical comparison with other observatories. Both the site protection office and Ali observatory take responsibility for public education, including popular science lectures, light pollution and energy conservation education. Ali Night Sky Park has been constructed and opens in 2014, and provides a popular place and observational experience. The establishment of Ali Observatory and Night Sky Park brings unexpected social influence, and the starry sky trip to Ali becomes a new format of culture-oriented travels in China. The related news reports and network propaganda have drawn attention of national top leadership, instructing to further investigate national support policies.

Harmane and harmalan are bioactive components of classical clonidine-displacing substance.

PubMed

Parker, Christine A; Anderson, Neil J; Robinson, Emma S J; Price, Rhiannon; Tyacke, Robin J; Husbands, Stephen M; Dillon, Michael P; Eglen, Richard M; Hudson, Alan L; Nutt, David J; Crump, Matthew P; Crosby, John

2004-12-28

Elucidation of the structure of the endogenous ligand(s) for imidazoline binding sites, clonidine-displacing substance (CDS), has been a major goal for many years. Crude CDS from bovine lung was purified by reverse-phase high-pressure liquid chromatography. Electrospray mass spectrometry (ESMS) and nuclear magnetic resonance ((1)H NMR) analysis revealed the presence of L-tryptophan and 1-carboxy-1-methyltetrahydro-beta-carboline in the active CDS extract. Competition radioligand binding studies, however, failed to show displacement of specific [(3)H]clonidine binding to rat brain membranes for either compound. Further purification of the bovine lung extract allowed the isolation of the beta-carbolines harmane and harmalan as confirmed by ESMS, (1)H NMR, and comparison with synthetic standards. Both compounds exhibited a high (nanomolar) affinity for both type 1 and type 2 imidazoline binding sites, and the synthetic standards were shown to coelute with the active classical CDS extracts. We therefore propose that the beta-carbolines harmane and harmalan represent active components of classical CDS. The identification of these compounds will allow us to establish clear physiological roles for CDS.

Structural analysis of Clostridium acetobutylicum ATCC 824 glycoside hydrolase from CAZy family GH105

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

Germane, Katherine L., E-mail: katherine.germane.civ@mail.mil; Servinsky, Matthew D.; Gerlach, Elliot S.

2015-07-29

The crystal structure of the protein product of the C. acetobutylicum ATCC 824 gene CA-C0359 is structurally similar to YteR, an unsaturated rhamnogalacturonyl hydrolase from B. subtilis strain 168. Substrate modeling and electrostatic studies of the active site of the structure of CA-C0359 suggests that the protein can now be considered to be part of CAZy glycoside hydrolase family 105. Clostridium acetobutylicum ATCC 824 gene CA-C0359 encodes a putative unsaturated rhamnogalacturonyl hydrolase (URH) with distant amino-acid sequence homology to YteR of Bacillus subtilis strain 168. YteR, like other URHs, has core structural homology to unsaturated glucuronyl hydrolases, but hydrolyzes themore » unsaturated disaccharide derivative of rhamnogalacturonan I. The crystal structure of the recombinant CA-C0359 protein was solved to 1.6 Å resolution by molecular replacement using the phase information of the previously reported structure of YteR (PDB entry (http://scripts.iucr.org/cgi-bin/cr.cgi?rm)) from Bacillus subtilis strain 168. The YteR-like protein is a six-α-hairpin barrel with two β-sheet strands and a small helix overlaying the end of the hairpins next to the active site. The protein has low primary protein sequence identity to YteR but is structurally similar. The two tertiary structures align with a root-mean-square deviation of 1.4 Å and contain a highly conserved active pocket. There is a conserved aspartic acid residue in both structures, which has been shown to be important for hydration of the C=C bond during the release of unsaturated galacturonic acid by YteR. A surface electrostatic potential comparison of CA-C0359 and proteins from CAZy families GH88 and GH105 reveals the make-up of the active site to be a combination of the unsaturated rhamnogalacturonyl hydrolase and the unsaturated glucuronyl hydrolase from Bacillus subtilis strain 168. Structural and electrostatic comparisons suggests that the protein may have a slightly different substrate specificity from that of YteR.« less

A comparison of site index curves for northern hardwood species.

Treesearch

Willard H. Carmean

1979-01-01

Gives an inventory and compares site index curves for 13 northern hardwood species. Differences illustrate the need for more precise site index curves that are applicable to local soil and site conditions.

Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking.

PubMed

Prasanna, Sivaprakasam; Daga, Pankaj R; Xie, Aihua; Doerksen, Robert J

2009-02-01

Glycogen synthase kinase-3, a serine/threonine kinase, has been implicated in a wide variety of pathological conditions such as diabetes, Alzheimer's disease, stroke, bipolar disorder, malaria and cancer. Herein we report 3D-QSAR analyses using CoMFA and CoMSIA and molecular docking studies on 3-anilino-4-phenylmaleimides as GSK-3alpha inhibitors, in order to better understand the mechanism of action and structure-activity relationship of these compounds. Comparison of the active site residues of GSK-3alpha and GSK-3beta isoforms shows that all the key amino acids involved in polar interactions with the maleimides for the beta isoform are the same in the alpha isoform, except that Asp133 in the beta isoform is replaced by Glu196 in the alpha isoform. We prepared a homology model for GSK-3alpha, and showed that the change from Asp to Glu should not affect maleimide binding significantly. Docking studies revealed the binding poses of three subclasses of these ligands, namely anilino, N-methylanilino and indoline derivatives, within the active site of the beta isoform, and helped to explain the difference in their inhibitory activity.

Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking

NASA Astrophysics Data System (ADS)

Prasanna, Sivaprakasam; Daga, Pankaj R.; Xie, Aihua; Doerksen, Robert J.

2009-02-01

Glycogen synthase kinase-3, a serine/threonine kinase, has been implicated in a wide variety of pathological conditions such as diabetes, Alzheimer's disease, stroke, bipolar disorder, malaria and cancer. Herein we report 3D-QSAR analyses using CoMFA and CoMSIA and molecular docking studies on 3-anilino-4-phenylmaleimides as GSK-3α inhibitors, in order to better understand the mechanism of action and structure-activity relationship of these compounds. Comparison of the active site residues of GSK-3α and GSK-3β isoforms shows that all the key amino acids involved in polar interactions with the maleimides for the β isoform are the same in the α isoform, except that Asp133 in the β isoform is replaced by Glu196 in the α isoform. We prepared a homology model for GSK-3α, and showed that the change from Asp to Glu should not affect maleimide binding significantly. Docking studies revealed the binding poses of three subclasses of these ligands, namely anilino, N-methylanilino and indoline derivatives, within the active site of the β isoform, and helped to explain the difference in their inhibitory activity.

Influenza epidemiology and influenza vaccine effectiveness during the 2014-2015 season: annual report from the Global Influenza Hospital Surveillance Network.

PubMed

Puig-Barberà, Joan; Burtseva, Elena; Yu, Hongjie; Cowling, Benjamin J; Badur, Selim; Kyncl, Jan; Sominina, Anna

2016-08-22

The Global Influenza Hospital Surveillance Network (GIHSN) has established a prospective, active surveillance, hospital-based epidemiological study to collect epidemiological and virological data for the Northern and Southern Hemispheres over several consecutive seasons. It focuses exclusively on severe cases of influenza requiring hospitalization. A standard protocol is shared between sites allowing comparison and pooling of results. During the 2014-2015 influenza season, the GIHSN included seven coordinating sites from six countries (St. Petersburg and Moscow, Russian Federation; Prague, Czech Republic; Istanbul, Turkey; Beijing, China; Valencia, Spain; and Rio de Janeiro, Brazil). Here, we present the detailed epidemiological and influenza vaccine effectiveness findings for the Northern Hemisphere 2014-2015 influenza season.

Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

PubMed Central

Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

2014-01-01

While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils. PMID:25058658

The Structures of the C185S and C185A Mutants of Sulfite Oxidase Reveal Rearrangement of the Active Site

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

Qiu, James A.; Wilson, Heather L.; Pushie, M. Jake

Sulfite oxidase (SO) catalyzes the physiologically critical conversion of sulfite to sulfate. Enzymatic activity is dependent on the presence of the metal molybdenum complexed with a pyranopterin-dithiolene cofactor termed molybdopterin. Comparison of the amino acid sequences of SOs from a variety of sources has identified a single conserved Cys residue essential for catalytic activity. The crystal structure of chicken liver sulfite oxidase indicated that this residue, Cys185 in chicken SO, coordinates the Mo atom in the active site. To improve our understanding of the role of this residue in the catalytic mechanism of sulfite oxidase, serine and alanine variants atmore » position 185 of recombinant chicken SO were generated. Spectroscopic and kinetic studies indicate that neither variant is capable of sulfite oxidation. The crystal structure of the C185S variant was determined to 1.9 {angstrom} resolution and to 2.4 {angstrom} resolution in the presence of sulfite, and the C185A variant to 2.8 {angstrom} resolution. The structures of the C185S and C185A variants revealed that neither the Ser or Ala side chains appeared to closely interact with the Mo atom and that a third oxo group replaced the usual cysteine sulfur ligand at the Mo center, confirming earlier extended X-ray absorption fine structure spectroscopy (EXAFS) work on the human C207S mutant. An unexpected result was that in the C185S variant, in the absence of sulfite, the active site residue Tyr322 became disordered as did the loop region flanking it. In the C185S variant crystallized in the presence of sulfite, the Tyr322 residue relocalized to the active site. The C185A variant structure also indicated the presence of a third oxygen ligand; however, Tyr322 remained in the active site. EXAFS studies of the Mo coordination environment indicate the Mo atom is in the oxidized Mo{sup VI} state in both the C185S and C185A variants of chicken SO and show the expected trioxodithiolene active site. Density functional theory calculations of the trioxo form of the cofactor reasonably reproducd the Mo=O distances of the complex; however, the calculated Mo-S distances were slightly longer than either crystallographic or EXAFS measurements. Taken together, these results indicate that the active sites of the C185S and C185A variants are essentially catalytically inactive, the crystal structures of C185S and C185A variants contain a fully oxidized, trioxo form of the cofactor, and Tyr322 can undergo a conformational change that is relevant to the reaction mechanism. Additional DFT calculations demonstrated that such methods can reasonably reproduce the geometry and bond lengths of the active site.« less

A comparison between two algorithms for the retrieval of soil moisture using AMSR-E data

USDA-ARS?s Scientific Manuscript database

A comparison between two algorithms for estimating soil moisture with microwave satellite data was carried out by using the datasets collected on the four Agricultural Research Service (ARS) watershed sites in the US from 2002 to 2009. These sites collectively represent a wide range of ground condit...

Comparing the impacts of hiking, skiing and horse riding on trail and vegetation in different types of forest.

PubMed

Törn, A; Tolvanen, A; Norokorpi, Y; Tervo, R; Siikamäki, P

2009-03-01

Nature-based tourism in protected areas has increased and diversified dramatically during the last decades. Different recreational activities have a range of impacts on natural environments. This paper reports results from a comparison of the impacts of hiking, cross-country skiing and horse riding on trail characteristics and vegetation in northern Finland. Widths and depths of existing trails, and vegetation on trails and in the neighbouring forests were monitored in two research sites during 2001 and 2002. Trail characteristics and vegetation were clearly related to the recreational activity, research site and forest type. Horse trails were as deep as hiking trails, even though the annual number of users was 150-fold higher on the hiking trails. Simultaneously, cross-country skiing had the least effect on trails due to the protective snow cover during winter. Hiking trail plots had little or no vegetation cover, horse riding trail plots had lower vegetation cover than forest plots, while skiing had no impact on total vegetation cover. On the other hand, on horse riding trails there were more forbs and grasses, many of which did not grow naturally in the forest. These species that were limited to riding trails may change the structure of adjacent plant communities in the long run. Therefore, the type of activities undertaken and the sensitivity of habitats to these activities should be a major consideration in the planning and management of nature-based tourism. Establishment of artificial structures, such as stairs, duckboards and trail cover, or complete closure of the site, may be the only way to protect the most sensitive or deteriorated sites.

Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity.

PubMed

Skala, Wolfgang; Utzschneider, Daniel T; Magdolen, Viktor; Debela, Mekdes; Guo, Shihui; Craik, Charles S; Brandstetter, Hans; Goettig, Peter

2014-12-05

Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the "classical" KLKs 1-3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn(2+) concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn(2+), which located the Zn(2+) binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure-Function Analyses of Human Kallikrein-related Peptidase 2 Establish the 99-Loop as Master Regulator of Activity*

PubMed Central

Skala, Wolfgang; Utzschneider, Daniel T.; Magdolen, Viktor; Debela, Mekdes; Guo, Shihui; Craik, Charles S.; Brandstetter, Hans; Goettig, Peter

2014-01-01

Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the “classical” KLKs 1–3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn2+ concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn2+, which located the Zn2+ binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation. PMID:25326387

Evaluation of a quality improvement intervention to prevent mother-to-child transmission of HIV (PMTCT) at Zambia defence force facilities.

PubMed

Kim, Young Mi; Chilila, Maureen; Shasulwe, Hildah; Banda, Joseph; Kanjipite, Webby; Sarkar, Supriya; Bazant, Eva; Hiner, Cyndi; Tholandi, Maya; Reinhardt, Stephanie; Mulilo, Joyce Chongo; Kols, Adrienne

2013-09-08

The Zambian Defence Force (ZDF) is working to improve the quality of services to prevent mother-to-child transmission of HIV (PMTCT) at its health facilities. This study evaluates the impact of an intervention that included provider training, supportive supervision, detailed performance standards, repeated assessments of service quality, and task shifting of group education to lay workers. Four ZDF facilities implementing the intervention were matched with four comparison sites. Assessors visited the sites before and after the intervention and completed checklists while observing 387 antenatal care (ANC) consultations and 41 group education sessions. A checklist was used to observe facilities' infrastructure and support systems. Bivariate and multivariate analyses were conducted of findings on provider performance during consultations. Among 137 women observed during their initial ANC visit, 52% came during the first 20 weeks of pregnancy, but 19% waited until the 28th week or later. Overall scores for providers' PMTCT skills rose from 58% at baseline to 73% at endline (p=0.003) at intervention sites, but remained stable at 52% at comparison sites. Especially large gains were seen at intervention sites in family planning counseling (34% to 75%, p=0.026), HIV testing during return visits (13% to 48%, p=0.034), and HIV/AIDS management during visits that did not include an HIV test (1% to 34%, p=0.004). Overall scores for providers' ANC skills rose from 67% to 74% at intervention sites, but declined from 65% to 59% at comparison sites; neither change was significant in the multivariate analysis. Overall scores for group education rose from 87% to 91% at intervention sites and declined from 78% to 57% at comparison sites. The overall facility readiness score rose from 73% to 88% at intervention sites and from 75% to 82% at comparison sites. These findings are relevant to civilian as well as military health systems in Zambia because the two are closely coordinated. Lessons learned include: the ability of detailed performance standards to draw attention to and strengthen areas of weakness; the benefits of training lay workers to take over non-clinical PMTCT tasks; and the need to encourage pregnant women to seek ANC early.

Elastomeric enriched biodegradable polyurethane sponges for critical bone defects: a successful case study reducing donor site morbidity.

PubMed

Lavrador, Catarina; Mascarenhas, Ramiro; Coelho, Paulo; Brites, Cláudia; Pereira, Alfredo; Gogolewski, Sylwester

2016-03-01

Bone substitutes have been a critical issue as the natural source can seldom provide enough bone to support full healing. No bone substitute complies with all necessary functions and characteristics that an autograft does. Polyurethane sponges have been used as a surgical alternative to cancellous bone grafts for critical bone defect donor sites. Critical bone defects were created on the tibial tuberosity and iliac crest using an ovine model. In group I (control-untreated), no bone regeneration was observed in any animal. In group II (defects left empty but covered with a microporous polymeric membrane), the new bone bridged the top ends in all animals. In groups III and IV, bone defects were implanted with polyurethane scaffolds modified with biologically active compounds, and bone regeneration was more efficient than in group II. In groups III and IV there were higher values of bone regeneration specific parameters used for evaluation (P < 0.05) although the comparison between these groups was not possible. The results obtained in this study suggest that biodegradable polyurethane substitutes modified with biologically active substances may offer an alternative to bone graft, reducing donor site morbidity associated with autogenous cancellous bone harvesting.

Intercomparison of atmospheric water vapour measurements at a Canadian High Arctic site

NASA Astrophysics Data System (ADS)

Weaver, Dan; Strong, Kimberly; Schneider, Matthias; Rowe, Penny M.; Sioris, Chris; Walker, Kaley A.; Mariani, Zen; Uttal, Taneil; McElroy, C. Thomas; Vömel, Holger; Spassiani, Alessio; Drummond, James R.

2017-08-01

Water vapour is a critical component of the Earth system. Techniques to acquire and improve measurements of atmospheric water vapour and its isotopes are under active development. This work presents a detailed intercomparison of water vapour total column measurements taken between 2006 and 2014 at a Canadian High Arctic research site (Eureka, Nunavut). Instruments include radiosondes, sun photometers, a microwave radiometer, and emission and solar absorption Fourier transform infrared (FTIR) spectrometers. Close agreement is observed between all combination of datasets, with mean differences ≤ 1.0 kg m-2 and correlation coefficients ≥ 0.98. The one exception in the observed high correlation is the comparison between the microwave radiometer and a radiosonde product, which had a correlation coefficient of 0.92.A variety of biases affecting Eureka instruments are revealed and discussed. A subset of Eureka radiosonde measurements was processed by the Global Climate Observing System (GCOS) Reference Upper Air Network (GRUAN) for this study. Comparisons reveal a small dry bias in the standard radiosonde measurement water vapour total columns of approximately 4 %. A recently produced solar absorption FTIR spectrometer dataset resulting from the MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water) retrieval technique is shown to offer accurate measurements of water vapour total columns (e.g. average agreement within -5.2 % of GRUAN and -6.5 % of a co-located emission FTIR spectrometer). However, comparisons show a small wet bias of approximately 6 % at the high-latitude Eureka site. In addition, a new dataset derived from Atmospheric Emitted Radiance Interferometer (AERI) measurements is shown to provide accurate water vapour measurements (e.g. average agreement was within 4 % of GRUAN), which usefully enables measurements to be taken during day and night (especially valuable during polar night).

Planktonic food web structure at a coastal time-series site: II. Spatiotemporal variability of microbial trophic activities

NASA Astrophysics Data System (ADS)

Connell, Paige E.; Campbell, Victoria; Gellene, Alyssa G.; Hu, Sarah K.; Caron, David A.

2017-03-01

The grazing activities of phagotrophic protists on various microbial assemblages play key roles in determining the amount of carbon available for higher trophic levels and for export out of the photic zone. However, comparisons of the proportion of carbon consumed from the phytoplankton (cyanobacteria+photosynthetic eukaryotes) and heterotrophic bacteria (bacteria+archaea, excluding cyanobacteria) are rare. In this study, microbial community composition, phytoplankton growth and mortality rates (total chlorophyll a, Synechococcus, Prochlorococcus, and photosynthetic picoeukaryotes), and bacterial mortality rates were measured seasonally from 2012 to 2014 in the surface waters of three environmentally distinct sites in the San Pedro Channel, off the coast of southern CA, USA. Higher nutrient concentrations at the nearshore site supported community standing stocks that were 1.3-4.5x those found offshore, yet average growth and grazing rates of the phytoplankton and bacterial assemblages were generally similar between sites and across seasons. Thus, the amount of carbon consumed by the grazer assemblage was largely dictated by prey standing stocks. Heterotrophic bacteria constituted an important source of carbon for microbial consumers, particularly at the two offshore sites where bacterial carbon consumed was roughly equivalent to the amount of phytoplankton carbon consumed. Carbon removal by grazers at the nearshore station was predominantly from the diatoms, which were the primary component of the photosynthetic community at that site. This study highlights the significant contribution of protistan-bacterial trophic interactions to planktonic food webs and provides unique community composition and turnover data to inform biogeochemical models.

Designing Hydrolytic Zinc Metalloenzymes

PubMed Central

2015-01-01

Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up. PMID:24506795

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

Site index comparisons among hardwoods

Treesearch

Richard M. Godman

1992-01-01

Site index is one of the more easily measured indicators of the productive capacity of an area for a given species. In mixed stands, the site index of one species can be used to predict the site index of another. Site index also illustrates growth differences among species.

Structure-Activity Relationship Models for Rat Carcinogenesis and Assessing the Role Mutagens Play in Model Predictivity

PubMed Central

Carrasquer, C. Alex; Batey, Kaylind; Qamar, Shahid; Cunningham, Albert R.; Cunningham, Suzanne L.

2016-01-01

We previously demonstrated that fragment based cat-SAR carcinogenesis models consisting solely of mutagenic or non-mutagenic carcinogens varied greatly in terms of their predictive accuracy. This led us to investigate how well the rat cancer cat-SAR model predicted mutagens and non-mutagens in their learning set. Four rat cancer cat-SAR models were developed: Complete Rat, Transgender Rat, Male Rat, and Female Rat, with leave-one-out (LOO) validation concordance values of 69%, 74%, 67%, and 73%, respectively. The mutagenic carcinogens produced concordance values in the range of 69–76% as compared to only 47–53% for non-mutagenic carcinogens. As a surrogate for mutagenicity comparisons between single site and multiple site carcinogen SAR models was analyzed. The LOO concordance values for models consisting of 1-site, 2-site, and 4+-site carcinogens were 66%, 71%, and 79%, respectively. As expected, the proportion of mutagens to non-mutagens also increased, rising from 54% for 1-site to 80% for 4+-site carcinogens. This study demonstrates that mutagenic chemicals, in both SAR learning sets and test sets, are influential in assessing model accuracy. This suggests that SAR models for carcinogens may require a two-step process in which mutagenicity is first determined before carcinogenicity can be accurately predicted. PMID:24697549

Usefulness of ventricular endocardial electric reconstruction from body surface potential maps to noninvasively localize ventricular ectopic activity in patients

NASA Astrophysics Data System (ADS)

Lai, Dakun; Sun, Jian; Li, Yigang; He, Bin

2013-06-01

As radio frequency (RF) catheter ablation becomes increasingly prevalent in the management of ventricular arrhythmia in patients, an accurate and rapid determination of the arrhythmogenic site is of important clinical interest. The aim of this study was to test the hypothesis that the inversely reconstructed ventricular endocardial current density distribution from body surface potential maps (BSPMs) can localize the regions critical for maintenance of a ventricular ectopic activity. Patients with isolated and monomorphic premature ventricular contractions (PVCs) were investigated by noninvasive BSPMs and subsequent invasive catheter mapping and ablation. Equivalent current density (CD) reconstruction (CDR) during symptomatic PVCs was obtained on the endocardial ventricular surface in six patients (four men, two women, years 23-77), and the origin of the spontaneous ectopic activity was localized at the location of the maximum CD value. Compared with the last (successful) ablation site (LAS), the mean and standard deviation of localization error of the CDR approach were 13.8 and 1.3 mm, respectively. In comparison, the distance between the LASs and the estimated locations of an equivalent single moving dipole in the heart was 25.5 ± 5.5 mm. The obtained CD distribution of activated sources extending from the catheter ablation site also showed a high consistency with the invasively recorded electroanatomical maps. The noninvasively reconstructed endocardial CD distribution is suitable to predict a region of interest containing or close to arrhythmia source, which may have the potential to guide RF catheter ablation.

DEMETER Observations of ELF Waves Injected With the HAARP HF Transmitter

DTIC Science & Technology

2006-08-17

DEMETER observations of ELF waves injected with the HAARP HF transmitter M. Platino,1 U. S. Inan,1 T. F. Bell,1 M. Parrot,2 and E. J. Kennedy3...Frequency Active Auroral Research Program ( HAARP ) facility in Gakona, Alaska, (located at L 4.9). Simultaneous observations of all six components of the ELF...signals generated by the HAARP heater are also simultaneously observed at a nearby ground-based site, allowing a comparison of the ELF power in the

Transfer of innovation on allergic rhinitis and asthma multimorbidity in the elderly (MACVIA-ARIA) - EIP on AHA Twinning Reference Site (GARD research demonstration project).

PubMed

Bousquet, J; Agache, I; Aliberti, M R; Angles, R; Annesi-Maesano, I; Anto, J M; Arnavielhe, S; Asayag, E; Bacci, E; Bedbrook, A; Bachert, C; Baroni, I; Barreto, B A; Bedolla-Barajas, M; Bergmann, K C; Bertorello, L; Bewick, M; Bieber, T; Birov, S; Bindslev-Jensen, C; Blua, A; Bochenska Marciniak, M; Bogus-Buczynska, I; Bosnic-Anticevich, S; Bosse, I; Bourret, R; Bucca, C; Buonaiuto, R; Burguete Cabanas, M T; Caillaud, D; Caimmi, D P; Caiazza, D; Camargos, P; Canfora, G; Cardona, V; Carriazo, A M; Cartier, C; Castellano, G; Chavannes, N H; Cecci, L; Ciaravolo, M M; Cingi, C; Ciceran, A; Colas, L; Colgan, E; Coll, J; Conforti, D; Correia de Sousa, J; Cortés-Grimaldo, R M; Corti, F; Costa, E; Courbis, A L; Cousein, E; Cruz, A A; Custovic, A; Cvetkovski, B; Dario, C; da Silva, J; Dauvilliers, Y; De Blay, F; Dedeu, T; De Feo, G; De Martino, B; Demoly, P; De Vries, G; Di Capua Ercolano, S; Di Carluccio, N; Doulapsi, M; Dray, G; Dubakiene, R; Eller, E; Emuzyte, R; Espinoza-Contreras, J G; Estrada-Cardona, A; Farrell, J; Farsi, A; Ferrero, J; Fokkens, W J; Fonseca, J; Fontaine, J F; Forti, S; Gálvez-Romero, J L; García-Cobas, C I; Garcia Cruz, M H; Gemicioğlu, B; Gerth van Wijk, R; Guidacci, M; Gómez-Vera, J; Guldemond, N A; Gutter, Z; Haahtela, T; Hajjam, J; Hellings, P W; Hernández-Velázquez, L; Illario, M; Ivancevich, J C; Jares, E; Joos, G; Just, J; Kalayci, O; Kalyoncu, A F; Karjalainen, J; Keil, T; Khaltaev, N; Klimek, L; Kritikos, V; Kull, I; Kuna, P; Kvedariene, V; Kolek, V; Krzych-Fałta, E; Kupczyk, M; Lacwik, P; La Grutta, S; Larenas-Linnemann, D; Laune, D; Lauri, D; Lavrut, J; Lessa, M; Levato, G; Lewis, L; Lieten, I; Lipiec, A; Louis, R; Luna-Pech, J A; Magnan, A; Malva, J; Maspero, J F; Matta-Campos, J J; Mayora, O; Medina-Ávalos, M A; Melén, E; Menditto, E; Millot-Keurinck, J; Moda, G; Morais-Almeida, M; Mösges, R; Mota-Pinto, A; Mullol, J; Muraro, A; Murray, R; Noguès, M; Nalin, M; Napoli, L; Neffen, H; O'Hehir, R E; Onorato, G L; Palkonen, S; Papadopoulos, N G; Passalacqua, G; Pépin, J L; Pereira, A M; Persico, M; Pfaar, O; Pozzi, A C; Prokopakis, E; Pugin, B; Raciborski, F; Rimmer, J; Rizzo, J A; Robalo-Cordeiro, C; Rodríguez-González, M; Rolla, G; Roller-Wirnsberger, R E; Romano, A; Romano, M; Romano, M R; Salimäki, J; Samolinski, B; Serpa, F S; Shamai, S; Sierra, M; Sova, M; Sorlini, M; Stellato, C; Stelmach, R; Strandberg, T; Stroetmann, V; Stukas, R; Szylling, A; Tan, R; Tibaldi, V; Todo-Bom, A; Toppila-Salmi, S; Tomazic, P; Trama, U; Triggiani, M; Valero, A; Valovirta, E; Valiulis, A; van Eerd, M; Vasankari, T; Vatrella, A; Ventura, M T; Verissimo, M T; Viart, F; Williams, S; Wagenmann, M; Wanscher, C; Westman, M; Wickman, M; Young, I; Yorgancioglu, A; Zernotti, E; Zuberbier, T; Zurkuhlen, A; De Oliviera, B; Senn, A

2018-01-01

The overarching goals of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA) are to enable European citizens to lead healthy, active and independent lives whilst ageing. The EIP on AHA includes 74 Reference Sites. The aim of this study was to transfer innovation from an app developed by the MACVIA-France EIP on AHA reference site (Allergy Diary) to other reference sites. The phenotypic characteristics of rhinitis and asthma multimorbidity in adults and the elderly will be compared using validated information and communication technology (ICT) tools (i.e. the Allergy Diary and CARAT: Control of Allergic Rhinitis and Asthma Test) in 22 Reference Sites or regions across Europe. This will improve the understanding, assessment of burden, diagnosis and management of rhinitis in the elderly by comparison with an adult population. Specific objectives will be: (i) to assess the percentage of adults and elderly who are able to use the Allergy Diary, (ii) to study the phenotypic characteristics and treatment over a 1-year period of rhinitis and asthma multimorbidity at baseline (cross-sectional study) and (iii) to follow-up using visual analogue scale (VAS). This part of the study may provide some insight into the differences between the elderly and adults in terms of response to treatment and practice. Finally (iv) work productivity will be examined in adults. © 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.

On-site or off-site treatment of medical waste: a challenge

PubMed Central

2014-01-01

Treating hazardous-infectious medical waste can be carried out on-site or off-site of health-care establishments. Nevertheless, the selection between on-site and off-site locations for treating medical waste sometimes is a controversial subject. Currently in Iran, due to policies of Health Ministry, the hospitals have selected on-site-treating method as the preferred treatment. The objectives of this study were to assess the current condition of on-site medical waste treatment facilities, compare on-site medical waste treatment facilities with off-site systems and find the best location of medical waste treatment. To assess the current on-site facilities, four provinces (and 40 active hospitals) were selected to participate in the survey. For comparison of on-site and off-site facilities (due to non availability of an installed off-site facility) Analytical Hierarchy Process (AHP) was employed. The result indicated that most on-site medical waste treating systems have problems in financing, planning, determining capacity of installations, operation and maintenance. AHP synthesis (with inconsistency ratio of 0.01 < 0.1) revealed that, in total, the off-site treatment of medical waste was in much higher priority than the on-site treatment (64.1% versus 35.9%). According to the results of study it was concluded that the off-site central treatment can be considered as an alternative. An amendment could be made to Iran’s current medical waste regulations to have infectious-hazardous waste sent to a central off-site installation for treatment. To begin and test this plan and also receive the official approval, a central off-site can be put into practice, at least as a pilot in one province. Next, if it was practically successful, it could be expanded to other provinces and cities. PMID:24739145

A comparative study of rhodopsin function in the great bowerbird (P tilonorhynchus nuchalis): Spectral tuning and light‐activated kinetics

PubMed Central

van Hazel, Ilke; Dungan, Sarah Z.; Hauser, Frances E.; Morrow, James M.; Endler, John A.

2016-01-01

Abstract Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well‐characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein‐coupled receptors. While this substitution is present in some dim‐light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site‐directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue‐shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light‐activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure‐function as well as their evolutionary significance for dim‐light vision across vertebrates. PMID:26889650

A standards-based approach to quality improvement for HIV services at Zambia Defence Force facilities: results and lessons learned.

PubMed

Kols, Adrienne; Kim, Young-Mi; Bazant, Eva; Necochea, Edgar; Banda, Joseph; Stender, Stacie

2015-07-01

The Zambia Defence Force adopted the Standards-Based Management and Recognition approach to improve the quality of the HIV-related services at its health facilities. This quality improvement intervention relies on comprehensive, detailed assessment tools to communicate and verify adherence to national standards of care, and to test and implement changes to improve performance. A quasi-experimental evaluation of the intervention was conducted at eight Zambia Defence Force primary health facilities (four facilities implemented the intervention and four did not). Data from three previous analyses are combined to assess the effect of Standards-Based Management and Recognition on three domains: facility readiness to provide services; observed provider performance during antiretroviral therapy (ART) and antenatal care consultations; and provider perceptions of the work environment. Facility readiness scores for ART improved on four of the eight standards at intervention sites, and one standard at comparison sites. Facility readiness scores for prevention of mother-to-child transmission (PMTCT) of HIV increased by 15 percentage points at intervention sites and 7 percentage points at comparison sites. Provider performance improved significantly at intervention sites for both ART services (from 58 to 84%; P < 0.01) and PMTCT services (from 58 to 73%; P = 0.003); there was no significant change at comparison sites. Providers' perceptions of the work environment generally improved at intervention sites and declined at comparison sites; differences in trends between study groups were significant for eight items. A standards-based approach to quality improvement proved effective in supporting healthcare managers and providers to deliver ART and PMTCT services in accordance with evidence-based standards in a health system suffering from staff shortages.

Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain

PubMed Central

Djordjevic, Snezana; Goudreau, Paul N.; Xu, Qingping; Stock, Ann M.; West, Ann H.

1998-01-01

We report the x-ray crystal structure of the methylesterase CheB, a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors. Methylesterase CheB and methyltransferase CheR modulate signaling output of the chemotaxis receptors by controlling the level of receptor methylation. The structure of CheB, which consists of an N-terminal regulatory domain and a C-terminal catalytic domain joined by a linker, was solved by molecular replacement methods using independent search models for the two domains. In unphosphorylated CheB, the N-terminal domain packs against the active site of the C-terminal domain and thus inhibits methylesterase activity by directly restricting access to the active site. We propose that phosphorylation of CheB induces a conformational change in the regulatory domain that disrupts the domain interface, resulting in a repositioning of the domains and allowing access to the active site. Structural similarity between the two companion receptor modification enzymes, CheB and CheR, suggests an evolutionary and/or functional relationship. Specifically, the phosphorylated N-terminal domain of CheB may facilitate interaction with the receptors, similar to the postulated role of the N-terminal domain of CheR. Examination of surfaces in the N-terminal regulatory domain of CheB suggests that despite a common fold throughout the response regulator family, surfaces used for protein–protein interactions differ significantly. Comparison between CheB and other response regulators indicates that analogous surfaces are used for different functions and conversely, similar functions are mediated by different molecular surfaces. PMID:9465023

Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase B.

PubMed

Adler, Marc; Bryant, Judi; Buckman, Brad; Islam, Imadul; Larsen, Brent; Finster, Silke; Kent, Lorraine; May, Karen; Mohan, Raju; Yuan, Shendong; Whitlow, Marc

2005-07-05

This paper presents the crystal structure of porcine pancreatic carboxypeptidase B (pp-CpB) in complex with a variety of thiol-based inhibitors that were developed as antagonists of activated thrombin-activatable fibrinolysis inhibitor (TAFIa). Recent studies have indicated that a selective inhibitor of TAFIa could enhance the efficacy of existing thrombolytic agents for the treatment of acute myocardial infarction, one of the most prevalent forms of heart attacks. Unfortunately, activated TAFIa rapidly degrades in solution and cannot be used for crystallographic studies. In contrast, porcine pancreatic CpB is stable at room temperature and is available from commercial sources. Both pancreatic CpB and TAFIa are zinc-based exopeptidases, and the proteins share a 47% sequence identity. The homology improves considerably in the active site where nearly all of the residues are conserved. The inhibitors used in this study were designed to mimic a C-terminal arginine residue, one of the natural substrates of TAFIa. The X-ray structures show that the thiol group chelates the active site zinc, the carboxylic acid forms a salt bridge to Arg145, and the guanidine group forms two hydrogen bonds to Asp255. A meta-substituted phenyl was introduced into our inhibitors to reduce conformational freedom. This modification vastly improved the selectivity of compounds against other exopeptidases that cleave basic residues. Comparisons between structures indicate that selectivity derives from the interaction between the guanidine group in the inhibitors and an acidic active site residue. The location of this acidic residue is not conserved in the various carboxypeptidases.

Comparison of soil sampling and analytical methods for asbestos at the Sumas Mountain Asbestos Site-Working towards a toolbox for better assessment.

PubMed

Wroble, Julie; Frederick, Timothy; Frame, Alicia; Vallero, Daniel

2017-01-01

Established soil sampling methods for asbestos are inadequate to support risk assessment and risk-based decision making at Superfund sites due to difficulties in detecting asbestos at low concentrations and difficulty in extrapolating soil concentrations to air concentrations. Environmental Protection Agency (EPA)'s Office of Land and Emergency Management (OLEM) currently recommends the rigorous process of Activity Based Sampling (ABS) to characterize site exposures. The purpose of this study was to compare three soil analytical methods and two soil sampling methods to determine whether one method, or combination of methods, would yield more reliable soil asbestos data than other methods. Samples were collected using both traditional discrete ("grab") samples and incremental sampling methodology (ISM). Analyses were conducted using polarized light microscopy (PLM), transmission electron microscopy (TEM) methods or a combination of these two methods. Data show that the fluidized bed asbestos segregator (FBAS) followed by TEM analysis could detect asbestos at locations that were not detected using other analytical methods; however, this method exhibited high relative standard deviations, indicating the results may be more variable than other soil asbestos methods. The comparison of samples collected using ISM versus discrete techniques for asbestos resulted in no clear conclusions regarding preferred sampling method. However, analytical results for metals clearly showed that measured concentrations in ISM samples were less variable than discrete samples.

Present tectonics of the southeast of Russia as seen from GPS observations

NASA Astrophysics Data System (ADS)

Shestakov, N. V.; Gerasimenko, M. D.; Takahashi, H.; Kasahara, M.; Bormotov, V. A.; Bykov, V. G.; Kolomiets, A. G.; Gerasimov, G. N.; Vasilenko, N. F.; Prytkov, A. S.; Timofeev, V. Yu.; Ardyukov, D. G.; Kato, T.

2011-02-01

The present tectonics of Northeast Asia has been extensively investigated during the last 12 yr by using GPS techniques. Nevertheless, crustal velocity field of the southeast of Russia near the northeastern boundaries of the hypothesized Amurian microplate has not been defined yet. The GPS data collected between 1997 February and 2009 April at sites of the regional geodynamic network were used to estimate the recent geodynamic activity of this area. The calculated GPS velocities indicate almost internal (between network sites) and external (with respect to the Eurasian tectonic plate) stability of the investigated region. We have not found clear evidences of any notable present-day tectonic activity of the Central Sikhote-Alin Fault as a whole. This fault is the main tectonic unit that determines the geological structure of the investigated region. The obtained results speak in favour of the existence of a few separate blocks and a more sophisticated structure of the proposed Amurian microplate in comparison with an indivisible plate approach.

Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus.

PubMed

Collart, F R; Osipiuk, J; Trent, J; Olsen, G J; Huberman, E

1996-10-03

We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Pyrococcus furiosus (Pf), a hyperthermophillic archeon. Sequence analysis of the Pf gene indicated an open reading frame specifying a protein of 485 amino acids (aa) with a calculated M(r) of 52900. Canonical Archaea promoter elements, Box A and Box B, are located -49 and -17 nucleotides (nt), respectively, upstream of the putative start codon. The sequence of the putative active-site region conforms to the IMPDH signature motif and contains a putative active-site cysteine. Phylogenetic relationships derived by using all available IMPDH sequences are consistent with trees developed for other molecules; they do not precisely resolve the history of Pf IMPDH but indicate a close similarity to bacterial IMPDH proteins. The phylogenetic analysis indicates that a gene duplication occurred prior to the division between rodents and humans, accounting for the Type I and II isoforms identified in mice and humans.

Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

NASA Astrophysics Data System (ADS)

Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

2015-05-01

The immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles was investigated. For all particle sizes investigated, a leveling off of the frozen droplet fraction was observed reaching a plateau within the heterogeneous freezing temperature regime (T >- 38°C). The frozen fraction in the plateau region was proportional to the particle surface area. Based on these findings, an asymptotic value for ice active surface site density ns, which we named ns⋆, could be determined for the investigated feldspar sample. The comparison of these results with those of other studies not only elucidates the general feasibility of determining such an asymptotic value but also shows that the value of ns⋆ strongly depends on the method of the particle surface area determination. However, such an asymptotic value might be an important input parameter for atmospheric modeling applications. At least it shows that care should be taken when ns is extrapolated to lower or higher temperature.

Photosynthesis of boreal ground vegetation after a forest clear-cut

NASA Astrophysics Data System (ADS)

Kulmala, L.; Pumpanen, J.; Vesala, T.; Hari, P.

2009-11-01

Heather (Calluna vulgaris), rosebay willowherb (Epilobium angustifolium), wavy hair-grass (Deschampsia flexuosa) and raspberry (Rubus idaeus) are typical species at boreal clear-cut sites. In this study, we measured their photosynthesis separately in the growing season of 2005 using a manual chamber. All measured species showed clear and species-specific seasonal cycles of photosynthetic activity (Pmax). The maxima of C. vulgaris and E. angustifolium occurred around June and July, while that of R. idaeus occurred as late as August. A simple model of photosynthetic activity is presented, addressing the photosynthesis of C. vulgaris was mainly explained by temperature history when the soil moisture is high. The activity of deciduous D. flexuosa also followed the temperature history, unlike the activities of E. angustifolium and R. idaeus. During a short drought, some shoots decreased their Pmax levels but none of the species showed similar reactions between individuals. We also observed that the comparison of the whole-plant Pmax or respiration of different-sized individuals were less scattered than the results based on full-grown leaf mass, implying that species-specific rates of photosynthesis at ground level are rather similar regardless of the plant size. Using species composition and continuous temperature and light measurements, we upscaled the species-specific process rates and integrated fixed and respired CO2 of ground vegetation for the entire 2005 growing season. The photosynthetic production per surface area of soil was 760 g C m-2 y-1 at the fertile site and 300 g C m-2 y-1 at the infertile site. During the snow-free period (18 April-21 November), the above ground parts of measured species released 75 g C m-2 y-1 at the infertile site. At the fertile site, E. angustifolium and R. idaeus respired 22 and 12 g C m-2 y-1, respectively.

Regimes of association of arsenic and selenium during pulverized coal combustion

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

Wayne S. Seames; Jost O.L. Wendt

2007-07-01

A suite of six coals, of widely differing As, Se, Ca, Fe, and sulfur contents, was burned under self-sustaining conditions in a 17 kW downflow laboratory combustor. Size segregated ash-laden aerosol samples were isokinetically withdrawn and collected on a Berner low pressure impactor. Correlations between trace element concentration (As or Se) and that of major elements (as functions of particle size) were then used to infer chemical associations between trace metals and Ca and/or Fe, and how these depended on sulfur. These baseline data led to formation of the following hypotheses, namely: (1) dominant As and Se partitioning mechanisms dependmore » on the availability of Ca and/or Fe active sites for surface reaction; (2) increasing combustion temperature increases the availability of active cation sites, and increases partitioning of As and Se to fly ash by surface reaction; (3) sulfur competes with these surface reactions, decreasing As and Se partitioning to fly ash surfaces. These hypotheses were tested by manipulating the As, Se, Ca, Fe, and S contents for various coals by doping. Temperature was adjusted in order to achieve comparisons of different coals and different coal constituents at similar thermal conditions, through O{sub 2} and CO{sub 2} addition, as required. These results confirmed the hypotheses above, and allowed an association regime map to be constructed. This map shows that both As and Se associate with Fe and Ca, provided active sites are available. Se reacts preferentially with Fe over Ca when both are available while As reactions with both Fe and Ca are comparable. Sulfur can prevent association of both As and Se, by preferentially reacting with active sites, especially those on Fe. When sufficient sites are not available, the release of vapor-phase As and Se species is promoted. 23 refs., 4 figs., 4 tabs.« less

COMPARISON OF THE SPECIATED VOC COMPOSITION AT SELECTED HOUSTON, TEXAS AREA SITES FOR THE YEARS 1978 AND 2000

EPA Science Inventory

Comparisons are presented for the C2-C12 volatile organic compounds (VOCs) observed at Houston area sites used for ambient air monitoring during special ozone field study programs conducted in 1978 and 2000. In 1978 the special study called the Houston Ozone Modeling Study cons...

Functional and Neuroanatomical Specificity of Episodic Memory Dysfunction in Schizophrenia: An fMRI study of the Relational and Item-Specific Encoding Task

PubMed Central

Ragland, J. Daniel; Ranganath, Charan; Harms, Michael P.; Barch, Deanna M.; Gold, James M.; Layher, Evan; Lesh, Tyler A.; MacDonald, Angus W.; Niendam, Tara A.; Phillips, Joshua; Silverstein, Steven M.; Yonelinas, Andrew P.; Carter, Cameron S.

2015-01-01

Importance Individuals with schizophrenia (SZ) can encode item-specific information to support familiarity-based recognition, but are disproportionately impaired encoding inter-item relationships (relational encoding) and recollecting information. The Relational and Item-Specific Encoding (RiSE) paradigm has been used to disentangle these encoding and retrieval processes, which may be dependent on specific medial temporal lobe (MTL) and prefrontal cortex (PFC) subregions. Functional imaging during RiSE task performance could help to specify dysfunctional neural circuits in SZ that can be targeted for interventions to improve memory and functioning in the illness. Objectives To use functional magnetic resonance imaging (fMRI) to test the hypothesis that SZ disproportionately affects MTL and PFC subregions during relational encoding and retrieval, relative to item-specific memory processes. Imaging results from healthy comparison subjects (HC) will also be used to establish neural construct validity for RiSE. Design, Setting, and Participants This multi-site, case-control, cross-sectional fMRI study was conducted at five CNTRACS sites. The final sample included 52 clinically stable outpatients with SZ, and 57 demographically matched HC. Main Outcomes and Measures Behavioral performance speed and accuracy (d’) on item recognition and associative recognition tasks. Voxelwise statistical parametric maps for a priori MTL and PFC regions of interest (ROI), testing activation differences between relational and item-specific memory during encoding and retrieval. Results Item recognition was disproportionately impaired in SZ patients relative to controls following relational encoding. The differential deficit was accompanied by reduced dorsolateral prefrontal cortex (DLPFC) activation during relational encoding in SZ, relative to HC. Retrieval success (hits > misses) was associated with hippocampal (HI) activation in HC during relational item recognition and associative recognition conditions, and HI activation was specifically reduced in SZ for recognition of relational but not item-specific information. Conclusions In this unique, multi-site fMRI study, HC results supported RiSE construct validity by revealing expected memory effects in PFC and MTL subregions during encoding and retrieval. Comparison of SZ and HC revealed disproportionate memory deficits in SZ for relational versus item-specific information, accompanied by regionally and functionally specific deficits in DLPFC and HI activation. PMID:26200928

An In Vitro Comparison of PMMA and Calcium Sulfate as Carriers for the Local Delivery of Gallium(III) Nitrate to Staphylococcal Infected Surgical Sites

PubMed Central

Garcia, Rebecca A.; Tennent, David J.; Chang, David; Wenke, Joseph C.; Sanchez, Carlos J.

2016-01-01

Antibiotic-loaded bone cements, including poly(methyl methacrylate) (PMMA) and calcium sulfate (CaSO4), are often used for treatment of orthopaedic infections involving Staphylococcus spp., although the effectiveness of this treatment modality may be limited due to the emergence of antimicrobial resistance and/or the development of biofilms within surgical sites. Gallium(III) is an iron analog capable of inhibiting essential iron-dependent pathways, exerting broad antimicrobial activity against multiple microorganisms, including Staphylococcus spp. Herein, we evaluated PMMA and CaSO4 as carriers for delivery of gallium(III) nitrate (Ga(NO3)3) to infected surgical sites by assessing the release kinetics subsequent to incorporation and antimicrobial activity against S. aureus and S. epidermidis. PMMA and to a lesser extent CaSO4 were observed to be compatible as carriers for Ga(NO3)3, eluting concentrations with antimicrobial activity against planktonic bacteria, inhibiting bacterial growth, and preventing bacterial colonization of beads, and effective against established bacterial biofilms of S. aureus and S. epidermidis. Collectively, our in vitro results indicate that PMMA is a more suitable carrier compared to CaSO4 for delivery of Ga(NO3)3; moreover they provide evidence for the potential use of Ga(NO3)3 with PMMA as a strategy for the prevention and/or treatment for orthopaedic infections. PMID:26885514

Norwegian deep-water coral reefs: cultivation and molecular analysis of planktonic microbial communities.

PubMed

Jensen, Sigmund; Lynch, Michael D J; Ray, Jessica L; Neufeld, Josh D; Hovland, Martin

2015-10-01

Deep-sea coral reefs do not receive sunlight and depend on plankton. Little is known about the plankton composition at such reefs, even though they constitute habitats for many invertebrates and fish. We investigated plankton communities from three reefs at 260-350 m depth at hydrocarbon fields off the mid-Norwegian coast using a combination of cultivation and small subunit (SSU) rRNA gene and transcript sequencing. Eight months incubations of a reef water sample with minimal medium, supplemented with carbon dioxide and gaseous alkanes at in situ-like conditions, enabled isolation of mostly Alphaproteobacteria (Sulfitobacter, Loktanella), Gammaproteobacteria (Colwellia) and Flavobacteria (Polaribacter). The relative abundance of isolates in the original sample ranged from ∼ 0.01% to 0.80%. Comparisons of bacterial SSU sequences from filtered plankton of reef and non-reef control samples indicated high abundance and metabolic activity of primarily Alphaproteobacteria (SAR11 Ia), Gammaproteobacteria (ARCTIC96BD-19), but also of Deltaproteobacteria (Nitrospina, SAR324). Eukaryote SSU sequences indicated metabolically active microalgae and animals, including codfish, at the reef sites. The plankton community composition varied between reefs and differed between DNA and RNA assessments. Over 5000 operational taxonomic units were detected, some indicators of reef sites (e.g. Flavobacteria, Cercozoa, Demospongiae) and some more active at reef sites (e.g. Gammaproteobacteria, Ciliophora, Copepoda). © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Distinct regulators of Shh transcription in the floor plate and notochord indicate separate origins for these tissues in the mouse node.

PubMed

Jeong, Yongsu; Epstein, Douglas J

2003-08-01

The establishment of the floor plate at the ventral midline of the CNS is dependent on an inductive signaling process mediated by the secreted protein Sonic hedgehog (Shh). To understand molecularly how floor plate induction proceeds we identified a Shh-responsive regulatory element that directs transgene reporter expression to the ventral midline of the CNS and notochord in a Shh-like manner and characterized critical cis-acting sequences regulating this element. Cross-species comparisons narrowed the activity of the Shh floor plate enhancer to an 88-bp sequence within intron 2 of Shh that included highly conserved binding sites matching the consensus for homeodomain, Tbx and Foxa transcription factors. Mutational analysis revealed that the homeodomain and Foxa binding sites are each required for activation of the Shh floor plate enhancer, whereas the Tbx site was required for repression in regions of the CNS where Shh is not normally expressed. We further show that Shh enhancer activity was detected in the mouse node from where the floor plate and notochord precursors derive. Shh reporter expression was restricted to the ventral (mesodermal) layer of the node in a pattern similar to endogenous Shh. X-gal-positive cells emerging from the node were only detected in the notochord lineage, suggesting that the floor plate and notochord arise from distinct precursors in the mouse node.

Antibody-catalyzed benzoin oxidation as a mechanistic probe for nucleophilic catalysis by an active site lysine.

PubMed

Sklute, Genia; Oizerowich, Rachel; Shulman, Hagit; Keinan, Ehud

2004-05-03

Aldolase antibody 24H6, which was obtained by reactive immunization against a 1,3-diketone hapten, is shown to catalyze additional reactions, including H/D exchange and oxidation reactions. Comparison of the H/D exchange reaction at the alpha-position of a wide range of aldehydes and ketones by 24H6 and by other aldolase antibodies, such as 38C2, pointed at the significantly larger size of the 24H6 active site. This property allowed for the catalysis of the oxidation of substituted benzoins to benzils by potassium ferricyanide. This reaction was used as a mechanistic probe to learn about the initial steps of the 24H6-catalyzed aldol condensation reaction. The Hammett correlation (rho=4.7) of log(k(cat)) versus the substituent constant, sigma, revealed that the reaction involves rapid formation of a Schiff base intermediate from the ketone and an active site lysine residue. The rate-limiting step in this oxidation reaction is the conversion of the Schiff base to an enamine intermediate. In addition, linear correlation (rho=3.13) was found between log(K(M)) and sigma, indicating that electronic rather than steric factors are dominant in the antibody-substrate binding phenomenon and confirming that the reversible formation of a Schiff base intermediate comprises part of the substrate-binding mechanism.

An international land-biosphere model benchmarking activity for the IPCC Fifth Assessment Report (AR5)

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

Hoffman, Forrest M; Randerson, James T; Thornton, Peter E

2009-12-01

The need to capture important climate feedbacks in general circulation models (GCMs) has resulted in efforts to include atmospheric chemistry and land and ocean biogeochemistry into the next generation of production climate models, called Earth System Models (ESMs). While many terrestrial and ocean carbon models have been coupled to GCMs, recent work has shown that such models can yield a wide range of results (Friedlingstein et al., 2006). This work suggests that a more rigorous set of global offline and partially coupled experiments, along with detailed analyses of processes and comparisons with measurements, are needed. The Carbon-Land Model Intercomparison Projectmore » (C-LAMP) was designed to meet this need by providing a simulation protocol and model performance metrics based upon comparisons against best-available satellite- and ground-based measurements (Hoffman et al., 2007). Recently, a similar effort in Europe, called the International Land Model Benchmark (ILAMB) Project, was begun to assess the performance of European land surface models. These two projects will now serve as prototypes for a proposed international land-biosphere model benchmarking activity for those models participating in the IPCC Fifth Assessment Report (AR5). Initially used for model validation for terrestrial biogeochemistry models in the NCAR Community Land Model (CLM), C-LAMP incorporates a simulation protocol for both offline and partially coupled simulations using a prescribed historical trajectory of atmospheric CO2 concentrations. Models are confronted with data through comparisons against AmeriFlux site measurements, MODIS satellite observations, NOAA Globalview flask records, TRANSCOM inversions, and Free Air CO2 Enrichment (FACE) site measurements. Both sets of experiments have been performed using two different terrestrial biogeochemistry modules coupled to the CLM version 3 in the Community Climate System Model version 3 (CCSM3): the CASA model of Fung, et al., and the carbon-nitrogen (CN) model of Thornton. Comparisons of the CLM3 offline results against observational datasets have been performed and are described in Randerson et al. (2009). CLM version 4 has been evaluated using C-LAMP, showing improvement in many of the metrics. Efforts are now underway to initiate a Nitrogen-Land Model Intercomparison Project (N-LAMP) to better constrain the effects of the nitrogen cycle in biosphere models. Presented will be new results from C-LAMP for CLM4, initial N-LAMP developments, and the proposed land-biosphere model benchmarking activity.« less

Oxidative potential of on-road fine particulate matter (PM2.5) measured on major freeways of Los Angeles, CA, and a 10-year comparison with earlier roadside studies

NASA Astrophysics Data System (ADS)

Shirmohammadi, Farimah; Wang, Dongbin; Hasheminassab, Sina; Verma, Vishal; Schauer, James J.; Shafer, Martin M.; Sioutas, Constantinos

2017-01-01

This study describes on-road measurements of fine particulate matter (PM2.5) using a mobile instrumentation platform to assess the chemical composition and oxidative potential of PM2.5, using the dithiothreitol (DTT) assay, over three representative roadways in the Los Angeles Basin: the I-110 and I-710 freeways, the Wilshire/Sunset boulevards as well as the main campus of the University of Southern California (USC), used as a reference urban background site. Samples were chemically analyzed for elemental carbon (EC), organic carbon (OC), polycyclic aromatic hydrocarbons (PAHs) and 50 elements. The cumulative mass fraction of the measured PAHs was highest on the freeways (0.16 ± 0.01 and 0.15 ± 0.01 ng/μg PM, on I-110 and I-710, respectively); which on average was 3 and 3.3-fold higher than at Wilshire/Sunset and USC site, respectively. Mass fractions of Ba, Cr, Cu, Mn, Ni, Pb, Sb and Zn, tracers of vehicular abrasion, were 3.8 ± 0.8 times higher on both freeways in comparison to Wilshire/Sunset. The observed intrinsic (normalized per PM mass) DTT activity was greatest on freeways, averaging 30.13 ± 3.15 nmol/min mg PM and being roughly 1.9 and 2.1 times higher than the values obtained at Wilshire/Sunset and USC, respectively. Furthermore, comparison of our results with previous on-road and roadside studies conducted in the last decade in Los Angeles indicated an overall reduction in the contribution of carbonaceous species and PAHs (important tracers of exhaust emissions) to PM mass, especially on I-710 freeway with the higher heavy-duty diesel vehicle fraction, indicating the effectiveness of diesel vehicle emissions control policies implemented in recent years in California. In contrast, greater contributions of certain groups of metals and trace elements that are indicators of non-tailpipe emissions compared to previous studies provide evidence on the increasing importance of non-tailpipe emissions to the oxidative potential of on-road PM2.5 as vehicular exhaust emissions becomes cleaner. This finding was also reflected in the increased levels of on-road DTT activity by factors of 1.4-1.5 in comparison to the DTT activity of vehicular emissions estimated in previous dynamometer studies.

Biochemical analyses are instrumental in identifying the impact of mutations on holo and/or apo-forms and on the region(s) of alanine:glyoxylate aminotransferase variants associated with Primary Hyperoxaluria Type I☆

PubMed Central

Oppici, Elisa; Montioli, Riccardo; Lorenzetto, Antonio; Bianconi, Silvia; Borri Voltattorni, Carla; Cellini, Barbara

2012-01-01

Primary Hyperoxaluria Type I (PH1) is a disorder of glyoxylate metabolism caused by mutations in the human AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5′-phosphate (PLP) dependent enzyme. Previous investigations highlighted that, although PH1 is characterized by a significant variability in terms of enzymatic phenotype, the majority of the pathogenic variants are believed to share both structural and functional defects, as mainly revealed by data on AGT activity and expression level in crude cellular extracts. However, the knowledge of the defects of the AGT variants at a protein level is still poor. We therefore performed a side-by-side comparison between normal AGT and nine purified recombinant pathogenic variants in terms of catalytic activity, coenzyme binding mode and affinity, spectroscopic features, oligomerization, and thermal stability of both the holo- and apo-forms. Notably, we chose four variants in which the mutated residues are located in the large domain of AGT either within the active site and interacting with the coenzyme or in its proximity, and five variants in which the mutated residues are distant from the active site either in the large or in the small domain. Overall, this integrated analysis of enzymatic activity, spectroscopic and stability information is used to (i) reassess previous data obtained with crude cellular extracts, (ii) establish which form(s) (i.e. holoenzyme and/or apoenzyme) and region(s) (i.e. active site microenvironment, large and/or small domain) of the protein are affected by each mutation, and (iii) suggest the possible therapeutic approach for patients bearing the examined mutations. PMID:22018727

Binding and Inactivation Mechanism of a Humanized Fatty Acid Amide Hydrolase by [alpha]-Ketoheterocycle Inhibitors Revealed from Cocrystal Structures

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

Mileni, Mauro; Garfunkle, Joie; DeMartino, Jessica K.

The cocrystal X-ray structures of two isomeric {alpha}-ketooxazole inhibitors (1 (OL-135) and 2) bound to fatty acid amide hydrolase (FAAH), a key enzymatic regulator of endocannabinoid signaling, are disclosed. The active site catalytic Ser241 is covalently bound to the inhibitors electrophilic carbonyl groups, providing the first structures of FAAH bound to an inhibitor as a deprotonated hemiketal mimicking the enzymatic tetrahedral intermediate. The work also offers a detailed view of the oxyanion hole and an exceptional 'in-action' depiction of the unusual Ser-Ser-Lys catalytic triad. These structures capture the first picture of inhibitors that span the active site into the cytosolicmore » port providing new insights that help to explain FAAH's interaction with substrate leaving groups and their role in modulating inhibitor potency and selectivity. The role for the activating central heterocycle is clearly defined and distinguished from that observed in prior applications with serine proteases, reconciling the large electronic effect of attached substituents found unique to this class of inhibitors with FAAH. Additional striking active site flexibility is seen upon binding of the inhibitors, providing insights into the existence of a now well-defined membrane access channel with the disappearance of a spatially independent portion of the acyl chain-binding pocket. Finally, comparison of the structures of OL-135 (1) and its isomer 2 indicates that they bind identically to FAAH, albeit with reversed orientations of the central activating heterocycle, revealing that the terminal 2-pyridyl substituent and the acyl chain phenyl group provide key anchoring interactions and confirming the distinguishing role of the activating oxazole.« less

Real-time monitoring of beta-d-glucuronidase activity in sediment laden streams: A comparison of prototypes.

PubMed

Stadler, Philipp; Blöschl, Günter; Vogl, Wolfgang; Koschelnik, Juri; Epp, Markus; Lackner, Maximilian; Oismüller, Markus; Kumpan, Monika; Nemeth, Lukas; Strauss, Peter; Sommer, Regina; Ryzinska-Paier, Gabriela; Farnleitner, Andreas H; Zessner, Matthias

2016-09-15

Detection of enzymatic activities has been proposed as a rapid surrogate for the culture-based microbiological pollution monitoring of water resources. This paper presents the results of tests on four fully automated prototype instruments for the on-site monitoring of beta-d-glucuronidase (GLUC) activity. The tests were performed on sediment-laden stream water in the Hydrological Open Air Laboratory (HOAL) during the period of March 2014 to March 2015. The dominant source of faecal pollution in the stream was swine manure applied to the fields within the catchment. The experiments indicated that instrument pairs with the same construction design yielded highly consistent results (R(2) = 0.96 and R(2) = 0.94), whereas the results between different designs were less consistent (R(2) = 0.71). Correlations between the GLUC activity measured on-site and culture-based Escherichia coli analyses over the entire study period yielded R(2) = 0.52 and R(2) = 0.47 for the two designs, respectively. The correlations tended to be higher at the event scale. The GLUC activity was less correlated with suspended sediment concentrations than with E. coli, which is interpreted in terms of indicator applicability and the time since manure application. The study shows that this rapid assay can yield consistent results over a long period of on-site operation in technically challenging habitats. Although the use of GLUC activity as a proxy for culture-based assays could not be proven for the observed habitat, the study results suggest that this biochemical indicator has high potential for implementation in early warning systems. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biochemical analyses are instrumental in identifying the impact of mutations on holo and/or apo-forms and on the region(s) of alanine:glyoxylate aminotransferase variants associated with primary hyperoxaluria type I.

PubMed

Oppici, Elisa; Montioli, Riccardo; Lorenzetto, Antonio; Bianconi, Silvia; Borri Voltattorni, Carla; Cellini, Barbara

2012-01-01

Primary Hyperoxaluria Type I (PH1) is a disorder of glyoxylate metabolism caused by mutations in the human AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP) dependent enzyme. Previous investigations highlighted that, although PH1 is characterized by a significant variability in terms of enzymatic phenotype, the majority of the pathogenic variants are believed to share both structural and functional defects, as mainly revealed by data on AGT activity and expression level in crude cellular extracts. However, the knowledge of the defects of the AGT variants at a protein level is still poor. We therefore performed a side-by-side comparison between normal AGT and nine purified recombinant pathogenic variants in terms of catalytic activity, coenzyme binding mode and affinity, spectroscopic features, oligomerization, and thermal stability of both the holo- and apo-forms. Notably, we chose four variants in which the mutated residues are located in the large domain of AGT either within the active site and interacting with the coenzyme or in its proximity, and five variants in which the mutated residues are distant from the active site either in the large or in the small domain. Overall, this integrated analysis of enzymatic activity, spectroscopic and stability information is used to (i) reassess previous data obtained with crude cellular extracts, (ii) establish which form(s) (i.e. holoenzyme and/or apoenzyme) and region(s) (i.e. active site microenvironment, large and/or small domain) of the protein are affected by each mutation, and (iii) suggest the possible therapeutic approach for patients bearing the examined mutations. Copyright © 2011 Elsevier Inc. All rights reserved.

Docking modes of BB-3497 into the PDF active site--a comparison of the pure MM and QM/MM based docking strategies.

PubMed

Kumari, Tripti; Issar, Upasana; Kakkar, Rita

2014-01-01

Peptide deformylase (PDF) has emerged as an important antibacterial drug target. Considerable effort is being directed toward developing peptidic and non-peptidic inhibitors for this metalloprotein. In this work, the known peptidic inhibitor BB-3497 and its various ionization and tautomeric states are evaluated for their inhibition efficiency against PDF using a molecular mechanics (MM) approach as well as a mixed quantum mechanics/molecular mechanics (QM/MM) approach, with an aim to understand the interactions in the binding site. The evaluated Gibbs energies of binding with the mixed QM/MM approach are shown to have the best predictive power. The experimental pose is found to have the most negative Gibbs energy of binding, and also the smallest strain energy. A quantum mechanical evaluation of the active site reveals the requirement of strong chelation by the ligand with the metal ion. The investigated ligand chelates the metal ion through the two oxygens of its reverse hydroxamate moiety, particularly the N-O(-) oxygen, forming strong covalent bonds with the metal ion, which is penta-coordinated. In the uninhibited state, the metal ion is tetrahedrally coordinated, and hence chelation with the inhibitor is associated with an increase of the metal ion coordination. Thus, the strong binding of the ligand at the binding site is accounted for.

Interaction of external alkali metal ions with the Na-K pump of human erythrocytes: a comparison of their effects on activation of the pump and on the rate of ouabain binding

PubMed Central

1978-01-01

The effects of external alkali metal ions on the rate of ouabain binding and on the rate of the Na-K pump were examined in human red blood cells. In Na-containing solutions, K, Cs, and Li decreased the rate of ouabain binding. For K and Cs, the kinetics of this effect were similar to those for their activation of the pump. In Na-free (choline- substituted) solutions the rate of ouabain binding was decreased by K whereas it was promoted by Cs and Li. External Na increased the rate of ouabain binding whether or not external K was present, and the kinetics of this effect were not the same as those for inhibition of the pump by Na. These findings are interpreted to mean that not only do the cations affect ouabain binding at the external loading sites on the pump from which ions are translocated inward, but that there are additional sites on the external aspect of the pump at which cations can promote ouabain binding, and that these sites can be occupied by Li, Na, and Cs. It is postulated that these latter sites are those from which Na is discharged after outward translocation by the pump. PMID:702113

The Mediating Roles of Upward Social Comparison and Self-esteem and the Moderating Role of Social Comparison Orientation in the Association between Social Networking Site Usage and Subjective Well-Being.

PubMed

Wang, Jin-Liang; Wang, Hai-Zhen; Gaskin, James; Hawk, Skyler

2017-01-01

The increased pervasiveness of social media use has raised questions about potential effects on users' subjective well-being, with studies reaching contrasting conclusions. To reconcile these discrepancies and shed new light on this phenomenon, the current study examined: (1) whether upward social comparison and self-esteem mediate the association between social networking site (SNS) usage and users' subjective well-being, and (2) whether the association between SNS usage and upward social comparison is moderated by users' social comparison orientation. Data from 696 participants were collected. Structural equation modeling revealed that upward social comparison and self-esteem mediated the relationship between SNS usage and users' subjective well-being. We found that social comparison orientation moderated the association between passive SNS usage and users' upward social comparison. Specifically, social comparison orientation strengthened the association between passive SNS usage and upward social comparison. The results might suggest a process through which passive SNS usage is related to subjective well-being, and identify a context under which these associations may differ.

The Mediating Roles of Upward Social Comparison and Self-esteem and the Moderating Role of Social Comparison Orientation in the Association between Social Networking Site Usage and Subjective Well-Being

PubMed Central

Wang, Jin-Liang; Wang, Hai-Zhen; Gaskin, James; Hawk, Skyler

2017-01-01

The increased pervasiveness of social media use has raised questions about potential effects on users’ subjective well-being, with studies reaching contrasting conclusions. To reconcile these discrepancies and shed new light on this phenomenon, the current study examined: (1) whether upward social comparison and self-esteem mediate the association between social networking site (SNS) usage and users’ subjective well-being, and (2) whether the association between SNS usage and upward social comparison is moderated by users’ social comparison orientation. Data from 696 participants were collected. Structural equation modeling revealed that upward social comparison and self-esteem mediated the relationship between SNS usage and users’ subjective well-being. We found that social comparison orientation moderated the association between passive SNS usage and users’ upward social comparison. Specifically, social comparison orientation strengthened the association between passive SNS usage and upward social comparison. The results might suggest a process through which passive SNS usage is related to subjective well-being, and identify a context under which these associations may differ. PMID:28553256

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....

Site index comparisons among northern hardwoods in northern Wisconsin and Upper Michigan.

Treesearch

Willard H. Carmean

1979-01-01

Compares site index for 13 species found in even-aged northern hardwood stands. Shows that these species differ greatly in site index when growing together, but can be grouped into four general site index classes. Site relations between several species differed with soil drainage.

The effect of changing the built environment on physical activity: a quantitative review of the risk of bias in natural experiments.

PubMed

Benton, Jack S; Anderson, Jamie; Hunter, Ruth F; French, David P

2016-10-07

Evidence regarding the association of the built environment with physical activity is influencing policy recommendations that advocate changing the built environment to increase population-level physical activity. However, to date there has been no rigorous appraisal of the quality of the evidence on the effects of changing the built environment. The aim of this review was to conduct a thorough quantitative appraisal of the risk of bias present in those natural experiments with the strongest experimental designs for assessing the causal effects of the built environment on physical activity. Eligible studies had to evaluate the effects of changing the built environment on physical activity, include at least one measurement before and one measurement of physical activity after changes in the environment, and have at least one intervention site and non-intervention comparison site. Given the large number of systematic reviews in this area, studies were identified from three exemplar systematic reviews; these were published in the past five years and were selected to provide a range of different built environment interventions. The risk of bias in these studies was analysed using the Cochrane Risk of Bias Assessment Tool: for Non-Randomized Studies of Interventions (ACROBAT-NRSI). Twelve eligible natural experiments were identified. Risk of bias assessments were conducted for each physical activity outcome from all studies, resulting in a total of fifteen outcomes being analysed. Intervention sites included parks, urban greenways/trails, bicycle lanes, paths, vacant lots, and a senior citizen's centre. All outcomes had an overall critical (n = 12) or serious (n = 3) risk of bias. Domains with the highest risk of bias were confounding (due to inadequate control sites and poor control of confounding variables), measurement of outcomes, and selection of the reported result. The present review focused on the strongest natural experiments conducted to date. Given this, the failure of existing studies to adequately control for potential sources of bias highlights the need for more rigorous research to underpin policy recommendations for changing the built environment to increase physical activity. Suggestions are proposed for how future natural experiments in this area can be improved.

How does precipitation become runoff? Comparison of hydrologic thresholds across hillslope and catchment scales

NASA Astrophysics Data System (ADS)

Ross, C.; Ali, G.; Oswald, C. J.; McMillan, H. K.; Walter, K.

2017-12-01

A hydrologic threshold is a critical point in time when runoff behavior rapidly changes, often in response to the activation of specific storage-driven or intensity-driven processes. Hydrologic thresholds can be viewed as characteristic signatures of hydrosystems, which makes them useful for site comparison as long as their presence (or lack thereof) can be evaluated in a standard manner across a range of environments. While several previous studies have successfully identified thresholds at a variety of individual sites, only a limited number have compared dynamics prevailing at the hillslope versus catchment scale, or distinguished the role of storage versus intensity thresholds. The objective of this study was therefore to examine precipitation input thresholds as well as "precipitation minus evapotranspiration" thresholds in environments with contrasted climatic and geographic characteristics. Historical climate and hydrometric datasets were consolidated for one hillslope site located at the Panola Mountain Research Watershed (Southeastern USA) and catchments located in the HJ Andrew's Experimental Forest (Northwestern USA), the Catfish Creek Watershed (Canadian prairies), the Experimental Lakes Area (Canadian boreal ecozone), the Tarrawarra catchment (Australia) and the Mahurangi catchment (New Zealand). Individual precipitation-runoff events were delineated using the newly introduced software HydRun to derive event-specific hydrograph parameters as well surrogate measures of antecedent moisture conditions and evapotranspiration in an automated and consistent manner. Various hydrograph parameters were then plotted against those surrogate measures to detect and evaluate site-specific threshold dynamics. Preliminary results show that a range of threshold shapes (e.g., "hockey stick", heaviside and dirac) were observed across sites. The influence of antecedent precipitation on threshold magnitude and shape also appeared stronger at sites with lower topographic relief and drier climate. Future analyses will focus on the interaction between storage and intensity thresholds in order to evaluate the importance of considering both for comparative hydrological studies.

Comparisons between vs30 and spectral response for 30 sites in Newcastle, Australia from collocated seismic cone penetrometer, active- and passive-source vs data

USGS Publications Warehouse

Volti, Theodora; Burbidge, David; Collins, Clive; Asten, Michael W.; Odum, Jackson K.; Stephenson, William J.; Pascal, Chris; Holzschuh, Josef

2016-01-01

Although the time‐averaged shear‐wave velocity down to 30 m depth (VS30) can be a proxy for estimating earthquake ground‐motion amplification, significant controversy exists about its limitations when used as a single parameter for the prediction of amplification. To examine this question in absence of relevant strong‐motion records, we use a range of different methods to measure the shear‐wave velocity profiles and the resulting theoretical site amplification factors (AFs) for 30 sites in the Newcastle area, Australia, in a series of blind comparison studies. The multimethod approach used here combines past seismic cone penetrometer and spectral analysis of surface‐wave data, with newly acquired horizontal‐to‐vertical spectral ratio, passive‐source surface‐wave spatial autocorrelation (SPAC), refraction microtremor (ReMi), and multichannel analysis of surface‐wave data. The various measurement techniques predicted a range of different AFs. The SPAC and ReMi techniques have the smallest overall deviation from the median AF for the majority of sites. We show that VS30 can be related to spectral response above a period T of 0.5 s but not necessarily with the maximum amplification according to the modeling done based on the measured shear‐wave velocity profiles. Both VS30 and AF values are influenced by the velocity ratio between bedrock and overlying sediments and the presence of surficial thin low‐velocity layers (<2  m thick and <150  m/s), but the velocity ratio is what mostly affects the AF. At 0.20.5  s do the amplification curves consistently show higher values for soft site classes and lower for hard classes.

Mass and number size distributions of particulate matter components: comparison of an industrial site and an urban background site.

PubMed

Taiwo, Adewale M; Beddows, David C S; Shi, Zongbo; Harrison, Roy M

2014-03-15

Size-resolved composition of particulate matter (PM) sampled in the industrial town of Port Talbot (PT), UK was determined in comparison to a typical urban background site in Birmingham (EROS). A Micro-Orifice Uniform Deposit Impactor (MOUDI) sampler was deployed for two separate sampling campaigns with the addition of a Grimm optical spectrometer at the PT site. MOUDI samples were analysed for water-soluble anions (Cl(-), NO₃(-) and SO₄(2-)) and cations (Na(+), NH4(+), K(+), Mg(2+) and Ca(2+)) and trace metals (Al, V, Cr, Mn, Fe, Cu, Zn, Sb, Ba and Pb). The PM mass distribution showed a predominance of fine particle (PM₂.₅) mass at EROS whereas the PT samples were dominated by the coarse fraction (PM₂.₅₋₁₀). SO₄(2-), Cl(-), NH4(+), Na(+), NO₃(-), and Ca(2+) were the predominant ionic species at both sites while Al and Fe were the metals with highest concentrations at both sites. Mean concentrations of Cl(-), Na(+), K(+), Ca(2+), Mg(2+), Cr, Mn, Fe and Zn were higher at PT than EROS due to industrial and marine influences. The contribution of regional pollution by sulphate, ammonium and nitrate was greater at EROS relative to PT. The traffic signatures of Cu, Sb, Ba and Pb were particularly prominent at EROS. Overall, PM at EROS was dominated by secondary aerosol and traffic-related particles while PT was heavily influenced by industrial activities and marine aerosol. Profound influences of wind direction are seen in the 72-hour data, especially in relation to the PT local sources. Measurements of particle number in 14 separate size bins plotted as a function of wind direction and speed are highly indicative of contributing sources, with local traffic dominant below 0.5 μm, steelworks emissions from 0.5 to 15 μm, and marine aerosol above 15 μm. Copyright © 2013 Elsevier B.V. All rights reserved.

1-3-A Resolution Structure of Human Glutathione S-Transferase With S-Hexyl Glutathione Bound Reveals Possible Extended Ligandin Binding Site

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

Trong, I.Le; Stenkamp, R.E.; Ibarra, C.

2005-08-22

Cytosolic glutathione S-transferases (GSTs) play a critical role in xenobiotic binding and metabolism, as well as in modulation of oxidative stress. Here, the high-resolution X-ray crystal structures of homodimeric human GSTA1-1 in the apo form and in complex with S-hexyl glutathione (two data sets) are reported at 1.8, 1.5, and 1.3A respectively. At this level of resolution, distinct conformations of the alkyl chain of S-hexyl glutathione are observed, reflecting the nonspecific nature of the hydrophobic substrate binding site (H-site). Also, an extensive network of ordered water, including 75 discrete solvent molecules, traverses the open subunit-subunit interface and connects the glutathionemore » binding sites in each subunit. In the highest-resolution structure, three glycerol moieties lie within this network and directly connect the amino termini of the glutathione molecules. A search for ligand binding sites with the docking program Molecular Operating Environment identified the ordered water network binding site, lined mainly with hydrophobic residues, suggesting an extended ligand binding surface for nonsubstrate ligands, the so-called ligandin site. Finally, detailed comparison of the structures reported here with previously published X-ray structures reveal a possible reaction coordinate for ligand-dependent conformational changes in the active site and the C-terminus.« less

Seismic site-response characterization of high-velocity sites using advanced geophysical techniques: application to the NAGRA-Net

NASA Astrophysics Data System (ADS)

Poggi, V.; Burjanek, J.; Michel, C.; Fäh, D.

2017-08-01

The Swiss Seismological Service (SED) has recently finalised the installation of ten new seismological broadband stations in northern Switzerland. The project was led in cooperation with the National Cooperative for the Disposal of Radioactive Waste (Nagra) and Swissnuclear to monitor micro seismicity at potential locations of nuclear-waste repositories. To further improve the quality and usability of the seismic recordings, an extensive characterization of the sites surrounding the installation area was performed following a standardised investigation protocol. State-of-the-art geophysical techniques have been used, including advanced active and passive seismic methods. The results of all analyses converged to the definition of a set of best-representative 1-D velocity profiles for each site, which are the input for the computation of engineering soil proxies (traveltime averaged velocity and quarter-wavelength parameters) and numerical amplification models. Computed site response is then validated through comparison with empirical site amplification, which is currently available for any station connected to the Swiss seismic networks. With the goal of a high-sensitivity network, most of the NAGRA stations have been installed on stiff-soil sites of rather high seismic velocity. Seismic characterization of such sites has always been considered challenging, due to lack of relevant velocity contrast and the large wavelengths required to investigate the frequency range of engineering interest. We describe how ambient vibration techniques can successfully be applied in these particular conditions, providing practical recommendations for best practice in seismic site characterization of high-velocity sites.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

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

Wang, Xianwei; State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062; Zhang, John Z. H.

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. Inmore » this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.« less

Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in Lepidoptera.

PubMed

Dias, Renata O; Via, Allegra; Brandão, Marcelo M; Tramontano, Anna; Silva-Filho, Marcio C

2015-03-01

Trypsins and chymotrypsins are well-studied serine peptidases that cleave peptide bonds at the carboxyl side of basic and hydrophobic L-amino acids, respectively. These enzymes are largely responsible for the digestion of proteins. Three primary processes regulate the activity of these peptidases: secretion, precursor (zymogen) activation and substrate-binding site recognition. Here, we present a detailed phylogenetic analysis of trypsins and chymotrypsins in three orders of holometabolous insects and reveal divergent characteristics of Lepidoptera enzymes in comparison with those of Coleoptera and Diptera. In particular, trypsin subsite S1 was more hydrophilic in Lepidoptera than in Coleoptera and Diptera, whereas subsites S2-S4 were more hydrophobic, suggesting different substrate preferences. Furthermore, Lepidoptera displayed a lineage-specific trypsin group belonging only to the Noctuidae family. Evidence for facilitated trypsin auto-activation events were also observed in all the insect orders studied, with the characteristic zymogen activation motif complementary to the trypsin active site. In contrast, insect chymotrypsins did not seem to have a peculiar evolutionary history with respect to their mammal counterparts. Overall, our findings suggest that the need for fast digestion allowed holometabolous insects to evolve divergent groups of peptidases with high auto-activation rates, and highlight that the evolution of trypsins led to a most diverse group of enzymes in Lepidoptera. Copyright © 2015 Elsevier Ltd. All rights reserved.

HPLC-Based Activity Profiling: Discovery of Piperine as a Positive GABAA Receptor Modulator Targeting a Benzodiazepine-Independent Binding Site

PubMed Central

Zaugg, Janine; Baburin, Igor; Strommer, Barbara; Kim, Hyun-Jung; Hering, Steffen; Hamburger, Matthias

2011-01-01

A plant extract library was screened for GABAA receptor activity making use of a two-microelectrode voltage clamp assay on Xenopus laevis oocytes. An ethyl acetate extract of black pepper fruits [Piper nigrum L. (Piperaceae) 100 μg/mL] potentiated GABA-induced chloride currents through GABAA receptors (composed of α1, β2, and γ2S subunits) by 169.1 ± 2.4%. With the aid of an HPLC-based activity profiling approach, piperine (5) was identified as the main active compound, together with 12 structurally related less active or inactive piperamides (1–4, 6–13). Identification was achieved by on-line high-resolution mass spectrometry and off-line microprobe 1D and 2D NMR spectroscopy, using only milligram amounts of extract. Compound 5 induced a maximum potentiation of the chloride currents by 301.9 ± 26.5% with an EC50 of 52.4 ± 9.4 μM. A comparison of the modulatory activity of 5 and other naturally occurring piperamides enabled insights into structural features critical for GABAA receptor modulation. The stimulation of chloride currents through GABAA receptors by compound 5 was not antagonized by flumazenil (10 μM). These data show that piperine (5) represents a new scaffold of positive allosteric GABAA receptor modulators targeting a benzodiazepine-independent binding site. PMID:20085307

Backbone modified TBA analogues endowed with antiproliferative activity.

PubMed

Esposito, Veronica; Russo, Annapina; Amato, Teresa; Varra, Michela; Vellecco, Valentina; Bucci, Mariarosaria; Russo, Giulia; Virgilio, Antonella; Galeone, Aldo

2017-05-01

The thrombin binding aptamer (TBA) is endowed with antiproliferative properties but its potential development is counteracted by the concomitant anticoagulant activity. Five oligonucleotides (ODNs) based on TBA sequence (GGTTGGTGTGGTTGG) and containing l-residues or both l-residues and inversion of polarity sites have been investigated by NMR and CD techniques for their ability to form G-quadruplex structures. Furthermore, their anticoagulant (PT assay) and antiproliferative properties (MTT assay), and their resistance in fetal bovine serum have been tested. CD and NMR data suggest that the investigated ODNs are able to form right- and left-handed G-quadruplex structures. All ODNs do not retain the anticoagulant activity characteristic of TBA but are endowed with a significant antiproliferative activity against two cancerous cell lines. Their resistance in biological environment after six days is variable, depending on the ODN. A comparison between results and literature data suggests that the antiproliferative activity of the TBA analogues investigated could depends on two factors: a) biological pathways and targets different from those already identified or proposed for other antiproliferative G-quadruplex aptamers, and b) the contribution of the guanine-based degradation products. Modified TBA analogues containing l-residues and inversion of polarity sites lose the anticoagulant activity but gain antiproliferative properties against two cancer cell lines. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio. Copyright © 2016 Elsevier B.V. All rights reserved.

Methane oxidation on Pd–Ceria: A DFT study of the mechanism over PdxCe1-xO2, Pd, and PdO

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

Mayernick, Adam D.; Janik, Michael J.

2011-02-14

Palladium/ceria exhibits unique catalytic activity for hydrocarbon oxidation; however, the chemical and structural properties of active sites on the palladium–ceria surface are difficult to characterize. Strong interactions between palladium and the ceria support stabilize oxidized Pdδ+ species, which may contribute to the significant activity of Pd/ceria for methane oxidation. We present a density functional theory (DFT + U) investigation into methane oxidation over Pd/ceria and quantify the activity of the Pd xCe 1-xO 2(1 1 1) mixed oxide surface in comparison with the PdO(1 0 0) and Pd(1 1 1) surfaces. The methane activation barrier is lowest over the Pdmore » xCe 1-xO 2(1 1 1) surface, even lower than over the Pd(1 1 1) surface or low coordinated stepped or kinked Pd sites. Subsequent reaction steps in complete oxidation, including product desorption and vacancy refilling, are considered to substantiate that methane activation remains the rate-limiting step despite the low barrier over Pd xCe 1-xO 2(1 1 1). The low barrier over the Pd xCe 1-xO 2(1 1 1) surface demonstrates that mixed ceria-noble metal oxides offer the potential for improved hydrocarbon oxidation performance with respect to dispersed noble metal particles on ceria.« less

Long-term observations of tropospheric particle number size distributions and equivalent black carbon mass concentrations in the German Ultrafine Aerosol Network (GUAN)

NASA Astrophysics Data System (ADS)

Birmili, W.; Weinhold, K.; Merkel, M.; Rasch, F.; Sonntag, A.; Wiedensohler, A.; Bastian, S.; Schladitz, A.; Löschau, G.; Cyrys, J.; Pitz, M.; Gu, J.; Kusch, T.; Flentje, H.; Quass, U.; Kaminski, H.; Kuhlbusch, T. A. J.; Meinhardt, F.; Schwerin, A.; Bath, O.; Ries, L.; Wirtz, K.; Fiebig, M.

2015-11-01

The German Ultrafine Aerosol Network (GUAN) is a cooperative atmospheric observation network, which aims at improving the scientific understanding of aerosol-related effects in the troposphere. The network addresses research questions dedicated to both, climate and health related effects. GUAN's core activity has been the continuous collection of tropospheric particle number size distributions and black carbon mass concentrations at seventeen observation sites in Germany. These sites cover various environmental settings including urban traffic, urban background, rural background, and Alpine mountains. In association with partner projects, GUAN has implemented a high degree of harmonisation of instrumentation, operating procedures, and data evaluation procedures. The quality of the measurement data is assured by laboratory intercomparisons as well as on-site comparisons with reference instruments. This paper describes the measurement sites, instrumentation, quality assurance and data evaluation procedures in the network as well as the EBAS repository, where the data sets can be obtained (doi:10.5072/guan).

Long-term observations of tropospheric particle number size distributions and equivalent black carbon mass concentrations in the German Ultrafine Aerosol Network (GUAN)

NASA Astrophysics Data System (ADS)

Birmili, Wolfram; Weinhold, Kay; Rasch, Fabian; Sonntag, André; Sun, Jia; Merkel, Maik; Wiedensohler, Alfred; Bastian, Susanne; Schladitz, Alexander; Löschau, Gunter; Cyrys, Josef; Pitz, Mike; Gu, Jianwei; Kusch, Thomas; Flentje, Harald; Quass, Ulrich; Kaminski, Heinz; Kuhlbusch, Thomas A. J.; Meinhardt, Frank; Schwerin, Andreas; Bath, Olaf; Ries, Ludwig; Gerwig, Holger; Wirtz, Klaus; Fiebig, Markus

2016-08-01

The German Ultrafine Aerosol Network (GUAN) is a cooperative atmospheric observation network, which aims at improving the scientific understanding of aerosol-related effects in the troposphere. The network addresses research questions dedicated to both climate- and health-related effects. GUAN's core activity has been the continuous collection of tropospheric particle number size distributions and black carbon mass concentrations at 17 observation sites in Germany. These sites cover various environmental settings including urban traffic, urban background, rural background, and Alpine mountains. In association with partner projects, GUAN has implemented a high degree of harmonisation of instrumentation, operating procedures, and data evaluation procedures. The quality of the measurement data is assured by laboratory intercomparisons as well as on-site comparisons with reference instruments. This paper describes the measurement sites, instrumentation, quality assurance, and data evaluation procedures in the network as well as the EBAS repository, where the data sets can be obtained (doi:10.5072/guan).

Staunton 1 reclamation demonstration project. Aquatic ecosystems. Final report

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

Vinikour, W. S.

1981-02-01

To provide long-term indications of the potential water quality improvements following reclamation efforts at the Staunton 1 Reclamation Demonstration Project, macroinvertebrates were collected from three on-site ponds and from the receiving stream (Cahokia Creek) for site drainage. Implications for potential benthic community differences resulting from site runoff were disclosed, but macroinvertebrate diversity throughout Cahokia Creek was limited due to an unstable, sandy substrate. The three ponds sampled were the New Pond, which was created as part of the reclamation activities; the Shed Pond, which and the Old Pond, which, because it was an existing, nonimpacted pond free of site runoff,more » served as a control. Comparisons of macroinvertebrates from the ponds indicated the potential for the New Pond to develop into a productive ecosystem. Macroinvertebrates in the New Pond were generally species more tolerant of acid mine drainage conditions. However, due to the present limited faunal densities and the undesirable physical and chemical characteristics of the New Pond, the pond should not be stocked with fish at this time.« less

Lead and mercury levels in an environmentally exposed population in the Central Brazil.

PubMed

Jesus, Leda Diva Freitas de; Moreira, Maria de Fátima Ramos; Azevedo, Sayonara Vieira de; Borges, Renato Marçullo; Gomes, Regina Aderne de Almeida; Bergamini, Fernanda Pereira Baptista; Teixeira, Liliane Reis

2018-03-01

The objective was to assess the level of exposure to lead and mercury in a population in the Pantanal region in Mato Grosso State, Brazil. Blood lead (PbB) (n = 119) and urinary mercury (HgU) (n = 109) in local residents were measured by atomic absorption spectrometry. Comparison of means and correlations between variables used analysis of variance (ANOVA) and linear regression, respectively, with 95% confidence intervals. Mean PbB was 2.82 ± 1.53µg dL-1. The comparison of PbB stratified by collection site (p ≤ 0.01), work activity (p ≤ 0.01), and consumption of locally produced cow's milk (p ≤ 0.05) showed statistically significant differences. There were also positive associations between PbB and collection site (p ≤ 0.01), participants' profession (p ≤ 0.05), local milk (p ≤ 0.01), and source of drinking water (p ≤ 0.01). Mean HgU was 1.41 ± 0.98µg L-1. The levels only showed significant differences for participants' profession (p ≤ 0.01), and positive associations emerged between HgU and work activity (p ≤ 0.01) and body mass index (p ≤ 0.01). The samples showed low lead and mercury levels, similar to those found in other environmentally exposed populations. Despite these low concentrations, current knowledge on the toxicity of these metals shows that health effects can already be felt at levels that were previously considered safe, thus characterizing a health hazard.

Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3

PubMed Central

Heaslet, Holly; Lin, Ying-Chuan; Tam, Karen; Torbett, Bruce E; Elder, John H; Stout, C David

2007-01-01

We have obtained the 1.7 Å crystal structure of FIV protease (PR) in which 12 critical residues around the active site have been substituted with the structurally equivalent residues of HIV PR (12X FIV PR). The chimeric PR was crystallized in complex with the broad-based inhibitor TL-3, which inhibits wild type FIV and HIV PRs, as well as 12X FIV PR and several drug-resistant HIV mutants [1-4]. Biochemical analyses have demonstrated that TL-3 inhibits these PRs in the order HIV PR > 12X FIV PR > FIV PR, with Ki values of 1.5 nM, 10 nM, and 41 nM, respectively [2-4]. Comparison of the crystal structures of the TL-3 complexes of 12X FIV and wild-typeFIV PR revealed theformation of additinal van der Waals interactions between the enzyme inhibitor in the mutant PR. The 12X FIV PR retained the hydrogen bonding interactions between residues in the flap regions and active site involving the enzyme and the TL-3 inhibitor in comparison to both FIV PR and HIV PR. However, the flap regions of the 12X FIV PR more closely resemble those of HIV PR, having gained several stabilizing intra-flap interactions not present in wild type FIV PR. These findings offer a structural explanation for the observed inhibitor/substrate binding properties of the chimeric PR. PMID:17212810

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

Comparisons of Prostate Cancer Inhibitors Abiraterone and TOK-001 Binding with CYP17A1 through Molecular Dynamics.

PubMed

Xiao, Fei; Yang, Maohua; Xu, Youjun; Vongsangnak, Wanwipa

2015-01-01

Cytochrome P450 17A1 (CYP17A1) is associated in the steroid hormone biosynthesis in human. As cell proliferation of prostate cancer in response to androgen steroid, an inhibition of CYP17A1 becomes an alternative approach to inhibit biosynthesis of androgen and support treatment of prostate cancer. However, biology-driven inhibitor development of prostate cancer is poorly elucidated. The aims of this study are to address structural differences at atomic-level between CYP17A1 and inhibitors i.e., abiraterone and TOK-001, and further investigate the effect of point mutation of CYP17A1 on the active site stability and the local interactions that are hydrophobic interaction and hydrogen bonding throughout molecular dynamics (MD) simulation. After performing multiple comparisons among four different complexes across CYP17A1 and inhibitors, interestingly TOK-001 oriented toward the active pocket and formed larger volume with I-helix of CYP17A1 than abiraterone, whereas abiraterone showed tighter binding and more active site stability. Considering on the effect of hydrophobic interaction and hydrogen bonding between abiraterone and CYP17A1, the key residues of Phe114, Ile371, Val482, and Asn202 were identified. This contributes into tight binding interactions; however abiraterone is effectively weakened along with the global conformation mobility increased in A105L mutation. Surprisingly, overall conformation of the CYP17A1 remained stable when bound to TOK-001. This basic knowledge can guide future experiments on design of efficient inhibitors for CYP17A1, which provides theoretical basis of androgen-dependent disease therapy.

Comparisons of Prostate Cancer Inhibitors Abiraterone and TOK-001 Binding with CYP17A1 through Molecular Dynamics

PubMed Central

Xiao, Fei; Yang, Maohua; Xu, Youjun; Vongsangnak, Wanwipa

2015-01-01

Cytochrome P450 17A1 (CYP17A1) is associated in the steroid hormone biosynthesis in human. As cell proliferation of prostate cancer in response to androgen steroid, an inhibition of CYP17A1 becomes an alternative approach to inhibit biosynthesis of androgen and support treatment of prostate cancer. However, biology-driven inhibitor development of prostate cancer is poorly elucidated. The aims of this study are to address structural differences at atomic-level between CYP17A1 and inhibitors i.e., abiraterone and TOK-001, and further investigate the effect of point mutation of CYP17A1 on the active site stability and the local interactions that are hydrophobic interaction and hydrogen bonding throughout molecular dynamics (MD) simulation. After performing multiple comparisons among four different complexes across CYP17A1 and inhibitors, interestingly TOK-001 oriented toward the active pocket and formed larger volume with I-helix of CYP17A1 than abiraterone, whereas abiraterone showed tighter binding and more active site stability. Considering on the effect of hydrophobic interaction and hydrogen bonding between abiraterone and CYP17A1, the key residues of Phe114, Ile371, Val482, and Asn202 were identified. This contributes into tight binding interactions; however abiraterone is effectively weakened along with the global conformation mobility increased in A105L mutation. Surprisingly, overall conformation of the CYP17A1 remained stable when bound to TOK-001. This basic knowledge can guide future experiments on design of efficient inhibitors for CYP17A1, which provides theoretical basis of androgen-dependent disease therapy. PMID:26682016

Total dissolved gas and water temperature in the lower Columbia River, Oregon and Washington, 2007: Quality-assurance data and comparison to water-quality standards

USGS Publications Warehouse

Tanner, Dwight Q.; Bragg, Heather M.; Johnston, Matthew W.

2007-01-01

For the eight monitoring sites in water year 2007, an average of 99.5% of the total-dissolved-gas data were received in real time by the USGS satellite downlink and were within 1% saturation of the expected value on the basis of calibration data, replicate quality-control measurements in the river, and comparison to ambient river conditions at adjacent sites. Data received from the sites ranged from 97.9% to 100.0% complete.

Correlations of OGO-V plasmapause crossing with observations of type Pi micropulsations on the ground.

NASA Technical Reports Server (NTRS)

Heacock, R. R.; Mullen, A. J.; Hessler, V. P.; Sucksdorff, C.; Kivinen, M.; Kataja, E.

1971-01-01

Comparison of plasmapause positions with Pi micropulsation events observed at College (L 5.4) or at Sodankyla (L 5.1), showing that in almost all cases the plasmapause was inside the field line of the observing site when the Pi event was recorded. Strong Pi events were seen at Nurmijaarvi (L 3.4) only when Kp was very high, when the plasmapause would be expected to be inside L 3.4. When Pi events and structure Pc 1 events were observed nearly simultaneously, the Pi activity was always more prominent at the poleward site. A demarcation line seems to exist, separating the Pi and structured Pc 1 source regions. This line may be the plasmapause, with structured Pc 1 inside and Pi outside.

Multicellular automaticity of cardiac cell monolayers: effects of density and spatial distribution of pacemaker cells

NASA Astrophysics Data System (ADS)

Elber Duverger, James; Boudreau-Béland, Jonathan; Le, Minh Duc; Comtois, Philippe

2014-11-01

Self-organization of pacemaker (PM) activity of interconnected elements is important to the general theory of reaction-diffusion systems as well as for applications such as PM activity in cardiac tissue to initiate beating of the heart. Monolayer cultures of neonatal rat ventricular myocytes (NRVMs) are often used as experimental models in studies on cardiac electrophysiology. These monolayers exhibit automaticity (spontaneous activation) of their electrical activity. At low plated density, cells usually show a heterogeneous population consisting of PM and quiescent excitable cells (QECs). It is therefore highly probable that monolayers of NRVMs consist of a heterogeneous network of the two cell types. However, the effects of density and spatial distribution of the PM cells on spontaneous activity of monolayers remain unknown. Thus, a simple stochastic pattern formation algorithm was implemented to distribute PM and QECs in a binary-like 2D network. A FitzHugh-Nagumo excitable medium was used to simulate electrical spontaneous and propagating activity. Simulations showed a clear nonlinear dependency of spontaneous activity (occurrence and amplitude of spontaneous period) on the spatial patterns of PM cells. In most simulations, the first initiation sites were found to be located near the substrate boundaries. Comparison with experimental data obtained from cardiomyocyte monolayers shows important similarities in the position of initiation site activity. However, limitations in the model that do not reflect the complex beat-to-beat variation found in experiments indicate the need for a more realistic cardiomyocyte representation.

A natural product based DOS library of hybrid systems.

PubMed

Prabhu, Ganesh; Agarwal, Shalini; Sharma, Vijeta; Madurkar, Sanjay M; Munshi, Parthapratim; Singh, Shailja; Sen, Subhabrata

2015-05-05

Here we described a natural product inspired modular DOS strategy for the synthesis of a library of hybrid systems that are structurally and stereochemically disparate. The main scaffold is a pyrroloisoquinoline motif, that is synthesized from tandem Pictet-Spengler lactamization. The structural diversity is generated via "privileged scaffolds" that are attached at the appropriate site of the motif. Screening of the library compounds for their antiplasmodial activity against chloroquine sensitive 3D7 cells indicated few compounds with moderate activity (20-50 μM). A systematic comparison of structural intricacy between the library members and a natural product dataset obtained from ZINC(®) revealed comparable complexity. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Use of strategic environmental assessment in the site selection process for a radioactive waste disposal facility in Slovenia.

PubMed

Dermol, Urška; Kontić, Branko

2011-01-01

The benefits of strategic environmental considerations in the process of siting a repository for low- and intermediate-level radioactive waste (LILW) are presented. The benefits have been explored by analyzing differences between the two site selection processes. One is a so-called official site selection process, which is implemented by the Agency for radwaste management (ARAO); the other is an optimization process suggested by experts working in the area of environmental impact assessment (EIA) and land-use (spatial) planning. The criteria on which the comparison of the results of the two site selection processes has been based are spatial organization, environmental impact, safety in terms of potential exposure of the population to radioactivity released from the repository, and feasibility of the repository from the technical, financial/economic and social point of view (the latter relates to consent by the local community for siting the repository). The site selection processes have been compared with the support of the decision expert system named DEX. The results of the comparison indicate that the sites selected by ARAO meet fewer suitability criteria than those identified by applying strategic environmental considerations in the framework of the optimization process. This result stands when taking into account spatial, environmental, safety and technical feasibility points of view. Acceptability of a site by a local community could not have been tested, since the formal site selection process has not yet been concluded; this remains as an uncertain and open point of the comparison. Copyright © 2010 Elsevier Ltd. All rights reserved.

Pd n Ag (4-n) and Pd n Pt (4-n) clusters on MgO (100): a density functional surface genetic algorithm investigation

DOE PAGES

Heard, Christopher J.; Heiles, Sven; Vajda, Stefan; ...

2014-08-07

We employed the novel surface mode of the Birmingham Cluster Genetic Algorithm (S-BCGA) for the global optimisation of noble metal tetramers upon an MgO(100) substrate at the GGA-DFT level of theory. The effect of element identity and alloying in surface-bound neutral subnanometre clusters is determined by energetic comparison between all compositions of Pd nAg (4-n) and Pd nPt (4-n). And while the binding strengths to the surface increase in the order Pt > Pd > Ag, the excess energy profiles suggest a preference for mixed clusters for both cases. The binding of CO is also modelled, showing that the adsorptionmore » site can be predicted solely by electrophilicity. Comparison to CO binding on a single metal atom shows a reversal of the 5s-d activation process for clusters, weakening the cluster surface interaction on CO adsorption. Charge localisation determines homotop, CO binding and surface site preferences. Furthermore, the electronic behaviour, which is intermediate between molecular and metallic particles allows for tunable features in the subnanometre size range.« less

Analysis of Raman Lidar and radiosonde measurements from the AWEX-G field campaign and its relation to Aqua validation

NASA Technical Reports Server (NTRS)

Whiteman, D. N.; Russo, F.; Demoz, B.; Miloshevich, L. M.; Veselovskii, I.; Hannon, S.; Wang, Z.; Vomel, H.; Schmidlin, F.; Lesht, B.

2005-01-01

Early work within the Aqua validation activity revealed there to be large differences in water vapor measurement accuracy among the various technologies in use for providing validation data. The validation measurements were made at globally distributed sites making it difficult to isolate the sources of the apparent measurement differences among the various sensors, which included both Raman lidar and radiosonde. Because of this, the AIRS Water Vapor Experiment-Ground (AWEX-G) was held in October - November, 2003 with the goal of bringing validation technologies to a common site for intercomparison and resolution of the measurement discrepancies. Using the University of Colorado Cryogenic Frostpoint Hygrometer (CFH) as the water vapor reference, the AWEX-G field campaign resulted in new correction techniques for both Raman lidar, Vaisala RS80-H and RS90/92 measurements that significantly improve the absolute accuracy of those measurement systems particularly in the upper troposphere. Mean comparisons of radiosondes and lidar are performed demonstrating agreement between corrected sensors and the CFH to generally within 5% thereby providing data of sufficient accuracy for Aqua validation purposes. Examples of the use of the correction techniques in radiance and retrieval comparisons are provided and discussed.

Hydrolysis at One of the Two Nucleotide-binding Sites Drives the Dissociation of ATP-binding Cassette Nucleotide-binding Domain Dimers

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

Zoghbi, M. E.; Altenberg, G. A.

The functional unit of ATP-binding cassette (ABC) transporters consists of two transmembrane domains and two nucleotide-binding domains (NBDs). ATP binding elicits association of the two NBDs, forming a dimer in a head-to-tail arrangement, with two nucleotides “sandwiched” at the dimer interface. Each of the two nucleotide-binding sites is formed by residues from the two NBDs. We recently found that the prototypical NBD MJ0796 from Methanocaldococcus jannaschii dimerizes in response to ATP binding and dissociates completely following ATP hydrolysis. However, it is still unknown whether dissociation of NBD dimers follows ATP hydrolysis at one or both nucleotide-binding sites. Here, we usedmore » luminescence resonance energy transfer to study heterodimers formed by one active (donor-labeled) and one catalytically defective (acceptor-labeled) NBD. Rapid mixing experiments in a stop-flow chamber showed that NBD heterodimers with one functional and one inactive site dissociated at a rate indistinguishable from that of dimers with two hydrolysis-competent sites. Comparison of the rates of NBD dimer dissociation and ATP hydrolysis indicated that dissociation followed hydrolysis of one ATP. We conclude that ATP hydrolysis at one nucleotide-binding site drives NBD dimer dissociation.« less

Cloud Computing for Protein-Ligand Binding Site Comparison

PubMed Central

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824

Cloud computing for protein-ligand binding site comparison.

PubMed

Hung, Che-Lun; Hua, Guan-Jie

2013-01-01

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

Variability in carbon dioxide fluxes for dense urban, suburban and woodland environments in southern England

NASA Astrophysics Data System (ADS)

Ward, Helen; Kotthaus, Simone; Grimmond, C. Sue; Bjorkegren, Alex; Wilkinson, Matt; Morrison, Will; Evans, Jon; Morison, James; Christen, Andreas

2014-05-01

The net exchange of carbon dioxide between the surface and atmosphere can be measured using the eddy covariance technique. Fluxes from a dense urban environment (central London), a suburban landscape (Swindon) and a woodland ecosystem (Alice Holt) are compared. All sites are located in southern England and experience similar climatic and meteorological conditions, yet have very different land cover. The signatures of anthropogenic and biogenic processes are explored at various (daily, seasonal and annual) timescales. Particular emphasis is placed on identifying the mixture of controls that determine the flux. In summer, there are clear similarities between the suburban and woodland sites, as the diurnal behaviour is dominated by photosynthetic uptake. In winter, however, vegetation is largely dormant and human activity determines the pattern of fluxes at the urban and suburban sites. Emissions from building heating augment the net release of carbon dioxide in cold months. Road use is a major contributor to the total emissions, and the diurnal cycle in the observed fluxes reflects this: in central London roads are busy throughout the day, whereas in Swindon a double-peaked rush-hour signal is evident. The net exchange of carbon dioxide is estimated for each site and set in context with other studies around the world. Central London has the smallest proportion of vegetation and largest emissions amongst study sites in the literature to date. Although Swindon's appreciable vegetation fraction helps to offset the anthropogenic emissions, even in summertime the 24h total flux is usually positive, indicating carbon release. Comparison of these three sites in a similar region demonstrates the effects of increasing urban density and changing land use on the atmosphere. Findings are relevant in terms of characterising the behaviour of urban surfaces and for quantifying the impact of anthropogenic activities.

Enhancement of plaque removal by baking soda toothpastes from less accessible areas in the dentition.

PubMed

Thong, S; Hooper, W; Xu, Y; Ghassemi, A; Winston, A

2011-01-01

To determine if baking soda toothpastes are relatively more effective than non-baking soda toothpastes in promoting plaque removal from less accessible sites in the dentition. Several single-brushing comparisons of baking soda and non-baking soda toothpastes for their overall ability to remove plaque have been published. In this study, individual comparisons of these published data, comparing the plaque removal performance of baking soda and non-baking soda toothpastes at various sites in the dentition, were examined to see if there were any site-dependant performance trends. The site-specific single-brushing data were then combined and analyzed in two ways. Meta-analyses of the clinical studies were performed to compare baking soda's relative plaque removal advantage at various sites in the mouth using paired t-testing at p <0.05. Also, plaque index reductions at various sites due to brushing with baking soda toothpastes were graphically compared with plaque index reductions due to brushing with non-baking soda dentifrices. The percent relative plaque removal advantage for baking soda toothpastes at various sites were plotted against the reduction in plaque index due to brushing with non-baking soda toothpastes. Individual comparisons showed that brushing with the toothpastes containing baking soda generally removed significantly more plaque from each site than brushing with toothpastes without baking soda. The relative efficacy advantage for baking soda toothpastes was consistently higher at sites where the non-baking soda toothpastes removed less plaque. Meta-analytical comparisons confirmed baking soda toothpastes to be relatively more effective in enhancing plaque removal from sites where less plaque was removed compared to brushing with non-baking soda toothpastes (p < 0.05). Graphically, the baking soda toothpastes' relative plaque removal advantage could be seen to increase hyperbolically with decreasing plaque removal by the non-baking soda toothpastes with which they were compared. We presuppose that the reason less plaque is removed by non-baking soda toothpastes at some sites than others is that these sites are less accessible to the toothbrush. These results show that baking soda toothpastes are relatively more effective in enhancing plaque removal from harder-to-reach areas of the dentition (p <0.05), i.e., from lingual than facial surfaces, from posterior than anterior areas, and from proximal than mid-surface sites.

Evaluation of plant species composition after thirteen years post coal mining rehabilitation in East Kutai District of East Kalimantan, Indonesia

NASA Astrophysics Data System (ADS)

Komara, L. L.; Murtinah, V.; Arbain

2018-04-01

Coal mining leaving large overburden which needs to be rehabilitated by conducting reclamation and re-vegetation. This study objective was to evaluate plant species composition after thirteen years of re-vegetation activities in a coal mining rehabilitation site in KutaiTimur District, East Kalimantan, with coordinate 00º33’23”-00º38’17” NL and 117º23’55”-117º23’20” EL. This study compared rehabilitation site with the natural forest conditions sites. There were found 28 plant species in the rehabilitation site, consisting of 19 wood species (Cassia siamea and Ficus uncinata) and 9 non-wood species (Nephrolepis biserata and Miscanthus javanica).In comparison, 36 species were found in the natural forest condition, consisting of 25 woody species (Nephelium eriopetalum and Macaranga hypoleuca)and 11 non-wood species (Fordia splendidisima and Saurauia umbellata). Woody species diversity indices in the rehabilitation site after 13 years post mining (i.e., 2,21) was lower than in the natural forest sites (3,01); while the diversity indices for non-wood species were relatively similar (1,48 and 1,96 in the rehabilitation and natural forest sites respectively). Species richness of non-wood species was low, but it has a high coverage per species in this site.To restore rehabilitation site woody species to its assumed natural conditions, 22woody species should be planted.

Plutonium isotopes and 241Am in the atmosphere of Lithuania: A comparison of different source terms

NASA Astrophysics Data System (ADS)

Lujanienė, G.; Valiulis, D.; Byčenkienė, S.; Šakalys, J.; Povinec, P. P.

2012-12-01

137Cs, 241Am and Pu isotopes collected in aerosol samples during 1994-2011 were analyzed with special emphasis on better understanding of Pu and Am behavior in the atmosphere. The results from long-term measurements of 240Pu/239Pu atom ratios showed a bimodal frequency distribution with median values of 0.195 and 0.253, indicating two main sources contributing to the Pu activities at the Vilnius sampling station. The low Pu atom ratio of 0.141 could be attributed to the weapon-grade plutonium derived from the nuclear weapon test sites. The frequency of air masses arriving from the North-West and North-East correlated with the Pu atom ratio indicating the input from the sources located in these regions (the Novaya Zemlya test site, Siberian nuclear plants), while no correlation with the Chernobyl region was observed. Measurements carried out during the Fukushima accident showed a negligible impact of this source with Pu activities by four orders of magnitude lower as compared to the Chernobyl accident. The activity concentration of actinides measured in the integrated sample collected in March-April, 2011 showed a small contribution of Pu with unusual activity and atom ratios indicating the presence of the spent fuel of different origin than that of the Chernobyl accident.

Structural and Biochemical Studies of TIGAR (TP53-induced Glycolysis and Apoptosis Regulator)

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

Li, H.; Jogl, G

2009-01-01

Activation of the p53 tumor suppressor by cellular stress leads to variable responses ranging from growth inhibition to apoptosis. TIGAR is a novel p53-inducible gene that inhibits glycolysis by reducing cellular levels of fructose-2,6-bisphosphate, an activator of glycolysis and inhibitor of gluconeogenesis. Here we describe structural and biochemical studies of TIGAR from Danio rerio. The overall structure forms a histidine phosphatase fold with a phosphate molecule coordinated to the catalytic histidine residue and a second phosphate molecule in a position not observed in other phosphatases. The recombinant human and zebra fish enzymes hydrolyze fructose-2,6-bisphosphate as well as fructose-1,6-bisphosphate but notmore » fructose 6-phosphate in vitro. The TIGAR active site is open and positively charged, consistent with its enzymatic function as bisphosphatase. The closest related structures are the bacterial broad specificity phosphatase PhoE and the fructose-2,6-bisphosphatase domain of the bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. The structural comparison shows that TIGAR combines an accessible active site as observed in PhoE with a charged substrate-binding pocket as seen in the fructose-2,6-bisphosphatase domain of the bifunctional enzyme.« less

Quantitative structure--property relationships for enhancing predictions of synthetic organic chemical removal from drinking water by granular activated carbon.

PubMed

Magnuson, Matthew L; Speth, Thomas F

2005-10-01

Granular activated carbon is a frequently explored technology for removing synthetic organic contaminants from drinking water sources. The success of this technology relies on a number of factors based not only on the adsorptive properties of the contaminant but also on properties of the water itself, notably the presence of substances in the water which compete for adsorption sites. Because it is impractical to perform field-scale evaluations for all possible contaminants, the pore surface diffusion model (PSDM) has been developed and used to predict activated carbon column performance using single-solute isotherm data as inputs. Many assumptions are built into this model to account for kinetics of adsorption and competition for adsorption sites. This work further evaluates and expands this model, through the use of quantitative structure-property relationships (QSPRs) to predict the effect of natural organic matter fouling on activated carbon adsorption of specific contaminants. The QSPRs developed are based on a combination of calculated topographical indices and quantum chemical parameters. The QSPRs were evaluated in terms of their statistical predictive ability,the physical significance of the descriptors, and by comparison with field data. The QSPR-enhanced PSDM was judged to give results better than what could previously be obtained.

Face to (face)book: the two faces of social behavior?

PubMed

Ivcevic, Zorana; Ambady, Nalini

2013-06-01

Social networking sites such as Facebook represent a unique and dynamic social environment. This study addresses three theoretical issues in personality psychology in the context of online social networking sites: (a) the temporal consistency of Facebook activity, (b) people's awareness of their online behavior, and (c) comparison of social behavior on Facebook with self- and informant-reported behavior in real life. Facebook Wall pages of 99 college students (mean age = 19.72) were downloaded six times during 3 weeks and coded for quantity and quality of activity. Everyday social interactions were assessed by self- and friend report. Facebook activity showed significant consistency across time, and people demonstrated awareness of their online behavior. There was significant similarity between everyday traits and interactions and Facebook behavior (e.g., more posts by friends are related to Agreeableness). Some differences between online and everyday interactions warrant further research (e.g., individuals with more positive offline relationships are less likely to engage in back-and-forth conversations on Facebook). The results indicate substantial similarity between online and offline social behavior and identify avenues for future research on the possible use of Facebook to compensate for difficulty in everyday interactions. © 2012 Wiley Periodicals, Inc.

Micromorphology of past urban soils: method and results (France, Iron Age - Middle Age)

NASA Astrophysics Data System (ADS)

Cammas, Cécilia

2014-05-01

Urban soils in French protohistoric and Roman towns and present-day towns of roman origin are several meters thick accumulations, with great spatial and vertical variability due to long duration of occupation. In order to improve our knowledge of both sedimentary and pedological characteristics as well as formation processes of urban soils, micromorphological analysis was carried out on buried towns. The studied sites include Iron Age towns (floodplain sites: Lattes or Lattara, Le Cailar; oppidum: Pech-Maho in the south of France), a roman buried town (Famars or Fanum Martis, North of France), and various towns occupied from the Roman period until now (urban and periurban sites in Paris, Strasbourg, Mâcon… North and East of France). Original method and sampling strategy were elaborated in order to try to encompass both spatial and vertical variability as well as the "mitage" of the present-day cities. In Lattes, representative elementary urban areas such as streets, courtyard, and houses were sampled for micromorphology during extensive excavation. These analyses revealed specific microscopic features related to complex anthropogenic processes (craft and domestic activities discarding, trampling, backfill, building), moisture and heat, and biological activity, which defined each kind of area. Comparison between well preserved buried town and current cities of roman origin, where the sequence of past urban soils is preserved in few place ("mitage") help to identify past activities, building rhythms as well as specific building materials. For example, in Paris, compacted sandy backfills alternate with watertight hardfloors during the Roman period (soils similar to Technosols). At the opposite, various kinds of loose bioturbated laminated dark earth resulting from activities such as craft refuses, backfills, compost or trampled layers were discriminated for Early Medieval Period (soils similar to Cumulic Anthroposol). Moreover, biological activity is usually considered destructive and an evidence of abandonment of the towns during Early Medieval Period by the archaeologists. These results show that in the studied sites the nature, location and intensity of biological activity (Lumbricidae, Enchytraeidae) is dependent on human activities (moisture, organic input) and is an evidence of human presence in town. Thus, the methodology allows identifying past activities and their location in the town, as well as their evolution with time. It highlights cultural and micro-local conditions specificities of each period, and it helps to elucidate urban site formation processes. It shows that soils and sub-soils of present-day cities are composed of a succession of different kinds of urban soils, and that micromorphology is a powerful tool to identify their characteristics such as their physical and biological properties and their discontinuities as well as their functioning. Key words: site formation processes, Iron Age towns, Roman towns, dark earth, biological activity, Enchytraeidae, Lumbricidae, Technosols, cumulic soils.

Implementation of Policy, Systems, and Environmental Community-Based Interventions for Cardiovascular Health Through a National Not-for-Profit: A Multiple Case Study.

PubMed

Garney, Whitney R; Szucs, Leigh E; Primm, Kristin; King Hahn, Laura; Garcia, Kristen M; Martin, Emily; McLeroy, Kenneth

2018-05-01

In 2014, the Centers for Disease Control and Prevention funded the American Heart Association to implement policy, systems, and environment-focused strategies targeting access to healthy food and beverages, physical activity, and smoke-free environments. To understand factors affecting implementation and variations in success across sites, evaluators conducted a multiple case study. Based on past literature, community sites were categorized as capacity-building or implementation-ready, for comparison. A sample of six communities were selected using a systematic selection tool. Through site visits, evaluators conducted interviews with program staff and community partners and assessed action plans. Evaluators identified important implications for nationally coordinated community-based prevention programming. Differences in implementation varied by the communities' readiness, with the most notable differences in how they planned activities and defined success. Existing partner relationships (or lack thereof) played a significant role, regardless of the American Heart Association's existing presence within the communities, in the progression of initiatives and the differences observed among phases. Last, goals in capacity-building sites were tied to organizational goals while goals in implementation-ready sites were more incremental with increased community influence and buy-in. Using national organizations as a mechanism to carry out large-scale community-based prevention work is a viable option that provides coordinated, wide-scale implementation without sacrificing a community's priorities or input. In funding future initiatives, the presence of relationships and the time needed to cultivate such relationships should be accounted for in the planning and implementation processes, as well as both local and national expectations.

Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair

PubMed Central

Shinohara, Takeshi; Ikawa, Shukuko; Iwasaki, Wakana; Hiraki, Toshiki; Hikima, Takaaki; Mikawa, Tsutomu; Arai, Naoto; Kamiya, Nobuo; Shibata, Takehiko

2015-01-01

In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions. PMID:25561575

Environmental risk assessment in five rivers of Parana River basin, Southern Brazil, through biomarkers in Astyanax spp.

PubMed

Barros, Ivaldete Tijolin; Ceccon, Juliana Parolin; Glinski, Andressa; Liebel, Samuel; Grötzner, Sonia Regina; Randi, Marco Antonio Ferreira; Benedito, Evanilde; Ortolani-Machado, Claudia Feijó; Filipak Neto, Francisco; de Oliveira Ribeiro, Ciro Alberto

2017-07-01

In the current study, water quality of five river sites in Parana River basin (Brazil), utilized for public water supply, was assessed through a set of biomarkers in fish Astyanax spp. Population growth and inadequate use of land are challenges to the preservation of biodiversity and resources such as water. Some physicochemical parameters as well as somatic indexes, gills and liver histopathology, genotoxicity, and biochemical biomarkers were evaluated. The highest gonadosomatic index (GSI) and antioxidant parameters (catalase and glutathione S-transferase activities, non-protein thiols), as well as the lowest damage to biomolecules (lipid peroxidation, protein carbonylation, DNA damage) were observed in site 0 (Piava River), which is located at an environmental protected area. Site 1, located in the same river, but downstream site 0 and outside the protection area, presents some level of impact. Fish from site 2 (Antas River), which lack of riparian forest and suffer from silting, presented the highest micronucleus incidence and no melanomacrophages. Differently, individuals from site 3 (Xambrê River) and site 4 (Pinhalzinho River) which receive surface runoff from Umuarama city, urban and industrial sewage, have the highest incidences of liver and gill histopathological alterations, including neoplasia, which indicated the worst health conditions of all sites. In particular, site 4 had high levels of total nitrogen and ammonia, high turbidity, and very low oxygen levels, which indicate important chemical impact. Comparison of the biomarkers in fish allowed classification of the five sites in terms of environmental impact and revealed that sites 3 and 4 had particular poor water quality.

The dextromethorphan analog dimemorfan attenuates kainate-induced seizures via σ1 receptor activation: comparison with the effects of dextromethorphan

PubMed Central

Shin, Eun-Joo; Nah, Seung-Yeol; Kim, Won-Ki; Ko, Kwang Ho; Jhoo, Wang-Kee; Lim, Yong-Kwang; Cha, Joo Young; Chen, Chieh-Fu; Kim, Hyoung-Chun

2005-01-01

In a previous study, we demonstrated that a dextromethorphan analog, dimemorfan, has neuroprotective effects. Dextromethorphan and dimemorfan are high-affinity ligands at σ1 receptors. Dextromethorphan has moderate affinities for phencyclidine sites, while dimemorfan has very low affinities for such sites, suggesting that these sites are not essential for the anticonvulsant actions of dimemorfan. Kainate (KA) administration (10 mg kg−1, i.p.) produced robust convulsions lasting 4–6 h in rats. Pre-treatment with dimemorfan (12 or 24 mg kg−1) reduced seizures in a dose-dependent manner. Dimemorfan pre-treatment also attenuated the KA-induced increases in c-fos/c-jun expression, activator protein (AP)-1 DNA-binding activity, and loss of cells in the CA1 and CA3 fields of the hippocampus. These effects of dimemorfan were comparable to those of dextromethorphan. The anticonvulsant action of dextromethorphan or dimemorfan was significantly counteracted by a selective σ1 receptor antagonist BD 1047, suggesting that the anticonvulsant action of dextromethorphan or dimemorfan is, at least in part, related to σ1 receptor-activated modulation of AP-1 transcription factors. We asked whether dimemorfan produces the behavioral side effects seen with dextromethorphan or dextrorphan (a phencyclidine-like metabolite of dextromethorphan). Conditioned place preference and circling behaviors were significantly increased in mice treated with phencyclidine, dextrorphan or dextromethorphan, while mice treated with dimemorfan showed no behavioral side effects. Our results suggest that dimemorfan is equipotent to dextromethorphan in preventing KA-induced seizures, while it may lack behavioral effects, such as psychotomimetic reactions. PMID:15723099

Carbonic anhydrase inhibitors. Comparison of chlorthalidone, indapamide, trichloromethiazide, and furosemide X-ray crystal structures in adducts with isozyme II, when several water molecules make the difference.

PubMed

Temperini, Claudia; Cecchi, Alessandro; Scozzafava, Andrea; Supuran, Claudiu T

2009-02-01

Thiazide and high ceiling diuretics were recently shown to inhibit all mammalian isoforms of carbonic anhydrase (CA, EC 4.2.1.1) with a very different profile as compared to classical inhibitors, such as acetazolamide, methazolamide, and ethoxzolamide. Some of these structurally related compounds have a very different behavior against the widespread isozyme CA II, with chlorthalidone, trichloromethiazide, and furosemide being efficient inhibitors against CA II (K(I)s of 65-138 nM), whereas indapamide is a much weaker one (K(I) of 2520 nM). Furthermore, some of these diuretics are quite efficient (low nanomolar) inhibitors of other isoforms, for example, chlorthalidone against hCA VB, VII, IX, and XIII; indapamide against CA VII, IX, XII, and XIII, trichloromethiazide against CA VII and IX, and furosemide against CA I and XIV. Examining the four X-ray crystal structures of their CA II adducts, we observed several (2-3) active site water molecules interacting with the chlorthalidone, trichloromethiazide, and furosemide scaffolds which may be responsible for this important difference of activity. Indeed, indapamide bound to CA II has no interactions with active site water molecules. Chlorthalidone bound within the CA II active site is in an enolic (lactimic) tautomeric form, with the enolic OH also participating in two strong hydrogen bonds with Asn67 and a water molecule. The newly evidenced binding modes of these diuretics may be exploited for designing better CA II inhibitors as well as compounds with selectivity/affinity for various isoforms with medicinal chemistry applications.

A Novel N-Acetylglutamate Synthase Architecture Revealed by the Crystal Structure of the Bifunctional Enzyme from Maricaulis maris

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

Shi, Dashuang; Li, Yongdong; Cabrera-Luque, Juan

2012-05-24

Novel bifunctional N-acetylglutamate synthase/kinases (NAGS/K) that catalyze the first two steps of arginine biosynthesis and are homologous to vertebrate N-acetylglutamate synthase (NAGS), an essential cofactor-producing enzyme in the urea cycle, were identified in Maricaulis maris and several other bacteria. Arginine is an allosteric inhibitor of NAGS but not NAGK activity. The crystal structure of M. maris NAGS/K (mmNAGS/K) at 2.7 {angstrom} resolution indicates that it is a tetramer, in contrast to the hexameric structure of Neisseria gonorrhoeae NAGS. The quaternary structure of crystalline NAGS/K from Xanthomonas campestris (xcNAGS/K) is similar, and cross-linking experiments indicate that both mmNAGS/K and xcNAGS aremore » tetramers in solution. Each subunit has an amino acid kinase (AAK) domain, which is likely responsible for N-acetylglutamate kinase (NAGK) activity and has a putative arginine binding site, and an N-acetyltransferase (NAT) domain that contains the putative NAGS active site. These structures and sequence comparisons suggest that the linker residue 291 may determine whether arginine acts as an allosteric inhibitor or activator in homologous enzymes in microorganisms and vertebrates. In addition, the angle of rotation between AAK and NAT domains varies among crystal forms and subunits within the tetramer. A rotation of 26{sup o} is sufficient to close the predicted AcCoA binding site, thus reducing enzymatic activity. Since mmNAGS/K has the highest degree of sequence homology to vertebrate NAGS of NAGS and NAGK enzymes whose structures have been determined, the mmNAGS/K structure was used to develop a structural model of human NAGS that is fully consistent with the functional effects of the 14 missense mutations that were identified in NAGS-deficient patients.« less

Enhancement of activity and sulfur resistance of CeO2 supported on TiO2-SiO2 for the selective catalytic reduction of NO by NH3.

PubMed

Liu, Caixia; Chen, Liang; Li, Junhua; Ma, Lei; Arandiyan, Hamidreza; Du, Yu; Xu, Jiayu; Hao, Jiming

2012-06-05

A series of novel metal-oxide-supported CeO(2) catalysts were prepared via the wet impregnation method, and their NH(3)-SCR activities were investigated. The Ce/TiO(2)-SiO(2) catalyst with a Ti/Si mass ratio of 3/1 exhibited superior NH(3)-SCR activity and high N(2) selectivity in the temperature range of 250-450 °C. The characterization results revealed that the activity enhancement was correlated with the properties of the support material. Cerium was highly dispersed on the TiO(2)-SiO(2) binary metal oxide support, and the interaction of Ti and Si resulted in greater conversion of Ce(4+) to Ce(3+) on the surface of the catalyst compared to that on the single metal oxide supports. As a result of in the increased number of acid sites on Ce/TiO(2)-SiO(2) that resulted from the addition of SiO(2), the NH(3) adsorption capacity was significantly improved. All of these factors played significant roles in the high SCR activity. More importantly, Ce/TiO(2)-SiO(2) exhibited strong resistance to SO(2) and H(2)O poisoning. After the addition of SiO(2), the number of Lewis-acid sites was not decreased, but the number of Brønsted-acid sites on the TiO(2)-SiO(2) carrier was increased. The introduction of SiO(2) further weakened the alkalinity over the surface of the Ce/TiO(2)-SiO(2) catalyst, which resulted in sulfate not easily accumulating on the surface of the Ce/TiO(2)-SiO(2) catalyst in comparison with Ce/TiO(2).

A Framework for Managing Diver Impacts on Historic Shipwrecks

NASA Astrophysics Data System (ADS)

Edney, Joanne

2016-12-01

Shipwrecks are becoming increasingly popular and, therefore important attractions for recreational scuba divers. Divers' usage of these sites has the potential to create a range of adverse impacts on their cultural heritage values. Impacts associated with recreational scuba diving include boat anchor and mooring damage, impairment of site integrity and stability, the effects of intentional and unintentional contact with shipwrecks and artifacts, as well as divers' exhaled air bubbles coming into contact with shipwrecks. While these consequences may not present a major threat in comparison to other human impacts, such as fishing activities, extractive industries or commercial salvage, their cumulative effect can be significant, particularly at sites where visitation levels are high. Unlike natural events such as storms, diver impacts can be controlled and managing these impacts is an important component of a heritage management strategy for any site. Heritage managers face the difficult challenge of, on the one hand, balancing divers' access to important underwater cultural heritage sites, and on the other hand, protecting these sites. This paper outlines the causes and nature of potential recreational diver impacts on shipwrecks, briefly describing a range of management approaches that can mitigate such impacts, and presents a framework for the management of diver impacts on cultural heritage values of historic shipwrecks. The framework is designed to assist managers in deciding on appropriate management actions and priorities for particular sites.

An Analysis of Fish Communities on Structured Habitat in the Northwestern Gulf of Mexico: Potential Impacts of "Rigs-to-Reefs" Programs and a Comparison with Natural Banks

NASA Astrophysics Data System (ADS)

Wetz, J. J.; Ajemian, M. J.; Streich, M.; Stunz, G. W.

2016-02-01

Artificial habitat in the northwestern Gulf of Mexico is predominantly comprised of both active and reefed oil and gas platforms. In the last few decades, Texas alone has converted over 140 decommissioned oil and gas platforms into permitted artificial reefs. Despite the predominance of this habitat type, the associated fish communities remain poorly studied and few comparisons with natural habitat have been done. Using remotely operated vehicles in 2012 and 2013, we documented fish assemblages surrounding 15 artificial structures and several natural banks located on the Texas shelf. Artificial sites were variable in depth (30-84 m), number of structures, and vertical relief. Both structure type and relief influenced species richness and community structure at these sites. However, bottom depth was most influential with a shift in community composition and high diversity observed at approximately 60 m depth. In this same region, drowned coralgal reefs (the South Texas Banks) provide natural hard substrate with relief up to 20 m. Comparisons between these natural habitats and artificial reefs with similar depths and relief clearly demonstrate fish community differences, perhaps indicating differences in habitat function. To attain species-specific management goals, reefing programs should carefully consider the ambient environmental conditions (i.e., depth) and proximity of natural habitats, as these will most certainly affect the fish assemblage and characteristics of exploited fisheries species.

Mutation screening of melatonin-related genes in patients with autism spectrum disorders

PubMed Central

2010-01-01

Background One consistent finding in autism spectrum disorders (ASD) is a decreased level of the pineal gland hormone melatonin and it has recently been demonstrated that this decrease to a large extent is due to low activity of the acetylserotonin O-methyltransferase (ASMT), the last enzyme in the melatonin synthesis pathway. Moreover, mutations in the ASMT gene have been identified, including a splice site mutation, that were associated with low ASMT activity and melatonin secretion, suggesting that the low ASMT activity observed in autism is, at least partly, due to variation within the ASMT gene. Methods In the present study, we have investigated all the genes involved in the melatonin pathway by mutation screening of AA-NAT (arylalkylamine N-acetyltransferase), ASMT, MTNR1A, MTNR1B (melatonin receptor 1A and 1B) and GPR50 (G protein-coupled receptor 50), encoding both synthesis enzymes and the three main receptors of melatonin, in 109 patients with autism spectrum disorders (ASD). A cohort of 188 subjects from the general population was used as a comparison group and was genotyped for the variants identified in the patient sample. Results Several rare variants were identified in patients with ASD, including the previously reported splice site mutation in ASMT (IVS5+2T>C). Of the variants affecting protein sequence, only the V124I in the MTNR1B gene was absent in our comparison group. However, mutations were found in upstream regulatory regions in three of the genes investigated, ASMT, MTNR1A, and MTNR1B. Conclusions Our report of another ASD patient carrying the splice site mutation IVS5+2T>C, in ASMT further supports an involvement of this gene in autism. Moreover, our results also suggest that other melatonin related genes might be interesting candidates for further investigation in the search for genes involved in autism spectrum disorders and related neurobehavioral phenotypes. However, further studies of the novel variants identified in this study are warranted to shed light on their potential role in the pathophysiology of these disorders. PMID:20377855

Mutation screening of melatonin-related genes in patients with autism spectrum disorders.

PubMed

Jonsson, Lina; Ljunggren, Elin; Bremer, Anna; Pedersen, Christin; Landén, Mikael; Thuresson, Kent; Giacobini, Maibritt; Melke, Jonas

2010-04-08

One consistent finding in autism spectrum disorders (ASD) is a decreased level of the pineal gland hormone melatonin and it has recently been demonstrated that this decrease to a large extent is due to low activity of the acetylserotonin O-methyltransferase (ASMT), the last enzyme in the melatonin synthesis pathway. Moreover, mutations in the ASMT gene have been identified, including a splice site mutation, that were associated with low ASMT activity and melatonin secretion, suggesting that the low ASMT activity observed in autism is, at least partly, due to variation within the ASMT gene. In the present study, we have investigated all the genes involved in the melatonin pathway by mutation screening of AA-NAT (arylalkylamine N-acetyltransferase), ASMT, MTNR1A, MTNR1B (melatonin receptor 1A and 1B) and GPR50 (G protein-coupled receptor 50), encoding both synthesis enzymes and the three main receptors of melatonin, in 109 patients with autism spectrum disorders (ASD). A cohort of 188 subjects from the general population was used as a comparison group and was genotyped for the variants identified in the patient sample. Several rare variants were identified in patients with ASD, including the previously reported splice site mutation in ASMT (IVS5+2T>C). Of the variants affecting protein sequence, only the V124I in the MTNR1B gene was absent in our comparison group. However, mutations were found in upstream regulatory regions in three of the genes investigated, ASMT, MTNR1A, and MTNR1B. Our report of another ASD patient carrying the splice site mutation IVS5+2T>C, in ASMT further supports an involvement of this gene in autism. Moreover, our results also suggest that other melatonin related genes might be interesting candidates for further investigation in the search for genes involved in autism spectrum disorders and related neurobehavioral phenotypes. However, further studies of the novel variants identified in this study are warranted to shed light on their potential role in the pathophysiology of these disorders.

A Design Analysis Model for Developing World Wide Web Sites.

ERIC Educational Resources Information Center

Ma, Yan

2002-01-01

Examines the relationship between and among designers, text, and users of the Galter Health Sciences Library Web site at Northwestern University by applying reader-response criticism. Highlights include Web site design; comparison of designers' intentions with the actual organization of knowledge on the Web site; and compares designer's intentions…

Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide

PubMed Central

Omura, Hiroki; Oikawa, Daisuke; Nakane, Takanori; Kato, Megumi; Ishii, Ryohei; Ishitani, Ryuichiro; Tokunaga, Fuminori; Nureki, Osamu

2016-01-01

In the innate immune system, pattern recognition receptors (PRRs) specifically recognize ligands derived from bacteria or viruses, to trigger the responsible downstream pathways. DEAD box protein 41 (DDX41) is an intracellular PRR that triggers the downstream pathway involving the adapter STING, the kinase TBK1, and the transcription factor IRF3, to activate the type I interferon response. DDX41 is unique in that it recognizes two different ligands; i.e., double-stranded DNA (dsDNA) and cyclic dinucleotides (CDN), via its DEAD domain. However, the structural basis for the ligand recognition by the DDX41 DEAD domain has remained elusive. Here, we report two crystal structures of the DDX41 DEAD domain in apo forms, at 1.5 and 2.2 Å resolutions. A comparison of the two crystal structures revealed the flexibility in the ATP binding site, suggesting its formation upon ATP binding. Structure-guided functional analyses in vitro and in vivo demonstrated the overlapped binding surface for dsDNA and CDN, which is distinct from the ATP-binding site. We propose that the structural rearrangement of the ATP binding site is crucial for the release of ADP, enabling the fast turnover of DDX41 for the dsDNA/CDN-induced STING activation pathway. PMID:27721487

APPLICATION OF BAYESIAN AND GEOSTATISTICAL MODELING TO THE ENVIRONMENTAL MONITORING OF CS-137 AT THE IDAHO NATIONAL LABORATORY

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

Kara G. Eby

2010-08-01

At the Idaho National Laboratory (INL) Cs-137 concentrations above the U.S. Environmental Protection Agency risk-based threshold of 0.23 pCi/g may increase the risk of human mortality due to cancer. As a leader in nuclear research, the INL has been conducting nuclear activities for decades. Elevated anthropogenic radionuclide levels including Cs-137 are a result of atmospheric weapons testing, the Chernobyl accident, and nuclear activities occurring at the INL site. Therefore environmental monitoring and long-term surveillance of Cs-137 is required to evaluate risk. However, due to the large land area involved, frequent and comprehensive monitoring is limited. Developing a spatial model thatmore » predicts Cs-137 concentrations at unsampled locations will enhance the spatial characterization of Cs-137 in surface soils, provide guidance for an efficient monitoring program, and pinpoint areas requiring mitigation strategies. The predictive model presented herein is based on applied geostatistics using a Bayesian analysis of environmental characteristics across the INL site, which provides kriging spatial maps of both Cs-137 estimates and prediction errors. Comparisons are presented of two different kriging methods, showing that the use of secondary information (i.e., environmental characteristics) can provide improved prediction performance in some areas of the INL site.« less

Human Manganese Superoxide Dismutase Tyrosine 34 Contribution to Structure and Catalysis

PubMed Central

Perry, J. Jefferson P.; Hearn, Amy S.; Cabelli, Diane E.; Nick, Harry S.; Tainer, John A.; Silverman, David N.

2009-01-01

Superoxide dismutase (SOD) enzymes are critical in controlling levels of reactive oxygen species (ROS) that are linked to aging, cancer and neurodegenerative disease. Superoxide (O2 •−) produced during respiration is removed by the product of the SOD2 gene, the homotetrameric manganese superoxide dismutase (MnSOD). Here, we examine the structural and catalytic roles of the highly conserved active-site residue Tyr34, based upon structure-function studies of MnSOD enzymes with mutations at this site. Substitution of Tyr34 with five different amino acids retained the active site protein structure and assembly, but causes a substantial decrease in the catalytic rate constant for the reduction of superoxide. The rate constant for formation of product inhibition complex also decreases but to a much lesser extent, resulting in a net increase in the product inhibition form of the mutant enzymes. Comparisons of crystal structures and catalytic rates also suggest that one mutation, Y34V, interrupts the hydrogen-bonded network, which is associated with a rapid dissociation of the product-inhibited complex. Notably, with three of the Tyr34 mutants we also observe an intermediate in catalysis, which has not been reported previously. Thus, these mutants establish a means to trap a catalytic intermediate that promises to help elucidate the mechanism of catalysis. PMID:19265433

Distribution, vertical position and ecological implications of shallow gas in Bahía Blanca estuary (Argentina)

NASA Astrophysics Data System (ADS)

Bravo, M. E.; Aliotta, S.; Fiori, S.; Ginsberg, S.

2018-03-01

There has been a growing interest in the study of shallow gas due its importance in relation to the marine environment, climate change and human activities. In Bahía Blanca estuary, Argentina, shallow gas has a wide distribution. Acoustic turbidity and blanking are the main seismic evidence for the presence of shallow gas in the estuary. The former prevails in the inner sector of the estuary where gas is either near or in contact with the seabed. Gas deposits are generally associated with paleochannels corresponding to the Holocene paleodeltaic environment. Distribution studies of shallow gas in this estuary are necessary because its presence implies not only a geological risk for harbor activities but also because it may have noxious effects on the marine ecosystem, mainly on benthic communities. The comparison of benthic communities at a gas site (GS) with those at a control site (CS) indicated that gas could generate impoverishment in terms of individuals' abundance (GS: N = 357; CS: N = 724). Also, diversity indices showed great differences in the community structure at each site. This indicates that methane gas may act as a natural disturbance agent in estuarine ecosystems. The presence of gas in seabed sediments must therefore be taken into account when distribution studies are conducted of estuarine benthic communities.

Apollo 17

NASA Technical Reports Server (NTRS)

Garrett, David

1972-01-01

This is the Press Kit that was given to the various media outlets that were interested in covering the Apollo 17 mission. It includes information about the moon, lunar science, concentrating on the planned mission. The kit includes information about the flight, and the trajectory, planned orbit insertion maneuvers, the extravehicular mission events, a comparison with the Apollo 16, a map of the lunar surface, and the surface activity, information about the Taurus-Littrow landing site, the planned science experiments, the power source for the experiment package and diagrams of some of the instrumentation that was used to perform the experiments.

STS-114: Discovery Day 6 Post MMT Meeting

NASA Technical Reports Server (NTRS)

2005-01-01

Wane Hill, Deputy Manager of the Space Shuttle Program, and Steve Poulos, Manager, Orbiter Project Office discussed damage assessments caused during ascent. Steve further detailed the damage analysis and assessments with chart presentation of composite tile damage and gap filler sites evaluation, protruding ceramic shim, left wing tile damage, comparisons of ground test results versus FD5 focused inspection, and the window 1 blanket. Gap fillers, the STS-73, thermal protection, temperature range, heating and heating range, aerodynamics, aerothermodynamics, risk, foam damage, tile adhesions, and extravehicular activities are topics covered with the News media.

Reconstruction of 137Cs activity in the ocean following the Fukushima Daiichi Nuclear Power Plant Accident

NASA Astrophysics Data System (ADS)

Tsumune, Daisuke; Aoyama, Michio; Tsubono, Takaki; Tateda, Yutaka; Misumi, Kazuhiro; Hayami, Hiroshi; Toyoda, Yasuhiro; Maeda, Yoshiaki; Yoshida, Yoshikatsu; Uematsu, Mitsuo

2014-05-01

A series of accidents at the Fukushima Dai-ichi Nuclear Power Plant following the earthquake and tsunami of 11 March 2011 resulted in the release of radioactive materials to the ocean by two major pathways, direct release from the accident site and atmospheric deposition. We reconstructed spatiotemporal variability of 137Cs activity in the ocean by the comparison model simulations and observed data. We employed a regional scale and the North Pacific scale oceanic dispersion models, an atmospheric transport model, a sediment transport model, a dynamic biological compartment model for marine biota and river runoff model to investigate the oceanic contamination. Direct releases of 137Cs were estimated for more than 2 years after the accident by comparing simulated results and observed activities very close to the site. The estimated total amounts of directly released 137Cs was 3.6±0.7 PBq. Directly release rate of 137Cs decreased exponentially with time by the end of December 2012 and then, was almost constant. The daily release rate of 137Cs was estimated to be 3.0 x 1010 Bq day-1 by the end of September 2013. The activity of directly released 137Cs was detectable only in the coastal zone after December 2012. Simulated 137Cs activities attributable to direct release were in good agreement with observed activities, a result that implies the estimated direct release rate was reasonable, while simulated 137Cs activities attributable to atmospheric deposition were low compared to measured activities. The rate of atmospheric deposition onto the ocean was underestimated because of a lack of measurements of dose rate and air activity of 137Cs over the ocean when atmospheric deposition rates were being estimated. Observed 137Cs activities attributable to atmospheric deposition in the ocean helped to improve the accuracy of simulated atmospheric deposition rates. Although there is no observed data of 137Cs activity in the ocean from 11 to 21 March 2011, observed data of marine biota should reflect the history of 137Cs activity in this early period. The comparisons between simulated 137Cs activity of marine biota by a dynamic biological compartment and observed data also suggest that simulated 137Cs activity attributable to atmospheric deposition was underestimated in this early period. In addition, river runoff model simulations suggest that the river flux of 137Cs to the ocean was effective to the 137Cs activity in the ocean in this early period. The sediment transport model simulations suggests that the inventory of 137Cs in sediment was less than 10

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

PubMed Central

Lexa, Katrina W.; Carlson, Heather A.

2013-01-01

Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective - or even erroneous - atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. Based on comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future MSCS crystallographic structures. PMID:23327200

Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts

PubMed Central

HATAKEYAMA, YOSHINORI; SHIBUYA, NORIHIRO; NISHIYAMA, TAKASHI; NAKASHIMA, NOBUHIKO

2004-01-01

The intergenic region (IGR) located upstream of the capsid protein gene in dicistroviruses contains an internal ribosome entry site (IRES). Translation initiation mediated by the IRES does not require initiator methionine tRNA. Comparison of the IGRs among dicistroviruses suggested that Taura syndrome virus (TSV) and acute bee paralysis virus have an extra side stem loop in the predicted IRES. We examined whether the side stem is responsible for translation activity mediated by the IGR using constructs with compensatory mutations. In vitro translation analysis showed that TSV has an IGR-IRES that is structurally distinct from those previously described. Because IGR-IRES elements determine the translation initiation site by virtue of their own tertiary structure formation, the discovery of this initiation mechanism suggests the possibility that eukaryotic mRNAs might have more extensive coding regions than previously predicted. To test this hypothesis, we searched full-length cDNA databases and whole genome sequences of eukaryotes using the pattern matching program, Scan For Matches, with parameters that can extract sequences containing secondary structure elements resembling those of IGR-IRES. Our search yielded several sequences, but their predicted secondary structures were suggested to be unstable in comparison to those of dicistroviruses. These results suggest that RNAs structurally similar to dicistroviruses are not common. If some eukaryotic mRNAs are translated independently of an initiator methionine tRNA, their structures are likely to be significantly distinct from those of dicistroviruses. PMID:15100433

Scale-dependent spatial variability in peatland lead pollution in the southern Pennines, UK.

PubMed

Rothwell, James J; Evans, Martin G; Lindsay, John B; Allott, Timothy E H

2007-01-01

Increasingly, within-site and regional comparisons of peatland lead pollution have been undertaken using the inventory approach. The peatlands of the Peak District, southern Pennines, UK, have received significant atmospheric inputs of lead over the last few hundred years. A multi-core study at three peatland sites in the Peak District demonstrates significant within-site spatial variability in industrial lead pollution. Stochastic simulations reveal that 15 peat cores are required to calculate reliable lead inventories at the within-site and within-region scale for this highly polluted area of the southern Pennines. Within-site variability in lead pollution is dominant at the within-region scale. The study demonstrates that significant errors may be associated with peatland lead inventories at sites where only a single peat core has been used to calculate an inventory. Meaningful comparisons of lead inventories at the regional or global scale can only be made if the within-site variability of lead pollution has been quantified reliably.

The Vertical Dynamics of Larval Chironomids on Artificial Substrates in Lake Lido (Bogor, Indonesia)

PubMed Central

Wardiatno, Yusli; Krisanti, Majariana

2013-01-01

The composition and abundance of chironomid larval communities was studied on artificial substrates in Lido Lake, located in Bogor, West Java, Indonesia. The lake is organically enriched as a result of fish farming activity. Seventy two artificial substrates were deployed at three depths (2.0, 3.5 and 5.0 m) at two sites: a cage culture site and a non-cage culture site (control). Larval chironomid larvae were collected 7, 14, 28 and 56 days after the artificial substrates were deployed. In addition, selected physical and chemical parameters of the water were simultaneously measured. Three chironomid subfamilies, the Chironominae, Tanypodinae and Orthocladiinae, were found at both sites. At the cage culture site, both diversity and total abundance were significantly higher at the 2.0 and 3.5 m depths than at the 5.0 m depth, but this was not the case at the non-cage culture site. Based on pooling of the data from all depths, a Mann-Whitney U test showed that the non-cage culture site had a significantly higher diversity and total abundance than the cage culture site. Dissolved oxygen (DO) and turbidity showed significant differences between the 2.0 m depth and the 2 greater depths at the cage culture site, whereas none of the environmental parameters showed significant differences among the three depths at the non-cage culture site. A comparison of the environmental parameters at the same depth at the two sites showed significant differences in turbidity, pH and DO. A Spearman rank correlation analysis at the cage culture site showed that abundance and DO were positively correlated, whereas abundance and turbidity were negatively correlated. However, only pH was negatively correlated with abundance at the non-cage culture site. PMID:24575246

Effect of neohesperidin dihydrochalcone on the activity and stability of alpha-amylase: a comparative study on bacterial, fungal, and mammalian enzymes.

PubMed

Kashani-Amin, Elaheh; Ebrahim-Habibi, Azadeh; Larijani, Bagher; Moosavi-Movahedi, Ali Akbar

2015-10-01

Neohesperidin dihydrochalcone (NHDC) was recently introduced as an activator of mammalian alpha-amylase. In the current study, the effect of NHDC has been investigated on bacterial and fungal alpha-amylases. Enzyme assays and kinetic analysis demonstrated the capability of NHDC to significantly activate both tested alpha-amylases. The ligand activation pattern was found to be more similar between the fungal and mammalian enzyme in comparison with the bacterial one. Further, thermostability experiments indicated a stability increase in the presence of NHDC for the bacterial enzyme. In silico (docking) test locates a putative binding site for NHDC on alpha-amylase surface in domain B. This domain shows differences in various alpha-amylase types, and the different behavior of the ligand toward the studied enzymes may be attributed to this fact. Copyright © 2015 John Wiley & Sons, Ltd.

Soil hydrological and soil property changes resulting from termite activity on agricultural fields in Burkina Faso

NASA Astrophysics Data System (ADS)

Mettrop, I.; Cammeraat, L. H.; Verbeeten, E.

2009-04-01

Termites are important ecosystem-engineers in subtropical and tropical regions. The effect of termite activity affecting soil infiltration is well documented in the Sahelian region. Most studies find increased infiltration rates on surfaces that are affected by termite activity in comparison to crusted areas showing non-termite presence. Crusted agricultural fields in the Sanmatenga region in Burkina Faso with clear termite activity were compared to control fields without visual ground dwelling termite activity. Fine scale rainfall simulations were carried out on crusted termite affected and control sites. Furthermore soil moisture change, bulk density, soil organic matter as well as general soil characteristics were studied. The top soils in the study area were strongly crusted (structural crust) after the summer rainfall and harvest of millet. They have a loamy sand texture underlain by a shallow sandy loam Bt horizon. The initial soil moisture conditions were significantly higher on the termite plots when compared to control sites. It was found that the amount of runoff produced on the termite plots was significantly higher, and also the volumetric soil moisture content after the experiments was significantly lower if compared to the control plots. Bulk density showed no difference whereas soil organic matter was significantly higher under termite affected areas, in comparison to the control plots. Lab tests showed no significant difference in hydrophobic behavior of the topsoil and crust material. Micro and macro-structural properties of the topsoil did not differ significantly between the termite sites and the control sites. The texture of the top 5 cm of the soil was also found to be not significantly different. The infiltration results are contradictory to the general literature, which reports increased infiltration rates after prolonged termite activity although mostly under different initial conditions. The number of nest entrances was clearly higher in the termite areas, but apparently did not significantly affect infiltration. The increased soil organic matter contents in the termite affected areas however, are as expected from literature, but did not improve soil aggregation which would be expected given the importance of organic matter in soil aggregation in this type of soils. One of the explanations for the reduced infiltration rates might be that termites bring clay from the finer textured subsoil to the surface to build casts over the organic material on the surface (mainly millet stems). It is speculated that the excavated clay material could be involved in crust formation, only present is in the upper 0.5 cm of the soil crust, which is enough to block pores in the crust surface, hampering infiltration. The topsoil aggregates are slaking under the summer rainfall and the increase in fine textured material, excavated by the termites, could be incorporated into the crust and reduce infiltration. Furthermore this specific effect might also be related to the type of termite involved, as impacts from ecosystem engineers on their environment is highly dependent on the specific species involved.

External quality-assurance results for the National Atmospheric Deposition Program/National Trends Network during 1991

USGS Publications Warehouse

Nilles, M.A.; Gordon, J.D.; Schroder, L.J.; Paulin, C.E.

1995-01-01

The U.S. Geological Survey used four programs in 1991 to provide external quality assurance for the National Atmospheric Deposition Program/National Trends Network (NADP/NTN). An intersite-comparison program was used to evaluate onsite pH and specific-conductance determinations. The effects of routine sample handling, processing, and shipping of wet-deposition samples on analyte determinations and an estimated precision of analyte values and concentrations were evaluated in the blind-audit program. Differences between analytical results and an estimate of the analytical precision of four laboratories routinely measuring wet deposition were determined by an interlaboratory-comparison program. Overall precision estimates for the precipitation-monitoring system were determined for selected sites by a collocated-sampler program. Results of the intersite-comparison program indicated that 93 and 86 percent of the site operators met the NADP/NTN accuracy goal for pH determinations during the two intersite-comparison studies completed during 1991. The results also indicated that 96 and 97 percent of the site operators met the NADP/NTN accuracy goal for specific-conductance determinations during the two 1991 studies. The effects of routine sample handling, processing, and shipping, determined in the blind-audit program indicated significant positive bias (a=.O 1) for calcium, magnesium, sodium, potassium, chloride, nitrate, and sulfate. Significant negative bias (or=.01) was determined for hydrogen ion and specific conductance. Only ammonium determinations were not biased. A Kruskal-Wallis test indicated that there were no significant (*3t=.01) differences in analytical results from the four laboratories participating in the interlaboratory-comparison program. Results from the collocated-sampler program indicated the median relative error for cation concentration and deposition exceeded eight percent at most sites, whereas the median relative error for sample volume, sulfate, and nitrate concentration at all sites was less than four percent. The median relative error for hydrogen ion concentration and deposition ranged from 4.6 to 18.3 percent at the four sites and as indicated in previous years of the study, was inversely proportional to the acidity of the precipitation at a given site. Overall, collocated-sampling error typically was five times that of laboratory error estimates for most analytes.

The Crystal Structure of the Ivy delta4-16:0-ACP Desaturase Reveals Structural Details of the Oxidized Active Site and Potential Determinants of Regioselectivity

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

Guy,J.; Whittle, E.; Kumaran, D.

2007-01-01

The multifunctional acyl-acyl carrier protein (ACP) desaturase from Hedera helix (English ivy) catalyzes the {Delta}{sup 4} desaturation of 16:0-ACP and the{Delta}{sup 9} desaturation of 18:0-ACP and further desaturates{Delta}{sup 9}-16:1 or {Delta}{sup 9}-18:1 to the corresponding {Delta}{sup 4,9} dienes. The crystal structure of the enzyme has been solved to 1.95{angstrom} resolution, and both the iron-iron distance of 3.2{angstrom} and the presence of a {mu}-oxo bridge reveal this to be the only reported structure of a desaturase in the oxidized FeIII-FeIII form. Significant differences are seen between the oxidized active site and the reduced active site of the Ricinus communis (castor) desaturase;more » His{sup 227} coordination to Fe2 is lost, and the side chain of Glu{sup 224}, which bridges the two iron ions in the reduced structure, does not interact with either iron. Although carboxylate shifts have been observed on oxidation of other diiron proteins, this is the first example of the residue moving beyond the coordination range of both iron ions. Comparison of the ivy and castor structures reveal surface amino acids close to the annulus of the substrate-binding cavity and others lining the lower portion of the cavity that are potential determinants of their distinct substrate specificities. We propose a hypothesis that differences in side chain packing explains the apparent paradox that several residues lining the lower portion of the cavity in the ivy desaturase are bulkier than their equivalents in the castor enzyme despite the necessity for the ivy enzyme to accommodate three more carbons beyond the diiron site.« less

Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design.

PubMed

Krajewski, Wojciech W; Collins, Ruairi; Holmberg-Schiavone, Lovisa; Jones, T Alwyn; Karlberg, Tobias; Mowbray, Sherry L

2008-01-04

Glutamine synthetase (GS) catalyzes the ligation of glutamate and ammonia to form glutamine, with concomitant hydrolysis of ATP. In mammals, the activity eliminates cytotoxic ammonia, at the same time converting neurotoxic glutamate to harmless glutamine; there are a number of links between changes in GS activity and neurodegenerative disorders, such as Alzheimer's disease. In plants, because of its importance in the assimilation and re-assimilation of ammonia, the enzyme is a target of some herbicides. GS is also a central component of bacterial nitrogen metabolism and a potential drug target. Previous studies had investigated the structures of bacterial and plant GSs. In the present publication, we report the first structures of mammalian GSs. The apo form of the canine enzyme was solved by molecular replacement and refined at a resolution of 3 A. Two structures of human glutamine synthetase represent complexes with: a) phosphate, ADP, and manganese, and b) a phosphorylated form of the inhibitor methionine sulfoximine, ADP and manganese; these structures were refined to resolutions of 2.05 A and 2.6 A, respectively. Loop movements near the active site generate more closed forms of the eukaryotic enzymes when substrates are bound; the largest changes are associated with the binding of the nucleotide. Comparisons with earlier structures provide a basis for the design of drugs that are specifically directed at either human or bacterial enzymes. The site of binding the amino acid substrate is highly conserved in bacterial and eukaryotic GSs, whereas the nucleotide binding site varies to a much larger degree. Thus, the latter site offers the best target for specific drug design. Differences between mammalian and plant enzymes are much more subtle, suggesting that herbicides targeting GS must be designed with caution.

Energetic Constraints of Subseafloor Life

NASA Astrophysics Data System (ADS)

D'Hondt, S.; Spivack, A. J.; Wang, G.

2014-12-01

Mean per-cell rates of catabolic activity, energy flux, and biomass turnover are orders of magnitude slower in subseafloor sediment than in the surface world. Despite extreme scarcity of electron donors, competing metabolic pathways co-occur for hundreds of meters deep in subseafloor sediment deposited over millions of years. Our study of an example site (ODP Site 1226) indicates that the energy yields of these competing reactions are pinned to a thermodynamic minimum (Wang et al., 2010). The simplest explanation of this long-term co-existence is thermodynamic cooperation, where microorganisms utilize different but co-existing pathways that remove each other's reaction products. Our Site 1226 results indicate that the energy flux to subseafloor sedimentary microbes is extremely low. Comparison to biomass turnover rates at other sites suggests that most of this flux may be used for building biomolecules from existing components (e.g., amino acids in the surrounding sediment), rather than for de novo biosynthesis from inorganic chemicals. Given these discoveries, ocean drilling provides a tremendous opportunity to address several mysteries of microbial survival and natural selection under extreme energy limitation. Some of these mysteries are centered on microbial communities. To what extent do counted cells in subseafloor sediment constitute a deep microbial necrosphere? How do different kinds of microbes interact to sustain their mean activity at low average rates for millions of years? Other mysteries relate to individual cells. How slowly can a cell metabolize? How long can a cell survive at such low rates of activity? What properties allow microbes to be sustained by low fluxes of energy? In what ways do subseafloor organisms balance the benefit(s) of maximizing energy recovery with the need to minimize biochemical cost(s) of energy recovery? References Wang, G., et al., 2010. Geochimica et Cosmochimica Acta 74, 3938-3947.

Modelling of the acid-base properties of natural and synthetic adsorbent materials used for heavy metal removal from aqueous solutions.

PubMed

Pagnanelli, Francesca; Vegliò, Francesco; Toro, Luigi

2004-02-01

In this paper a comparison about kinetic behaviour, acid-base properties and copper removal capacities was carried out between two different adsorbent materials used for heavy metal removal from aqueous solutions: an aminodiacetic chelating resin as commercial product (Lewatit TP207) and a lyophilised bacterial biomass of Sphaerotilus natans. The acid-base properties of a S. natans cell suspension were well described by simplified mechanistic models without electrostatic corrections considering two kinds of weakly acidic active sites. In particular the introduction of two-peak distribution function for the proton affinity constants allows a better representation of the experimental data reproducing the site heterogeneity. A priori knowledge about resin functional groups (aminodiacetic groups) is the base for preliminary simulations of titration curve assuming a Donnan gel structure for the resin phase considered as a concentrated aqueous solution of aminodiacetic acid (ADA). Departures from experimental and simulated data can be interpreted by considering the heterogeneity of the functional groups and the effect of ionic concentration in the resin phase. Two-site continuous model describes adequately the experimental data. Moreover the values of apparent protonation constants (as adjustable parameters found by non-linear regression) are very near to the apparent constants evaluated by a Donnan model assuming the intrinsic constants in resin phase equal to the equilibrium constants in aqueous solution of ADA and considering the amphoteric nature of active sites for the evaluation of counter-ion concentration in the resin phase. Copper removal outlined the strong affinity of the active groups of the resin for this ion in solution compared to the S. natans biomass according to the complexation constants between aminodiacetic and mono-carboxylic groups and copper ions.

A method for assessing the physical recovery of Antarctic desert pavements following human-induced disturbances: a case study in the Ross Sea region of Antarctica.

PubMed

O'Neill, Tanya A; Balks, Megan R; López-Martínez, Jerónimo; McWhirter, Judi L

2012-12-15

With increasing visitor numbers an understanding of the impacts of human activities in Antarctic terrestrial environments has become important. The objective of this study was to develop a means for assessing recovery of the ground surface desert pavement following physical disturbance. A set of 11 criteria were identified to assess desert pavement recovery. Assessed criteria were: embeddedness of surface clasts; impressions of removed clasts; degree of clast surface weathering; % overturned clasts; salt on underside of clasts; development of salt coatings; armouring per m(2); colour contrast; evidence of subsidence/melt out; accumulation of salt on cut surfaces; and evidence of patterned ground development. Recovery criteria were assigned a severity/extent rating on a scale from zero to four, zero being highly disturbed, and four being undisturbed. A relative % recovery for each criteria was calculated for each site by comparison with a nearby undisturbed control area, and an overall Mean Recovery Index (MRI) was assigned to each pavement surface. To test the method, 54 sites in the Ross Sea region of Antarctica were investigated including areas disturbed by: bulldozer scraping for road-fill, contouring for infrastructure, geotechnical investigations, and experimental treading trial sites. Disturbances had occurred at timescales ranging from one week to 50 years prior to assessment. The extent of desert pavement recovery at the sites investigated in this study was higher than anticipated. Fifty of the 54 sites investigated were in an intermediate, or higher, stage of desert pavement recovery, 30 sites were in an advanced stage of recovery, and four sites were indistinguishable from adjacent control sites (MRI = 100%). It was found that active surfaces, such as the gravel beach deposits at the Greenpeace World Park Base site at Cape Evans, the aeolian sand deposits at Bull Pass, and the alluvial fan deposits of the Loop Moraine field campsite, recovered relatively quickly, whereas less active sites, such as the bulldozed tracks at Marble Point, and Williams Field to McMurdo Station pipeline site on Ross Island, showed only intermediate recovery 20-30 years after disturbance. The slabby grano-diorite surface material at the former Vanda Station site, meant that the impacts that had occurred were hard to detect following decommissioning of the station and site remediation. Desert pavements disturbed by randomly dispersed footprints, temporary field campsites at the Loop Moraine and VXE6 Pond in the Wright Valley, recovered to be undetectable (MRI = 100%) within five years, whereas track formation from repeated trampling, particularly the concentration of larger clasts along the margin of a confined track, persisted for over 15 years (MRI = 82%). The recovery assessment method developed in this study has environmental management applications and potential to advance our ability to predict the recovery of desert pavement following human impacts from activities in Antarctica. Copyright © 2012 Elsevier Ltd. All rights reserved.

Sediment loads and transport at constructed chutes along the Missouri River - Upper Hamburg Chute near Nebraska City, Nebraska, and Kansas Chute near Peru, Nebraska

USGS Publications Warehouse

Densmore, Brenda K.; Rus, David L.; Moser, Matthew T.; Hall, Brent M.; Andersen, Michael J.

2016-02-04

Comparisons of concentrations and loads from EWI samples collected from different transects within a study site resulted in few significant differences, but comparisons are limited by small sample sizes and large within-transect variability. When comparing the Missouri River upstream transect to the chute inlet transect, similar results were determined in 2012 as were determined in 2008—the chute inlet affected the amount of sediment entering the chute from the main channel. In addition, the Kansas chute is potentially affecting the sediment concentration within the Missouri River main channel, but small sample size and construction activities within the chute limit the ability to fully understand either the effect of the chute in 2012 or the effect of the chute on the main channel during a year without construction. Finally, some differences in SSC were detected between the Missouri River upstream transects and the chute downstream transects; however, the effect of the chutes on the Missouri River main-channel sediment transport was difficult to isolate because of construction activities and sampling variability.

A comparison of two cloudwater/fogwater collectors: The rotating arm collector and the caltech active strand cloudwater collector

NASA Astrophysics Data System (ADS)

Collett, Jeffrey L.; Daube, Bruce C.; Munger, J. William; Hoffmann, Michael R.

A side-by-side comparison of the Rotating Arm Collector (RAC) and the Caltech Active Strand Cloudwater Collector (CASCC) was conducted at an elevated coastal site near the eastern end of the Santa Barbara Channel in southern California. The CASCC was observed to collect cloudwater at rates of up to 8.5 ml min -1. The ratio of cloudwater collection rates was found to be close to the theoretical prediction of 4.2:1 (CASCC:RAC) over a wide range of liquid water contents (LWC). At low LWC, however, this ratio climbed rapidly, possibly reflecting a predominance of small droplets under these conditions, coupled with a greater collection efficiency of small droplets by the CASCC. Cloudwater samples collected by the RAC had significantly higher concentrations of Na +, Ca 2+, Mg 2+ and Cl - than those collected by the CASCC. These higher concentrations may be due to differences in the chemical composition of large vs small droplets. No significant differences were observed in concentrations of NO 3-, SO 42- or NH 4+ in samples collected by the two instruments.

Synthetic Active Site Model of the [NiFeSe] Hydrogenase

PubMed Central

Wombwell, Claire; Reisner, Erwin

2015-01-01

A dinuclear synthetic model of the [NiFeSe] hydrogenase active site and a structural, spectroscopic and electrochemical analysis of this complex is reported. [NiFe(‘S2Se2’)(CO)3] (H2‘S2Se2’=1,2-bis(2-thiabutyl-3,3-dimethyl-4-selenol)benzene) has been synthesized by reacting the nickel selenolate complex [Ni(‘S2Se2’)] with [Fe(CO)3bda] (bda=benzylideneacetone). X-ray crystal structure analysis confirms that [NiFe(‘S2Se2’)(CO)3] mimics the key structural features of the enzyme active site, including a doubly bridged heterobimetallic nickel and iron center with a selenolate terminally coordinated to the nickel center. Comparison of [NiFe(‘S2Se2’)(CO)3] with the previously reported thiolate analogue [NiFe(‘S4’)(CO)3] (H2‘S4’=H2xbsms=1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) showed that the selenolate groups in [NiFe(‘S2Se2’)(CO)3] give lower carbonyl stretching frequencies in the IR spectrum. Electrochemical studies of [NiFe(‘S2Se2’)(CO)3] and [NiFe(‘S4’)(CO)3] demonstrated that both complexes do not operate as homogenous H2 evolution catalysts, but are precursors to a solid deposit on an electrode surface for H2 evolution catalysis in organic and aqueous solution. PMID:25847470

Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer

PubMed Central

Drewell, Robert A.; Nevarez, Michael J.; Kurata, Jessica S.; Winkler, Lauren N.; Li, Lily; Dresch, Jacqueline M.

2013-01-01

Summary In Drosophila, the 330 kb bithorax complex regulates cellular differentiation along the anterio-posterior axis during development in the thorax and abdomen and is comprised of three homeotic genes: Ultrabithorax, abdominal-A, and Abdominal-B. The expression of each of these genes is in turn controlled through interactions between transcription factors and a number of cis-regulatory modules in the neighboring intergenic regions. In this study, we examine how the sequence architecture of transcription factor binding sites mediates the functional activity of one of these cis-regulatory modules. Using computational, mathematical modeling and experimental molecular genetic approaches we investigate the IAB7b enhancer, which regulates Abdominal-B expression specifically in the presumptive seventh and ninth abdominal segments of the early embryo. A cross-species comparison of the IAB7b enhancer reveals an evolutionarily conserved signature motif containing two FUSHI-TARAZU activator transcription factor binding sites. We find that the transcriptional repressors KNIRPS, KRUPPEL and GIANT are able to restrict reporter gene expression to the posterior abdominal segments, using different molecular mechanisms including short-range repression and competitive binding. Additionally, we show the functional importance of the spacing between the two FUSHI-TARAZU binding sites and discuss the potential importance of cooperativity for transcriptional activation. Our results demonstrate that the transcriptional output of the IAB7b cis-regulatory module relies on a complex set of combinatorial inputs mediated by specific transcription factor binding and that the sequence architecture at this enhancer is critical to maintain robust regulatory function. PMID:24514265

The 1.25 Å resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis

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

Javid-Majd, Farah; Yang, Dong; Ioerger, Thomas R.

2008-06-23

Phosphoribosyl-ATP pyrophosphohydrolase is the second enzyme in the histidine-biosynthetic pathway, irreversibly hydrolyzing phosphoribosyl-ATP to phosphoribosyl-AMP and pyrophosphate. It is encoded by the hisE gene, which is present as a separate gene in many bacteria and archaea but is fused to hisI in other bacteria, fungi and plants. Because of its essentiality for growth in vitro, HisE is a potential drug target for tuberculosis. The crystal structures of two native (uncomplexed) forms of HisE from Mycobacterium tuberculosis have been determined to resolutions of 1.25 and 1.79 {angstrom}. The structure of the apoenzyme reveals that the protein is composed of five -helicesmore » with connecting loops and is a member of the {alpha}-helical nucleoside-triphosphate pyrophosphatase superfamily. The biological unit of the protein is a homodimer, with an active site on each subunit composed of residues exclusively from that subunit. A comparison with the Campylobacter jejuni dUTPase active site allowed the identification of putative metal- and substrate-binding sites in HisE, including four conserved glutamate and glutamine residues in the sequence that are consistent with a motif for pyrophosphohydrolase activity. However, significant differences between family members are observed in the loop region between {alpha}-helices H1 and H3. The crystal structure of M. tuberculosis HisE provides insights into possible mechanisms of substrate binding and the diversity of the nucleoside-triphosphate pyrophosphatase superfamily.« less

Molecular Basis of Substrate Promiscuity for the SAM-Dependent O-Methyltransferase NcsB1, Involved in the Biosynthesis of the Enediyne Antitumor Antibiotic Neocarzinostatin

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

Cooke, H.; Guenther, E; Luo, Y

2009-01-01

The small molecule component of chromoprotein enediyne antitumor antibiotics is biosynthesized through a convergent route, incorporating amino acid, polyketide, and carbohydrate building blocks around a central enediyne hydrocarbon core. The naphthoic acid moiety of the enediyne neocarzinostatin plays key roles in the biological activity of the natural product by interacting with both the carrier protein and duplex DNA at the site of action. We have previously described the in vitro characterization of an S-adenosylmethionine-dependent O-methyltransferase (NcsB1) in the neocarzinostatin biosynthetic pathway [Luo, Y., Lin, S., Zhang, J., Cooke, H. A., Bruner, S. D., and Shen, B. (2008) J. Biol. Chem.more » 283, 14694-14702]. Here we provide a structural basis for NcsB1 activity, illustrating that the enzyme shares an overall architecture with a large family of S-adenosylmethionine-dependent proteins. In addition, NcsB1 represents the first enzyme to be structurally characterized in the biosynthetic pathway of neocarzinostatin. By cocrystallizing the enzyme with various combinations of the cofactor and substrate analogues, details of the active site structure have been established. Changes in subdomain orientation were observed via comparison of structures in the presence and absence of substrate, suggesting that reorientation of the enzyme is involved in binding of the substrate. In addition, residues important for substrate discrimination were predicted and probed through site-directed mutagenesis and in vitro biochemical characterization.« less

Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity.

PubMed

Findlay, S; Sinsabaugh, R L

2006-10-01

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.

Vs30 and spectral response from collocated shallow, active- and passive-source Vs data at 27 sites in Puerto Rico

USGS Publications Warehouse

Odum, Jack K.; Stephenson, William J.; Williams, Robert A.; von Hillebrandt-Andrade, Christa

2013-01-01

Shear‐wave velocity (VS) and time‐averaged shear‐wave velocity to 30 m depth (VS30) are the key parameters used in seismic site response modeling and earthquake engineering design. Where VS data are limited, available data are often used to develop and refine map‐based proxy models of VS30 for predicting ground‐motion intensities. In this paper, we present shallow VS data from 27 sites in Puerto Rico. These data were acquired using a multimethod acquisition approach consisting of noninvasive, collocated, active‐source body‐wave (refraction/reflection), active‐source surface wave at nine sites, and passive‐source surface‐wave refraction microtremor (ReMi) techniques. VS‐versus‐depth models are constructed and used to calculate spectral response plots for each site. Factors affecting method reliability are analyzed with respect to site‐specific differences in bedrock VS and spectral response. At many but not all sites, body‐ and surface‐wave methods generally determine similar depths to bedrock, and it is the difference in bedrock VS that influences site amplification. The predicted resonant frequencies for the majority of the sites are observed to be within a relatively narrow bandwidth of 1–3.5 Hz. For a first‐order comparison of peak frequency position, predictive spectral response plots from eight sites are plotted along with seismograph instrument spectra derived from the time series of the 16 May 2010 Puerto Rico earthquake. We show how a multimethod acquisition approach using collocated arrays compliments and corroborates VS results, thus adding confidence that reliable site characterization information has been obtained.

Characterization and analysis of temporal and spatial variations in habitat and macroinvertebrate community structure, Fountain Creek basin, Colorado Springs and vicinity, Colorado, 1998-2001

USGS Publications Warehouse

Bruce, James F.

2002-01-01

The Fountain Creek Basin in and around Colorado Springs, Colorado, is affected by various land- and water-use activities. Biological, hydrological, water-quality, and land-use data were collected at 10 sites in the Fountain Creek Basin from April 1998 through April 2001 to provide a baseline characterization of macroinvertebrate communities and habitat conditions for comparison in subsequent studies; and to assess variation in macroinvertebrate community structure relative to habitat quality. Analysis of variance results indicated that instream and riparian variables were not affected by season, but significant differences were found among sites. Nine metrics were used to describe and evaluate macroinvertebrate community structure. Statistical analysis indicated that for six of the nine metrics, significant variability occurred between spring and fall seasons for 60 percent of the sites. Cluster analysis (unweighted pair group method average) using macroinvertebrate presence-absence data showed a well-defined separation between spring and fall samples. Six of the nine metrics had significant spatial variation. Cluster analysis using Sorenson?s Coefficient of Community values computed from macroinvertebrate density (number of organisms per square meter) data showed that macroinvertebrate community structure was more similar among tributary sites than main-stem sites. Canonical correspondence analysis identified a substrate particle-size gradient from site-specific species-abundance data and environmental correlates that decreased the 10 sites to 5 site clusters and their associated taxa.

Ambient air quality at the wider area of an industrial mining facility at Stratoni, Chalkidiki, Greece.

PubMed

Gaidajis, Georgios; Angelakoglou, Komninos; Gazea, Emmy

2012-01-01

To assess ambient air quality at the wider area of a mining-industrial facility in Chalkidiki, Greece, the particulate matter with an aerodynamic diameter of 10 μm (PM(10)) and its content in characteristic elements, i.e., As, Cd, Cu, Fe, Mn, Pb, Zn were monitored for a period of three years (2008-2010). Gravimetric air samplers were employed for the particulate matter sampling at three sampling stations located in the immediate vicinity of the industrial facility and at a neighbouring residential site. Monitoring data indicated that the 3-year median PM(10) concentrations were 23.3 μg/m(3) at the residential site close to the facility and 28.7 μg/m(3) at the site within the facility indicating a minimal influence from the industrial activities to the air quality of the neighbouring residential area. Both annual average and median PM(10) concentration levels were below the indicative European standards, whereas similar spatial and temporal variation was observed for the PM(10) constituents. The average Pb concentrations measured for the three sampling sites were 0.2, 0.146 and 0.174 μg/m(3) respectively, well below the indicative limit of 0.5 μg/m(3). The quantitative and qualitative comparison of PM(10) concentrations and its elemental constituent for the three sampling stations did not indicate any direct influence of the mining-industrial activities to the air quality of the Stratoni residential area.

Probing the Role of N-Linked Glycans in the Stability and Activity of Fungal Cellobiohydrolases by Mutational Analysis

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

Adney, W. S.; Jeoh, T.; Beckham, G. T.

2009-01-01

The filamentous fungi Trichoderma reesei and Penicillium funiculosum produce highly effective enzyme mixtures that degrade the cellulose and hemicellulose components of plant cell walls. Many fungal species produce a glycoside hydrolase family 7 (Cel7A) cellobiohydrolase, a class of enzymes that catalytically process from the reducing end of cellulose. A direct amino acid comparison of these two enzymes shows that they not only have high amino acid homology, but also contain analogous N-linked glycosylation sites on the catalytic domain. We have previously shown (Jeoh et al. in Biotechnol Biofuels, 1:10, 2008) that expression of T. reesei cellobiohydrolase I in a commonlymore » used industrial expression host, Aspergillus niger var. awamori, results in an increase in the amount of N-linked glycosylation of the enzyme, which negatively affects crystalline cellulose degradation activity as well as thermal stability. This complementary study examines the significance of individual N-linked glycans on the surface of the catalytic domain of Cel7A cellobiohydrolases from T. reesei and P. funiculosum by genetically adding or removing N-linked glycosylation motifs using site directed mutagenesis. Modified enzymes, expressed in A. niger var. awamori, were tested for activity and thermal stability. It was concluded that N-linked glycans in peptide loops that form part of the active site tunnel have the greatest impact on both thermal stability and enzymatic activity on crystalline cellulose for both the T. reesei and P. funiculosum Cel7A enzymes. Specifically, for the Cel7A T. reesei enzyme expressed in A. niger var. awamori, removal of the N384 glycosylation site yields a mutant with 70% greater activity after 120 h compared to the heterologously expressed wild type T. reesei enzyme. In addition, similar activity improvements were found to be associated with the addition of a new glycosylation motif at N194 in P. funiculosum. This mutant also exhibits 70% greater activity after 120 h compared to the wild type P. funiculosum enzyme expressed in A. niger var. awamori. Overall, this study demonstrates that 'tuning' enzyme glycosylation for expression from heterologous expression hosts is essential for generating engineered enzymes with optimal stability and activity.« less

Optimum cable barrier design and placement for the state of Oklahoma.

DOT National Transportation Integrated Search

2013-01-01

This research evaluated the effectiveness of ODOTs cable barrier program. Site inspections of all known cable barrier systems were conducted. : Locations of most cable sites were found to be within guidelines for effective use. Comparison to sites...

Personal exposure monitoring of PM2.5 in indoor and outdoor microenvironments.

PubMed

Steinle, Susanne; Reis, Stefan; Sabel, Clive E; Semple, Sean; Twigg, Marsailidh M; Braban, Christine F; Leeson, Sarah R; Heal, Mathew R; Harrison, David; Lin, Chun; Wu, Hao

2015-03-01

Adverse health effects from exposure to air pollution are a global challenge and of widespread concern. Recent high ambient concentration episodes of air pollutants in European cities highlighted the dynamic nature of human exposure and the gaps in data and knowledge about exposure patterns. In order to support health impact assessment it is essential to develop a better understanding of individual exposure pathways in people's everyday lives by taking account of all environments in which people spend time. Here we describe the development, validation and results of an exposure method applied in a study conducted in Scotland. A low-cost particle counter based on light-scattering technology - the Dylos 1700 was used. Its performance was validated in comparison with equivalent instruments (TEOM-FDMS) at two national monitoring network sites (R(2)=0.9 at a rural background site, R(2)=0.7 at an urban background site). This validation also provided two functions to convert measured PNCs into calculated particle mass concentrations for direct comparison of concentrations with equivalent monitoring instruments and air quality limit values. This study also used contextual and time-based activity data to define six microenvironments (MEs) to assess everyday exposure of individuals to short-term PM2.5 concentrations. The Dylos was combined with a GPS receiver to track movement and exposure of individuals across the MEs. Seventeen volunteers collected 35 profiles. Profiles may have a different overall duration and structure with respect to times spent in different MEs and activities undertaken. Results indicate that due to the substantial variability across and between MEs, it is essential to measure near-complete exposure pathways to allow for a comprehensive assessment of the exposure risk a person encounters on a daily basis. Taking into account the information gained through personal exposure measurements, this work demonstrates the added value of data generated by the application of low-cost monitors. Copyright © 2014. Published by Elsevier B.V.

Moral panic versus the risk society: the implications of the changing sites of social anxiety.

PubMed

Ungar, S

2001-06-01

This paper compares moral panic with the potential political catastrophes of a risk society. The aim of the comparison is threefold: 1. to establish the position of risk society threats alongside more conventional moral panics; 2. to examine the conceptual shifts that accompany the new types of threats; and 3. to outline the changing research agenda. The paper suggests that as new sites of social anxiety have emerged around environmental, nuclear, chemical and medical threats, the questions motivating moral panic research have lost much of their utility. Conceptually, it examines how the roulette dynamics of the risk society accidents expose hidden institutional violations that redound into 'hot potatoes' that are passed among and fumbled by various actors. Changing conceptions of folk devils, claims making activities, and of a safety are also discussed.

Structures of Saccharomyces cerevisiae D-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.

PubMed

Hu, Xiao-Qian; Guo, Peng-Chao; Ma, Jin-Di; Li, Wei-Fang

2013-11-01

The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 Å resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.

Analysis of ILRS Site Ties

NASA Astrophysics Data System (ADS)

Husson, V. S.; Long, J. L.; Pearlman, M.

2001-12-01

By the end of 2000, 94% of ILRS stations had completed station and site information forms (i.e. site logs). These forms contain six types of information. These six categories include site identifiers, contact information, approximate coordinates, system configuration history, system ranging capabilities, and local survey ties. The ILRS Central Bureau, in conjunction with the ILRS Networks and Engineering Working Group, has developed procedures to quality control site log contents. Part of this verification entails data integrity checks of local site ties and is the primary focus of this paper. Local survey ties are critical to the combination of space geodetic network coordinate solutions (i.e. GPS, SLR, VLBI, DORIS) of the International Terrestrial Reference Frame (ITRF). Approximately 90% of active SLR sites are collocated with at least one other space geodetic technique. The process used to verify these SLR ties, at collocated sites, is identical to the approach used in ITRF2000. Local vectors (X, Y, Z) from each ILRS site log are differenced from its corresponding ITRF2000 position vectors (i.e. no transformations). These X, Y, and Z deltas are converted into North, East, and Up. Any deltas, in any component, larger than 5 millimeter is flagged for investigation. In the absence of ITRF2000 SLR positions, CSR positions were used. To further enhance this comparison and to fill gaps in information, local ties contained in site logs from the other space geodetic services (i.e. IGS, IVS, IDS) were used in addition to ITRF2000 ties. Case studies of two collocated sites (McDonald/Ft. Davis and Hartebeeshtoek) will be explored in-depth. Recommendations on how local site surveys should be conducted and how this information should be managed will also be presented.

Cobalamin-Independent Methionine Synthase (MetE): A Face-to-Face Double Barrel that Evolved by Gene Duplication

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

Pejcha, Robert; Ludwig, Martha L.

2010-03-08

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two ({beta}{alpha}){sub 8} barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domainmore » evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys){sub 3}Zn site in the related enzymes, MetH and betaine-homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E {center_dot} Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.« less

Transcriptional activation of the Escherichia coli adaptive response gene aidB is mediated by binding of methylated Ada protein. Evidence for a new consensus sequence for Ada-binding sites.

PubMed

Landini, P; Volkert, M R

1995-04-07

The Escherichia coli aidB gene is part of the adaptive response to DNA methylation damage. Genes belonging to the adaptive response are positively regulated by the ada gene; the Ada protein acts as a transcriptional activator when methylated in one of its cysteine residues at position 69. Through DNaseI protection assays, we show that methylated Ada (meAda) is able to bind a DNA sequence between 40 and 60 base pairs upstream of the aidB transcriptional startpoint. Binding of meAda is necessary to activate transcription of the adaptive response genes; accordingly, in vitro transcription of aidB is dependent on the presence of meAda. Unmethylated Ada protein shows no protection against DNaseI digestion in the aidB promoter region nor does it promote aidB in vitro transcription. The aidB Ada-binding site shows only weak homology to the proposed consensus sequences for Ada-binding sites in E. coli (AAANNAA and AAAGCGCA) but shares a higher degree of similarity with the Ada-binding regions from other bacterial species, such as Salmonella typhimurium and Bacillus subtilis. Based on the comparison of five different Ada-dependent promoter regions, we suggest that a possible recognition sequence for meAda might be AATnnnnnnG-CAA. Higher concentrations of Ada are required for the binding of aidB than for the ada promoter, suggesting lower affinity of the protein for the aidB Ada-binding site. Common features in the Ada-binding regions of ada and aidB are a high A/T content, the presence of an inverted repeat structure, and their position relative to the transcriptional start site. We propose that these elements, in addition to the proposed recognition sequence, are important for binding of the Ada protein.

Effect of single DNA lesions on in vitro replication with DNA polymerase III holoenzyme. Comparison with other polymerases.

PubMed

Belguise-Valladier, P; Maki, H; Sekiguchi, M; Fuchs, R P

1994-02-11

In the present work, we have studied in vitro replication of N-2-acetylaminofluorene (AAF) or cis-diamminedichloroplatinum II (cis-DDP) single modified DNA templates. We used the holoenzyme (pol III HE) or the alpha subunit of DNA polymerase III, which is involved in SOS mutagenesis, and other DNA polymerases in order to compare enzymes having different biological roles and properties. Single-stranded oligonucleotides (63-mer) bearing a single AAF adduct at one of the different guanine residues of the NarI sequence (-G1G2CG3CC-) have been used in primer extension assays. Site-specifically platinated 5'd(ApG) or 5'd(GpG) oligonucleotides were constructed and similarly used in primer extension assays. In all cases, irrespective of both the chemical nature of the lesion (i.e. AAF or cis-DDP) and its local sequence context (i.e. the 3 different sites for AAF adducts within the NarI site) replication by pol III HE and pol I Klenow fragment (pol I Kf) stops one base prior to the adduct site. Removal of the 3'-->5' proofreading activity alone was not sufficient to trigger bypass of DNA lesions. Indeed, when proofreading activity of pol I is inactivated by a point mutation (pol I Kf (exo-)), the major replication product corresponds to the position opposite the adduct site showing that incorporation across from the AAF adduct is possible. These results suggest that a polymerase with proofreading activity is actually found to stop one nucleotide before the adduct not because it is unable to insert a nucleotide opposite the adduct but most likely because elongation past the adduct is strongly impaired, giving thus an increased time frame for the proofreading exonuclease to remove the base inserted across from the adduct. These results are discussed in terms of their implications for error-free and error-prone bypass in vivo.

Heterogeneous electrochemical CO2 reduction using nonmetallic carbon-based catalysts: current status and future challenges

NASA Astrophysics Data System (ADS)

Ma, Tao; Fan, Qun; Tao, Hengcong; Han, Zishan; Jia, Mingwen; Gao, Yunnan; Ma, Wangjing; Sun, Zhenyu

2017-11-01

Electrochemical CO2 reduction (ECR) offers an important pathway for renewable energy storage and fuels production. It still remains a challenge in designing highly selective, energy-efficient, robust, and cost-effective electrocatalysts to facilitate this kinetically slow process. Metal-free carbon-based materials have features of low cost, good electrical conductivity, renewability, diverse structure, and tunability in surface chemistry. In particular, surface functionalization of carbon materials, for example by doping with heteroatoms, enables access to unique active site architectures for CO2 adsorption and activation, leading to interesting catalytic performances in ECR. We aim to provide a comprehensive review of this category of metal-free catalysts for ECR, providing discussions and/or comparisons among different nonmetallic catalysts, and also possible origin of catalytic activity. Fundamentals and some future challenges are also described.

Formulation of multifunctional oil-in-water nanosized emulsions for active and passive targeting of drugs to otherwise inaccessible internal organs of the human body.

PubMed

Tamilvanan, Shunmugaperumal

2009-10-20

Oil-in-water (o/w) type nanosized emulsions (NE) have been widely investigated as vehicles/carrier for the formulation and delivery of drugs with a broad range of applications. A comprehensive summary is presented on how to formulate the multifunctional o/w NE for active and passive targeting of drugs to otherwise inaccessible internal organs of the human body. The NE is classified into three generations based on its development over the last couple of decades to make ultimately a better colloidal carrier for a target site within the internal and external organs/parts of the body, thus allowing site-specific drug delivery and/or enhanced drug absorption. The third generation NE has tremendous application for drug absorption enhancement and for 'ferrying' compounds across cell membranes in comparison to its first and second generation counterparts. Furthermore, the third generation NE provides an interesting opportunity for use as drug delivery vehicles for numerous therapeutics that can range in size from small molecules to macromolecules.

A theoretical study of Zn++ interacting with models of ligands present at the thermolysin active site

NASA Astrophysics Data System (ADS)

Giessner-Prettre, Claude; Jacob, Olivier

1989-03-01

The binding energy and the geometrical arrangements of the complexes formed by the zinc dication with OH-, one, four, five or six water molecules, SH-, H2S, formic acid, the formate anion, imidazole, its anion and formamide are calculated using the MNDO method. The comparison of the results obtained with those of ab initio computations on the same complexes induced us to propose for Zn++ a set of parameters different from the one determined by Dewar for the neutral metal atom. Using the two MNDO parametrizations, similar calculations are carried out for Zn++ interacting with two molecules of 2-aminoethanethiol and with models of the four ligands which are present at the thermolysin active site, in order to evaluate the possibilities and limitations of this semiempirical method for theoretical studies concerning zinc metalloenzymes. In the last case, the results obtained suggest that, in the crystal state, the water molecule could be deprotonated. This finding is discussed in relation with the mechanism of action of the enzyme which has been proposed.

Testing coral-based tropical cyclone reconstructions: An example from Puerto Rico

USGS Publications Warehouse

Kilbourne, K. Halimeda; Moyer, Ryan P.; Quinn, Terrence M.; Grottoli, Andrea G.

2011-01-01

Complimenting modern records of tropical cyclone activity with longer historical and paleoclimatological records would increase our understanding of natural tropical cyclone variability on decadal to centennial time scales. Tropical cyclones produce large amounts of precipitation with significantly lower δ18O values than normal precipitation, and hence may be geochemically identifiable as negative δ18O anomalies in marine carbonate δ18O records. This study investigates the usefulness of coral skeletal δ18O as a means of reconstructing past tropical cyclone events. Isotopic modeling of rainfall mixing with seawater shows that detecting an isotopic signal from a tropical cyclone in a coral requires a salinity of ~ 33 psu at the time of coral growth, but this threshold is dependent on the isotopic composition of both fresh and saline end-members. A comparison between coral δ18O and historical records of tropical cyclone activity, river discharge, and precipitation from multiple sites in Puerto Rico shows that tropical cyclones are not distinguishable in the coral record from normal rainfall using this approach at these sites.

Molecular design of two sterol 14α-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole

NASA Astrophysics Data System (ADS)

Rupp, Bernd; Raub, Stephan; Marian, Christel; Höltje, Hans-Dieter

2005-03-01

Sterol 14α-demethylase (CYP51) is one of the known major targets for azole antifungals. Therapeutic side effects of these antifungals are based on interactions of the azoles with the human analogue enzyme. This study describes for the first time a comparison of a human CYP51 (HU-CYP51) homology model with a homology model of the fungal CYP51 of Candida albicans (CA-CYP51). Both models are constructed by using the crystal structure of Mycobacterium tuberculosis MT-CYP51 (PDB code: 1EA1). The binding mode of the azole ketoconazole is investigated in molecular dynamics simulations with the GROMACS force field. The usage of special parameters for the iron azole complex binding is necessary to obtain the correct complex geometry in the active site of the enzyme models. Based on the dynamics simulations it is possible to explain the enantioselectivity of the human enzyme and also to predict the binding mode of the isomers of ketoconazole in the active site of the fungal model.

IspE Inhibitors Identified by a Combination of In Silico and In Vitro High-Throughput Screening

PubMed Central

Tidten-Luksch, Naomi; Grimaldi, Raffaella; Torrie, Leah S.; Frearson, Julie A.; Hunter, William N.; Brenk, Ruth

2012-01-01

CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens. PMID:22563402

Comparison of breeding bird and vegetation communities in primary and secondary forests of Great Smoky Mountains National Park

USGS Publications Warehouse

Simons, Theodore R.; Shriner, Susan A.; Farnsworth, George L.

2006-01-01

We compared breeding bird communities and vegetation characteristics at paired point locations in primary (undisturbed) and mature secondary forest (70-100 years old) sites in Great Smoky Mountains National Park, USA to understand how sites logged prior to creation of the park compare to undisturbed sites following 70 years of protection from human disturbance. We found that bird and vegetation communities are currently similar, but retain some differences in species composition. Rank abundance curves for primary and secondary forest bird communities showed very similar patterns of species dominance. Species composition was also similar on the two sites which shared 24 of the 25 most frequently recorded species. Nonetheless, comparisons of density estimates derived from distance sampling showed three bird species were more abundant on primary forest sites and that one bird species was significantly more abundant on secondary forest sites. Notably, comparisons based on raw counts (unadjusted for potential differences in detectability) produced somewhat different results. Analyses of vegetation samples for the paired sites also showed relative similarity, but with some differences between primary and secondary forests. Primary forest sites had more large trees (trees greater than 50 cm diameter at breast height) and late successional species. Primary forest sites had a denser tall shrub layer while secondary forest sites had a denser canopy layer. Nonetheless, tree species richness, basal area of live trees and number of standing snags did not differ between primary and secondary forest sites. Results indicate that breeding bird communities on sites within the park that were logged commercially 70 years ago are currently quite similar to bird communities on sites with no history of human disturbance. Similarities between the bird communities on previously disturbed and undisturbed sites in Great Smoky Mountains National Park may exceed those on more fragmented landscapes because large patches of primary forest, adjacent to commercially logged sites, remained in the park when it was established in 1935. These patches of primary forest may have served as source areas for commercially logged sites.

The xanthine oxidase activity in different of secondary transformed peat-moorsh soils

NASA Astrophysics Data System (ADS)

Styła, Katarzyna; Wojciech Szajdak, Lech

2010-05-01

The investigations were carried out on the transect of peatland 4.5 km long, located in the Agroecological Landscape Park host D. Chlapowski in Turew (40 km South-West of Poznań, West Polish Lowland). The sites investigation were located along Wyskoć ditch. The following material was taken from four chosen sites marked as Zbęchy, Bridge, Shelterbelt and Hirudo in two layers: acrotelm (0-50 cm) and catotelm (50-100 cm). The object of this study was to characterize the biochemical properties by the determination of the xanthine oxidase activity in two layers (acrotelm and catotelm) of the four different peat-moorsh soils used as meadow. The xanthine oxidase activity was determined spectrophotometrically by measuring uric acid formation at λmax=290 nm with xanthine as substrate. In peat-moorsh soil the highest activities of xanthine oxidasewas observed in the Shelterbelt and whereas the lowest - in Zbęchy, Bridge and Hirudo. Activities of this enzyme in peat-moorsh soil ranged from 5.96 to 19.51 μmol h-1g d.m soil. Increased activities of xanthine oxidase have been recorded on the depth 50-100 cm - catotelm (from 11.71 to 19.51 μmol h-1g d.m soil) in comparison with the depth 0-50 cm - acrotelm (from 5.96 to 14.64 μmol h-1g d.m soil). This work was supported by a grant No. N N305 3204 36 founded by Polish Ministry of Education.

Uranium series dating of Allan Hills ice

NASA Technical Reports Server (NTRS)

Fireman, E. L.

1986-01-01

Uranium-238 decay series nuclides dissolved in Antarctic ice samples were measured in areas of both high and low concentrations of volcanic glass shards. Ice from the Allan Hills site (high shard content) had high Ra-226, Th-230 and U-234 activities but similarly low U-238 activities in comparison with Antarctic ice samples without shards. The Ra-226, Th-230 and U-234 excesses were found to be proportional to the shard content, while the U-238 decay series results were consistent with the assumption that alpha decay products recoiled into the ice from the shards. Through this method of uranium series dating, it was learned that the Allen Hills Cul de Sac ice is approximately 325,000 years old.

Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution

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

Timofeev, V. I., E-mail: inna@ns.crys.ras.ru, E-mail: tostars@mail.ru, E-mail: ugama@yandex.ru; Abramchik, Yu. A.; Zhukhlistova, N. E.

2016-01-15

Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sitesmore » were shown to be identical in both proteins.« less

Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

PubMed

Nebel, Jean-Christophe

2006-05-15

With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences.

PubMed

Nizam, Shadab; Gazara, Rajesh Kumar; Verma, Sandhya; Singh, Kunal; Verma, Praveen Kumar

2014-01-01

Old Yellow Enzyme (OYE1) was the first flavin-dependent enzyme identified and characterized in detail by the entire range of physical techniques. Irrespective of this scrutiny, true physiological role of the enzyme remains a mystery. In a recent study, we systematically identified OYE proteins from various fungi and classified them into three classes viz. Class I, II and III. However, there is no information about the structural organization of Class III OYEs, eukaryotic Class II OYEs and Class I OYEs of filamentous fungi. Ascochyta rabiei, a filamentous phytopathogen which causes Ascochyta blight (AB) in chickpea possesses six OYEs (ArOYE1-6) belonging to the three OYE classes. Here we carried out comparative homology modeling of six ArOYEs representing all the three classes to get an in depth idea of structural and functional aspects of fungal OYEs. The predicted 3D structures of A. rabiei OYEs were refined and evaluated using various validation tools for their structural integrity. Analysis of FMN binding environment of Class III OYE revealed novel residues involved in interaction. The ligand para-hydroxybenzaldehyde (PHB) was docked into the active site of the enzymes and interacting residues were analyzed. We observed a unique active site organization of Class III OYE in comparison to Class I and II OYEs. Subsequently, analysis of stereopreference through structural features of ArOYEs was carried out, suggesting differences in R/S selectivity of these proteins. Therefore, our comparative modeling study provides insights into the FMN binding, active site organization and stereopreference of different classes of ArOYEs and indicates towards functional differences of these enzymes. This study provides the basis for future investigations towards the biochemical and functional characterization of these enigmatic enzymes.

Observations of Thermospheric Horizontal Winds at Watson Lake, Yukon Territory (lambda=65 Deg N)

NASA Technical Reports Server (NTRS)

Niciejewski, R. J.; Killeen, T. L.; Solomon, Stanley C.

1996-01-01

Fabry-Perot interferometer observations of the thermospheric O I (6300 A) emission have been conducted from an airglow observatory at a dark field site in the southeastern Yukon Territory, Canada, for the period November 1991 to April 1993. The experiment operated in unattended, remote fashion, has resulted in a substantial data set from which mean neutral winds have been determined. Dependent upon geomagnetic activity, the nocturnal location of the site is either equatorward of the auroral oval or within oval boundaries. The data set is rich enough to permit hourly binning of neutral winds based upon the K(sub p) geomagnetic disturbance index as well as the season. For cases of low geomagnetic activity the averaged vector horizontal neutral wind exhibits the characteristics of a midlatitude site displaying antisunward pressure-gradient-driven winds. As the geomagnetic activity rises in the late afternoon and evening winds slowly rotate sunward in an anticlockwise direction, initially remaining near 100 m/s in speed but eventually increasing to 300 m/s for K(sub p) greater than 5. For the higher levels of activity the observed neutral wind flow pattern resembles a higher-latitude polar cap pattern characterized by ion drag forcing of thermospheric neutral gases. In addition, rotational Coriolis forcing on the dusk side enhances the ion drag forcing, resulting in dusk winds which trace out the clockwise dusk cell plasma flow. On the dawn side the neutral winds also rotate in an anticlockwise direction as the strength of geomagnetic disturbances increase. Since the site is located at a transition latitude between the midlatitude and the polar cap the data set provides a sensitive test for general circulation models which attempt to parameterize the contribution of magnetospheric processes. A comparison with the Vector Spherical Harmonic (VSH) model indicates several regions of poor correspondence for December solstice conditions but reasonable agreement for the vernal equinox.

The role of polymorphisms in the spliced leader addition domain in determining promoter activity in Brugia malayi.

PubMed

Bailey, Michelle; Chauhan, Chitra; Liu, Canhui; Unnasch, Thomas R

2011-03-01

Previous studies of Brugia malayi promoters have suggested that they are unusual in that they lack the CAAT or TATAA boxes that are often emblematic of eucaryotic core promoter domains. Instead, the region surrounding the spliced leader (SL) addition site appears to function as the core promoter domain in B. malayi. To test the hypothesis that polymorphisms in this SL addition domain are important determinants of promoter activity, a series of domain swap mutants were prepared replacing the SL addition domain of the B. malayi 13kDa large subunit ribosomal protein (BmRPL13) with those of other ribosomal protein (RP) promoters exhibiting a wide range of activities. These constructs were then tested for promoter activity in a homologous transient transfection system. On average, polymorphisms in the SL addition domain were found to be responsible for 80% of the variation in promoter activity exhibited by the RP promoters tested. Essentially all of this effect could be attributable to polymorphisms in the 10nt located directly upstream of the SL addition site. A comparison of the sequence of this domain to the promoter activity exhibited by the domain swap mutants suggested that promoter activity was related to the number of T residues present in the coding strand of the upstream domain. Confirming this, mutation of the upstream domain of the promoter of the BmRPS4 gene to a homogeneous stretch of 10 T residues resulted in a significant increase in promoter activity. Copyright © 2010 Elsevier B.V. All rights reserved.

Macrobenthos community structure and trophic relationships within active and inactive Pacific hydrothermal sediments

NASA Astrophysics Data System (ADS)

Levin, Lisa A.; Mendoza, Guillermo F.; Konotchick, Talina; Lee, Raymond

2009-09-01

Hydrothermal fluids passing through sediments create a habitat hypothesized to influence the community structure of infaunal macrobenthos. Here we characterize the density, biomass, species composition, diversity, distributions, lifestyle, and nutritional sources of macroinfauna in hydrothermal sediments in NE and SW Pacific settings, and draw comparisons in search of faunal attributes characteristic of this habitat. There is increasing likelihood that seafloor massive sulfide deposits, associated with active and inactive hydrothermal venting, will be mined commercially. This creates a growing imperative for a more thorough understanding of the structure, dynamics, and resilience of the associated sediment faunas, and has stimulated the research presented here. Macrobenthic assemblages were studied at Manus Basin (1430-1634 m, Papua New Guinea [PNG]) as a function of location (South Su vs. Solwara 1), and hydrothermal activity (active vs. inactive), and at Middle Valley (2406-2411 m, near Juan de Fuca Ridge) as a function of habitat (active clam bed, microbial mat, hot mud, inactive background sediment). The studies conducted in PNG formed part of the environmental impact assessment work for the Solwara 1 Project of Nautilus Minerals Niugini Limited. We hypothesized that hydrothermally active sites should support (a) higher densities and biomass, (b) greater dominance and lower diversity, (c) a higher fraction of deposit feeders, and (d) greater isotopic evidence for chemosynthetic food sources than inactive sites. Manus Basin macrofauna generally had low density (<1000 ind. m -2) and low biomass (0.1-1.07 g m -2), except for the South Su active site, which had higher density (3494 ind. m -2) and biomass (11.94 g m -2), greater dominance (R1D=76%), lower diversity and more spatial (between-core) homogeneity than the Solwara 1 and South Su inactive sites. Dominant taxa at Manus Basin were Spionidae ( Prionospio sp.) in active sediments, and tanaids and deposit-feeding nuculanoid bivalves in active and inactive sediments. At Middle Valley, hot mud sediments supported few animals (1011 ind m -2) and low biomass (1.34 g m -2), while active clam bed sediments supported a high-density (19,984 ind m -2), high-biomass (4.46 g m -2), low-diversity assemblage comprised of largely orbiniid and syllid polychaetes. Microbial mat sediments had the most diverse assemblage (mainly orbiniid, syllid, dorvilleid, and ampharetid polychaetes) with intermediate densities (8191 ind m -2) and high biomass (4.23 g m -2). Fauna at both Manus Basin active sites had heavy δ 13C signatures (-17‰ to -13‰) indicative of chemosynthetic, TCA-cycle microbes at the base of the food chain. In contrast, photosynthesis and sulfide oxidation appear to fuel most of the fauna at Manus Basin inactive sites (δ 13C=-29‰ to -20‰) and Middle Valley active clam beds and microbial mats (δ 13C=-36‰ to -20‰). The two hydrothermal regions, located at opposite ends of the Pacific Ocean, supported different habitats, sharing few taxa at the generic or family level, but both exhibited elevated infaunal density and high dominance at selected sites. Subsurface-deposit feeding and bacterivory were prevalent feeding modes. Both the Manus Basin and Middle Valley assemblages exhibit significant within-region heterogeneity, apparently conferred by variations in hydrothermal activity and associated biogenic habitats.

Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate.

PubMed

Chen, Yaozong; Jiang, Yiping; Guo, Zhihong

2016-12-06

o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.

Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation.

PubMed

Jamshidi, Shirin; Jalili, Seifollah; Rafii-Tabar, Hashem

2015-01-01

Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.

Design and implementation of an air monitoring program in support of a brownfields redevelopment program

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

Maisel, B.E.; Hunt, G.T.; Devaney, R.J. Jr.

EPA`s Brownfields Economic Redevelopment Initiative has sparked renewal of industrial and commercial parcels otherwise idled or under-utilized because of real or perceived environmental contamination. In certain cases, restoring such parcels to productive economic use requires a redevelopment effort protective of human health and welfare through minimizing offsite migration of environmental contaminants during cleanup, demolition and remediation activities. To support these objectives, an air monitoring program is often required as an integral element of a comprehensive brownfields redevelopment effort. This paper presents a strategic framework for design and execution of an ambient air monitoring program in support of a brownfields remediationmore » effort ongoing in Lawrence, MA. Based on site characterization, the program included sample collection and laboratory analysis of ambient air samples for polychlorinated biphenyls (PCBs), polychlorinated dibenzodioxins and polychlorinated dibenzofurans (PCDDs/PCDFs), total suspended particulate (TSP), inhalable particulate (PM10), and lead. The program included four monitoring phases, identified as background, wintertime, demolition/remediation and post-demolition. Air sampling occurred over a 16 month period during 1996--97, during which time nine sampling locations were utilized to produce approximately 1,500 ambient air samples. Following strict data review and validation procedures, ambient air data interpretation focused on the following: evaluation of upwind/downwind sample pairs, comparison of ambient levels to existing regulatory standards, relation of ambient levels to data reported in the open literature, and, determination of normal seasonal variations in existing background burden, comparison of ambient levels measured during site activity to background levels.« less

Comparison of self-processing of foot-and-mouth disease virus leader proteinase and porcine reproductive and respiratory syndrome virus leader proteinase nsp1α

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

Steinberger, Jutta; Kontaxis, Georg; Rancan, Chiara

The foot-and-mouth disease virus leader proteinase (Lb{sup pro}) cleaves itself off the nascent viral polyprotein. NMR studies on the monomeric variant Lb{sup pro} L200F provide structural evidence for intramolecular self-processing. {sup 15}N-HSQC measurements of Lb{sup pro} L200F showed specifically shifted backbone signals in the active and substrate binding sites compared to the monomeric variant sLb{sup pro}, lacking six C-terminal residues. This indicates transient intramolecular interactions between the C-terminal extension (CTE) of one molecule and its own active site. Contrastingly, the porcine reproductive and respiratory syndrome virus (PRRSV) leader proteinase nsp1α, with a papain-like fold like Lb{sup pro}, stably binds itsmore » own CTE. Parts of the β-sheet domains but none of the α-helical domains of Lb{sup pro} and nsp1α superimpose; consequently, the α-helical domain of nsp1α is oriented differently relative to its β-sheet domain. This provides a large interaction surface for the CTE with the globular domain, stabilising the intramolecular complex. Consequently, self-processing inactivates nsp1α but not Lb{sup pro}. - Highlights: • We examine self-processing of the leader protease of foot-and-mouth disease virus. • NMR analysis strongly supports intramolecular self-processing. • Self-processing is a dynamic process with no stable complex. • Structural comparison with nsp1α of PRRSV which forms stable intramolecular complex. • Subdomain orientation explains differences in stability of intramolecular complexes.« less

Geographic Variation in Daily Temporal Activity Patterns of a Neotropical Marsupial (Gracilinanus agilis)

PubMed Central

Vieira, Emerson M.; de Camargo, Nícholas F.; Colas, Paul F.; Ribeiro, Juliana F.; Cruz-Neto, Ariovaldo P.

2017-01-01

The temporal activity of animals is an outcome of both biotic and abiotic factors, which may vary along the geographic range of the species. Therefore, studies conducted with a species in different localities with distinct features could elucidate how animals deal with such factors. In this study, we used live traps equipped with timing devices to investigate the temporal activity patterns of the didelphid Gracilinanus agilis in two dry-woodland areas of the Brazilian savanna (Cerrado). These areas were located about 660 km apart, one in Central Brazil and the other in Southeastern Brazil. We compared such patterns considering both reproductive and non-reproductive periods, and how it varies as a function of temperature on a seasonal basis. In Central Brazil, we found a constant, and temperature-independent activity during the night in both reproductive and non-reproductive periods. On the other hand, in Southeastern Brazil, we detected a constant activity during the reproductive period, but in the non-reproductive period G. agilis presented a peak of activity between two and four hours after sunset. Moreover, in this latter we found a relation between temporal activity and temperature during the autumn and spring. These differences in temporal activity between areas, observed during the non-reproductive period, might be associated with the higher seasonal variability in temperature, and lower mean temperatures in the Southeastern site in comparison to the Central one. In Southeastern Brazil, the decrease in temperature during the non-reproductive season possibly forced G. agilis to be active only at certain hours of the night. However, likely due to the reproductive activities (intensive foraging and searching for mates) this marsupial showed constant, temperature-independent activity during the night in the reproductive period at both sites. PMID:28052077

Physicochemical characteristics, mutagenicity and genotoxicity of airborne particles under industrial and rural influences in Northern Lebanon.

PubMed

Melki, Pamela N; Ledoux, Frédéric; Aouad, Samer; Billet, Sylvain; El Khoury, Bilal; Landkocz, Yann; Abdel-Massih, Roula M; Courcot, Dominique

2017-08-01

In this work, the main objectives were to assess the mutagenic and genotoxic effects of fine particulate matter collected in an industrial influenced site in comparison with a non-industrial influenced one (rural site) and to relate the particulate matter (PM) composition to the observed genotoxic effects. At the industrial influenced site, higher concentrations of phosphates, trace metals, and polycyclic aromatic hydrocarbons (PAHs) in particles could be related to the contributions of quarries, fertilizer producer, cement plants, and tires burning. Gasoline and diesel combustion contributions were evidenced in particles collected at both sites. Particles collected under industrial influence showed a higher mutagenic potential on three tested strains of Salmonella typhimurium (TA98, YG1041, and TA102), and especially on the YG1041, compared to particles from the rural site. Furthermore, only particles collected in the vicinity of the industrial site showed a tendency to activate the SOS responses in Escherichia coli PQ37, which is indicative of DNA damage as a result of exposure of the bacteria cells to the action of mutagenic samples. The mutagenicity and genotoxicity of the industrial PM 2.5-0.3 particulates may be attributed to its composition especially in organic compounds. This study showed that proximity of industries can affect local PM composition as well as PM genotoxic and mutagenic potential.

Reconstructing the Qo Site of Plasmodium falciparum bc 1 Complex in the Yeast Enzyme

PubMed Central

Vallières, Cindy; Fisher, Nicholas; Meunier, Brigitte

2013-01-01

The bc 1 complex of the mitochondrial respiratory chain is essential for Plasmodium falciparum proliferation, the causative agent of human malaria. Therefore, this enzyme is an attractive target for antimalarials. However, biochemical investigations of the parasite enzyme needed for the study of new drugs are challenging. In order to facilitate the study of new compounds targeting the enzyme, we are modifying the inhibitor binding sites of the yeast Saccharomyces cerevisiae to generate a complex that mimics the P. falciparum enzyme. In this study we focused on its Qo pocket, the site of atovaquone binding which is a leading antimalarial drug used in treatment and causal prophylaxis. We constructed and studied a series of mutants with modified Qo sites where yeast residues have been replaced by P. falciparum equivalents, or, for comparison, by human equivalents. Mitochondria were prepared from the yeast Plasmodium-like and human-like Qo mutants. We measured the bc 1 complex sensitivity to atovaquone, azoxystrobin, a Qo site targeting fungicide active against P. falciparum and RCQ06, a quinolone-derivative inhibitor of P. falciparum bc 1 complex.The data obtained highlighted variations in the Qo site that could explain the differences in inhibitor sensitivity between yeast, plasmodial and human enzymes. We showed that the yeast Plasmodium-like Qo mutants could be useful and easy-to-use tools for the study of that class of antimalarials. PMID:23951230

A comparison of loblolly pine growth and yield on pure pine and mixed pine-hardwood sites

Treesearch

James D. Haywood; John R. Toliver

1989-01-01

The case histories of four loblolly pine (Pinus taeda L.) sites were examined to determine if differences in growth and yield could be associated with stand type. The stand types were pure loblolly pine and mixed loblolly pine-hardwood. All sites were located on silt loam soils and mechanical site preparation was carried out on all sites before...

Comparison of surficial CO2 efflux to other measures of subsurface crude oil degradation.

PubMed

Warren, Ean; Sihota, Natasha J; Hostettler, Frances D; Bekins, Barbara A

2014-08-01

At a spill site near Bemidji, Minnesota, crude oil at the water table has been undergoing anaerobic biodegradation for over 30years. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. To compare microbial activity measurement methods from multiple locations in the oil body, surficial carbon dioxide efflux, methanogen and methanotroph concentrations, and oil degradation state were collected. Carbon dioxide effluxes over the oil body averaged more than four times those at the background site. Methanotrophic bacteria concentrations measured using pmoA were over 10(5) times higher above the oil-contaminated sediments compared with the background site. Methanogenic archaea measured using mcrA ranged from 10(5) to over 10(7) in the oil and were below detection in the background. Methanogens correlated very well with methanotroph concentrations (r=0.99), n-alkylcyclohexane losses as a proxy for degradation state (r=-0.96), and somewhat less well with carbon dioxide efflux (r=0.92). Carbon dioxide efflux similarly correlated to methanotroph concentrations (r=0.90) and n-alkylcyclohexane losses (r=-0.91). Published by Elsevier B.V.

Comparison of surficial CO2 efflux to other measures of subsurface crude oil degradation

USGS Publications Warehouse

Warren, Ean; Sihota, Natasha J.; Hostettler, Frances D.; Bekins, Barbara A.

2014-01-01

At a spill site near Bemidji, Minnesota, crude oil at the water table has been undergoing anaerobic biodegradation for over 30 years. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. To compare microbial activity measurement methods from multiple locations in the oil body, surficial carbon dioxide efflux, methanogen and methanotroph concentrations, and oil degradation state were collected. Carbon dioxide effluxes over the oil body averaged more than four times those at the background site. Methanotrophic bacteria concentrations measured using pmoA were over 105 times higher above the oil-contaminated sediments compared with the background site. Methanogenic archaea measured using mcrA ranged from 105 to over 107 in the oil and were below detection in the background. Methanogens correlated very well with methanotroph concentrations (r = 0.99), n-alkylcyclohexane losses as a proxy for degradation state (r = − 0.96), and somewhat less well with carbon dioxide efflux (r = 0.92). Carbon dioxide efflux similarly correlated to methanotroph concentrations (r = 0.90) and n-alkylcyclohexane losses (r = − 0.91).

Boron Nitride-supported Sub-nanometer Pd 6 Clusters for Formic Acid Decomposition: A DFT Study

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

Schimmenti, Roberto; Cortese, Remedios; Duca, Dario

A periodic, self-consistent planewave DFT study was carried out to explore the potential use of Pd 6 clusters supported on a boron nitride sheet as a catalyst for the selective decomposition of formic acid (HCOOH) to CO 2 and H 2. The competition between formate (HCOO) and carboxyl (COOH) paths on catalytic sites, with different proximities to the support, was studied. Based on energetics alone, the reaction may mainly follow the HCOO route. Slightly lower activation energies were found at the lateral sites of the cluster as compared to top face sites. This is particularly true for the bidentate tomore » monodentate HCOO conversion. Through comparison of results with similar studies on HCOOH decomposition on extended Pd surfaces, it was demonstrated that the existence of undercoordinated sites in the sub-nanometer cluster could play a key role in preferentially stabilizing HCOO over COOH, which is a common CO precursor in this reaction. A hydrogen spillover mechanism was also investigated; migration toward the boron nitride support is not favorable, at least in the early stages of the reaction. However, hydrogen diffusion on the cluster has low barriers compared to those involved in formic acid decomposition.« less

Boron Nitride-supported Sub-nanometer Pd 6 Clusters for Formic Acid Decomposition: A DFT Study

DOE PAGES

Schimmenti, Roberto; Cortese, Remedios; Duca, Dario; ...

2017-04-25

A periodic, self-consistent planewave DFT study was carried out to explore the potential use of Pd 6 clusters supported on a boron nitride sheet as a catalyst for the selective decomposition of formic acid (HCOOH) to CO 2 and H 2. The competition between formate (HCOO) and carboxyl (COOH) paths on catalytic sites, with different proximities to the support, was studied. Based on energetics alone, the reaction may mainly follow the HCOO route. Slightly lower activation energies were found at the lateral sites of the cluster as compared to top face sites. This is particularly true for the bidentate tomore » monodentate HCOO conversion. Through comparison of results with similar studies on HCOOH decomposition on extended Pd surfaces, it was demonstrated that the existence of undercoordinated sites in the sub-nanometer cluster could play a key role in preferentially stabilizing HCOO over COOH, which is a common CO precursor in this reaction. A hydrogen spillover mechanism was also investigated; migration toward the boron nitride support is not favorable, at least in the early stages of the reaction. However, hydrogen diffusion on the cluster has low barriers compared to those involved in formic acid decomposition.« less

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery.

PubMed

Pérot, Stéphanie; Sperandio, Olivier; Miteva, Maria A; Camproux, Anne-Claude; Villoutreix, Bruno O

2010-08-01

Detection, comparison and analyses of binding pockets are pivotal to structure-based drug design endeavors, from hit identification, screening of exosites and de-orphanization of protein functions to the anticipation of specific and non-specific binding to off- and anti-targets. Here, we analyze protein-ligand complexes and discuss methods that assist binding site identification, prediction of druggability and binding site comparison. The full potential of pockets is yet to be harnessed, and we envision that better understanding of the pocket space will have far-reaching implications in the field of drug discovery, such as the design of pocket-specific compound libraries and scoring functions.

ASSESSMENT OF LARGE RIVER BENTHIC MACROINVERTEBRATE ASSEMBLAGES

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen in each river from those sampled in the 1999 methods comparison study to reflect a disturbance gradient. At each site, a total distanc...

ASSESSMENT OF LARGE RIVER MACROINVERTEBRATE ASSEMBLAGES

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen in each river from those sampled in the 1999 methods comparison study to reflect a disturbance gradient. At each site, a total distanc...

STANDARDIZED ASSESSMENT METHOD (SAM) FOR RIVERINE MACROINVERTEBRATES

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen in each river from those sampled in the 1999 methods comparison study to reflect a disturbance gradient. At each site, a total distanc...

ASSESSMENT OF LARGE RIVER MACROINVERTEBRATES: HOW FAR IS ENOUGH?

EPA Science Inventory

During the summer of 2001, twelve sites were sampled for macroinvertebrates, six each on the Great Miami and Kentucky Rivers. Sites were chosen to reflect a disturbance gradient in each river using sites sampled in a 1999 methods comparison study. Our sampling protocol improves...

COMPARISON OF RANDOM AND SYSTEMATIC SITE SELECTION FOR ASSESSING ATTAINMENT OF AQUATIC LIFE USES IN SEGMENTS OF THE OHIO RIVER

EPA Science Inventory

This report is a description of field work and data analysis results comparing a design comparable to systematic site selection with one based on random selection of sites. The report is expected to validate the use of random site selection in the bioassessment program for the O...

Direct Comparison of the Performance of a Bio-inspired Synthetic Nickel Catalyst and a [NiFe]-Hydrogenase, Both Covalently Attached to Electrodes

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

Rodriguez-Macia, Patricia; Dutta, Arnab; Lubitz, Wolfgang

2015-10-12

The active site of hydrogenases has been a source of inspiration for the development of molecular catalysts. However, direct comparisons between molecular catalysts and enzymes have not been possible because different techniques are used to evaluate both types of catalysts, minimizing our ability to determine how far we’ve come in mimicking the impressive enzymatic performance. Here we directly compare the catalytic properties of the [Ni(PCy2NGly2)2]2+ complex with the [NiFe]-hydrogenase from Desulfobivrio vulgaris Miyazaki F (DvMF) immobilized to a functionalized electrode under identical conditions. At pH=7, the enzyme has higher performance in both activity and overpotential, and is more stable, whilemore » at low pH, the molecular catalyst outperforms the enzyme in all respects. The Ni complex also has increased tolerance to CO. This is the first direct comparison of enzymes and molecular complexes, enabling a unique understanding of the benefits and detriments of both systems, and advancing our understanding of the utilization of these bioinspired complexes in fuel cells. AD and WJS acknowledge the Office of Science Early Career Research Program through the US Department of Energy (US DOE), Office of Science, Office of Basic Energy Sciences (BES), and Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the US DOE.« less

Structures of pyruvate kinases display evolutionarily divergent allosteric strategies

PubMed Central

Morgan, Hugh P.; Zhong, Wenhe; McNae, Iain W.; Michels, Paul A. M.; Fothergill-Gilmore, Linda A.; Walkinshaw, Malcolm D.

2014-01-01

The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (kcat/S0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (kcat/S0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors. PMID:26064527

Hair dosimetry following neutron irradiation.

PubMed

Lebaron-Jacobs, L; Gaillard-Lecanu, E; Briot, F; Distinguin, S; Boisson, P; Exmelin, L; Racine, Y; Berard, P; Flüry-Herard, A; Miele, A; Fottorino, R

2007-05-01

Use of hair as a biological dosimeter of neutron exposure was proposed a few years ago. To date, the (32)S(n,p)(32)P reaction in hair with a threshold of 2.5 MeV is the best choice to determine the fast neutron dose using body activation. This information is essential with regards to the heterogeneity of the neutron transfer to the organism. This is a very important parameter for individual dose reconstruction from the surface to the deeper tissues. This evaluation is essential to the adapted management of irradiated victims by specialized medical staff. Comparison exercises between clinical biochemistry laboratories from French sites (the CEA and COGEMA) and from the IRSN were carried out to validate the measurement of (32)P activity in hair and to improve the techniques used to perform this examination. Hair was placed on a phantom and was irradiated at different doses in the SILENE reactor (Valduc, France). Different parameters were tested: variation of hair type, minimum weight of hair sample, hair wash before measurement, delivery period of results, and different irradiation configurations. The results obtained in these comparison exercises by the different laboratories showed an excellent correlation. This allowed the assessment of a dose-activity relationship and confirmed the feasibility and the interest of (32)P measurement in hair following fast neutron irradiation.

Involvement of Sp1 and Microsatellite Repressor Sequences in the Transcriptional Control of the Human CD30 Gene

PubMed Central

Croager, Emma J.; Gout, Alexander M.; Abraham, Lawrence J.

2000-01-01

CD30, as a member of the tumor necrosis factor (TNF) receptor family, is expressed on the surface of activated lymphoid cells. CD30 overexpression is a characteristic of lymphoproliferative diseases such as Hodgkin’s/non-Hodgkin’s lymphomas, embryonal carcinoma, and a number of Th2-associated diseases. The CD30 gene has been mapped to a region of the murine genome that is involved in susceptibility to systemic lupus erythematosus. Functionally, CD30 may play a role in the deletion of autoreactive T cells. We were interested in determining the molecular nature of CD30 overexpression. Sequence comparison has revealed significant identity between the TATA-less human and murine CD30 promoters; they share a number of common consensus binding motifs. Transfection assays identified three regions of transcriptional importance; the region between position −1.2 kb and −336 bp, containing a CCAT microsatellite sequence, a conserved Sp1 site at positions −43 to −38, and a downstream promoter element (DPE) at positions +24 to +29. EMSA and DNase I footprinting showed specific DNA-protein interactions of the CD30 promoter with the Sp1 site and the CCAT repeat region. The DPE element was shown to be essential for start site selection. We conclude that the conserved Sp1 site at −43 to −38 is associated with maximum reporter gene activity, the DPE element is required for start site selection, and the CCAT tetranucleotide repeats act to repress transcription. We also have shown that the microsatellite is multiallelic, when we screened a random healthy population. Further studies are required to determine whether microsatellite instability in the repressor predisposes susceptible individuals to CD30 overexpression. PMID:10793083

REVIEW ARTICLE: A comparison of site response techniques using earthquake data and ambient seismic noise analysis in the large urban areas of Santiago de Chile

NASA Astrophysics Data System (ADS)

Pilz, Marco; Parolai, Stefano; Leyton, Felipe; Campos, Jaime; Zschau, Jochen

2009-08-01

Situated in an active tectonic region, Santiago de Chile, the country's capital with more than six million inhabitants, faces tremendous earthquake risk. Macroseismic data for the 1985 Valparaiso event show large variations in the distribution of damage to buildings within short distances, indicating strong effects of local sediments on ground motion. Therefore, a temporary seismic network was installed in the urban area for recording earthquake activity and a study was carried out aiming to estimate site amplification derived from horizontal-to-vertical (H/V) spectral ratios from earthquake data (EHV) and ambient noise (NHV), as well as using the standard spectral ratio (SSR) technique with a nearby reference station located on igneous rock. The results lead to the following conclusions: (1) The analysis of earthquake data shows significant dependence on the local geological structure with respect to amplitude and duration. (2) An amplification of ground motion at frequencies higher than the fundamental one can be found. This amplification would not be found when looking at NHV ratios alone. (3) The analysis of NHV spectral ratios shows that they can only provide a lower bound in amplitude for site amplification. (4) P-wave site responses always show lower amplitudes than those derived by S waves, and sometimes even fail to provide some frequencies of amplification. (5) No variability in terms of time and amplitude is observed in the analysis of the H/V ratio of noise. (6) Due to the geological conditions in some parts of the investigated area, the fundamental resonance frequency of a site is difficult to estimate following standard criteria proposed by the SESAME consortium, suggesting that these are too restrictive under certain circumstances.

Baseline Caesium-137 and Plutonium-239+240 inventory assessment for Central Europe

NASA Astrophysics Data System (ADS)

Meusburger, Katrin; Borelli, Pasquale; Evrard, Olivier; Ketterer, Michael; Mabit, Lionel; van Oost, Kristof; Alewell, Christine; Panagos, Panos

2017-04-01

Artificial fallout radionuclides (FRNs) such as Caesium-137 and Plutonium-239+240 released as products of the thermonuclear weapons testing that took place from the mid-1950s to the early 1980s and from nuclear power plant accidents (e.g. Chernobyl) are useful tools to quantify soil redistribution. In combination with geostatistics, FRNs may have the potential to bridge the gap between small scale process oriented studies and modelling that simplifies processes and effects over large spatial scales. An essential requirement for the application of FRNs as soil erosion tracers is the establishment of the baseline fallout at undisturbed sites before its comparison to those inventories found at sites undergoing erosion/accumulation. For this purpose, undisturbed topsoil (0-20cm) samples collected in 2009 within the framework of the Land Use/Cover Area frame Survey (LUCAS) have been measured by gamma-spectrometry and ICP-MS to determine 137Cs (n=145) and 239+240Pu (n=108) activities. To restrict the analysis to undisturbed reference sites a geospatial database query selecting only sites having a slope angle <2 degree, outside riparian zones (to avoid depositional sites) and under permanent grassland cover (according to CORINE Land Cover and Landsat) was applied. This study reports preliminary results on the feasibility of establishing a 137Cs and 239+240Pu baseline inventory map for Central Europe. The 137Cs/239+240Pu activity ratios will further allow assessing the rate and the spatial variability of 137Cs Chernobyl fallout. The establishment of such baseline inventory map will provide a unique opportunity to assess soil redistribution for a comparable time-frame (1953-2009) following a harmonised methodological protocol across national boundaries.

Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site

PubMed Central

Chang, Yun-Juan; Peacock, Aaron D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Macnaughton, Sarah J.; Hussain, A. K. M. Anwar; Saxton, Arnold M.; White, David C.

2001-01-01

Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from δ-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within δ-Proteobacteria were mainly recovered from low-uranium (≤302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. PMID:11425735

Early Site Permit Demonstration Program: Guidelines for determining design basis ground motions. Volume 2, Appendices

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

Not Available

This report develops and applies a methodology for estimating strong earthquake ground motion. The motivation was to develop a much needed tool for use in developing the seismic requirements for structural designs. An earthquake`s ground motion is a function of the earthquake`s magnitude, and the physical properties of the earth through which the seismic waves travel from the earthquake fault to the site of interest. The emphasis of this study is on ground motion estimation in Eastern North America (east of the Rocky Mountains), with particular emphasis on the Eastern United States and southeastern Canada. Eastern North America is amore » stable continental region, having sparse earthquake activity with rare occurrences of large earthquakes. While large earthquakes are of interest for assessing seismic hazard, little data exists from the region to empirically quantify their effects. The focus of the report is on the attributes of ground motion in Eastern North America that are of interest for the design of facilities such as nuclear power plants. This document, Volume II, contains Appendices 2, 3, 5, 6, and 7 covering the following topics: Eastern North American Empirical Ground Motion Data; Examination of Variance of Seismographic Network Data; Soil Amplification and Vertical-to-Horizontal Ratios from Analysis of Strong Motion Data From Active Tectonic Regions; Revision and Calibration of Ou and Herrmann Method; Generalized Ray Procedure for Modeling Ground Motion Attenuation; Crustal Models for Velocity Regionalization; Depth Distribution Models; Development of Generic Site Effects Model; Validation and Comparison of One-Dimensional Site Response Methodologies; Plots of Amplification Factors; Assessment of Coupling Between Vertical & Horizontal Motions in Nonlinear Site Response Analysis; and Modeling of Dynamic Soil Properties.« less

An aerial radiological survey of the Nevada Test Site

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

Hendricks, T J; Riedhauser, S R

1999-12-01

A team from the Remote Sensing Laboratory conducted an aerial radiological survey of the US Department of Energy's Nevada Test Site including three neighboring areas during August and September 1994. The survey team measured the terrestrial gamma radiation at the Nevada Test Site to determine the levels of natural and man-made radiation. This survey included the areas covered by previous surveys conducted from 1962 through 1993. The results of the aerial survey showed a terrestrial background exposure rate that varied from less than 6 microroentgens per hour (mR/h) to 50 mR/h plus a cosmic-ray contribution that varied from 4.5 mR/hmore » at an elevation of 900 meters (3,000 feet) to 8.5 mR/h at 2,400 meters (8,000 feet). In addition to the principal gamma-emitting, naturally occurring isotopes (potassium-40, thallium-208, bismuth-214, and actinium-228), the man-made radioactive isotopes found in this survey were cobalt-60, cesium-137, europium-152, protactinium-234m an indicator of depleted uranium, and americium-241, which are due to human actions in the survey area. Individual, site-wide plots of gross terrestrial exposure rate, man-made exposure rate, and americium-241 activity (approximating the distribution of all transuranic material) are presented. In addition, expanded plots of individual areas exhibiting these man-made contaminations are given. A comparison is made between the data from this survey and previous aerial radiological surveys of the Nevada Test Site. Some previous ground-based measurements are discussed and related to the aerial data. In regions away from man-made activity, the exposure rates inferred from the gamma-ray measurements collected during this survey agreed very well with the exposure rates inferred from previous aerial surveys.« less

Restoring and rehabilitating sagebrush habitats

USGS Publications Warehouse

Pyke, David A.; Knick, S.T.; Connelly, J.W.

2011-01-01

Less than half of the original habitat of the Greater Sage-Grouse (Centrocercus uropha-sianus) currently exists. Some has been perma-nently lost to farms and urban areas, but the remaining varies in condition from high quality to no longer adequate. Restoration of sagebrush (Artemisia spp.) grassland ecosystems may be pos-sible for resilient lands. However, Greater Sage-Grouse require a wide variety of habitats over large areas to complete their life cycle. Effective restoration will require a regional approach for prioritizing and identifying appropriate options across the landscape. A landscape triage method is recommended for prioritizing lands for restora-tion. Spatial models can indicate where to protect and connect intact quality habitat with other simi-lar habitat via restoration. The ecological site con-cept of land classification is recommended for characterizing potential habitat across the region along with their accompanying state and transi-tion models of plant community dynamics. These models assist in identifying if passive, manage-ment-based or active, vegetation manipulation?based restoration might accomplish the goals of improved Greater Sage-Grouse habitat. A series of guidelines help formulate questions that manag-ers might consider when developing restoration plans: (1) site prioritization through a landscape triage; (2) soil verification and the implications of soil features on plant establishment success; (3) a comparison of the existing plant community to the potential for the site using ecological site descriptions; (4) a determination of the current successional status of the site using state and transition models to aid in predicting if passive or active restoration is necessary; and (5) implemen-tation of post-treatment monitoring to evaluate restoration effectiveness and post-treatment man-agement implications to restoration success.

Comparison of the activities of extracts of Escherichia coli and Salmonella typhimurium in amino acid incorporation.

PubMed

Bassel, B A; Curry, M E

1973-11-01

We have compared the amino acid incorporating activities of extracts of Escherichia coli and Salmonella typhimurium in in vitro protein-synthesizing systems directed by bacterial messenger ribonucleic acid (mRNA) of both species and by the genomes of coliphages Qbeta and f2. E. coli and S. typhimurium extracts translate both homologous and heterologous bacterial mRNAs at comparable rates. S. typhimurium extracts translate phage RNAs only 10 to 15% as fast as E. coli extracts do. The presence of glucose in the growth medium increases the activity of S. typhimurium extracts three- to fourfold in the phage RNA-directed systems. Glucose has a much more limited effect on the activities of E. coli extracts. We show that similar amounts of phage RNA-ribosome complexes are formed in both the E. coli and the S. typhimurium systems, indicating that the different activities observed may be attributed to different rates of peptide elongation or to the formation of complexes at different sites on the RNA strand.

42 CFR 493.1281 - Standard: Comparison of test results.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 5 2012-10-01 2012-10-01 false Standard: Comparison of test results. 493.1281... Testing Analytic Systems § 493.1281 Standard: Comparison of test results. (a) If a laboratory performs the... between test results using the different methodologies, instruments, or testing sites. (b) The laboratory...

42 CFR 493.1281 - Standard: Comparison of test results.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Standard: Comparison of test results. 493.1281... Testing Analytic Systems § 493.1281 Standard: Comparison of test results. (a) If a laboratory performs the... between test results using the different methodologies, instruments, or testing sites. (b) The laboratory...

42 CFR 493.1281 - Standard: Comparison of test results.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 5 2013-10-01 2013-10-01 false Standard: Comparison of test results. 493.1281... Testing Analytic Systems § 493.1281 Standard: Comparison of test results. (a) If a laboratory performs the... between test results using the different methodologies, instruments, or testing sites. (b) The laboratory...

42 CFR 493.1281 - Standard: Comparison of test results.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Standard: Comparison of test results. 493.1281... Testing Analytic Systems § 493.1281 Standard: Comparison of test results. (a) If a laboratory performs the... between test results using the different methodologies, instruments, or testing sites. (b) The laboratory...

42 CFR 493.1281 - Standard: Comparison of test results.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 5 2014-10-01 2014-10-01 false Standard: Comparison of test results. 493.1281... Testing Analytic Systems § 493.1281 Standard: Comparison of test results. (a) If a laboratory performs the... between test results using the different methodologies, instruments, or testing sites. (b) The laboratory...

Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode.

PubMed

Chen, Yaozong; Li, Tin Lok; Lin, Xingbang; Li, Xin; Li, Xiang David; Guo, Zhihong

2017-07-21

o -Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent Bacillus subtilis mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 Å resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5° during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants.

PubMed

Stellmacher, Lena; Sandalova, Tatyana; Schneider, Sarah; Schneider, Gunter; Sprenger, Georg A; Samland, Anne K

2016-04-01

Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) from Escherichia coli are C-C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B from E. coli. The crystal structure of the variant TalB(F178Y) with bound sugar phosphate was solved to a resolution of 1.46 Å and revealed a novel mode of covalent inhibition. The sugar is bound covalently via its C2 atom to the ℇ-NH2 group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to β-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formed via a Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid-base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalB(E96Q) formed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20 Å. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.

Use of biomarkers in Nile tilapia (Oreochromis niloticus) to assess the impacts of pollution in Bolgoda Lake, an urban water body in Sri Lanka.

PubMed

Pathiratne, A; Chandrasekera, L W H U; Pathiratne, K A S

2009-09-01

The present study reports the first analysis of water pollutants in Sri Lankan waters using a suite of biomarkers in Nile tilapia (Oreochromis niloticus) residing in Bolgoda Lake which receives urban, industrial and domestic wastes from multiple sources. The fish were collected from the lake in the dry period (April 2005) and wet periods (September 2005, October 2006) and the levels of biomarkers viz. hepatic ethoxyresorufin O-deethylase (EROD), glutathione S-transferase (GST), metallothioneins, biliary fluorescent aromatic compounds, brain and muscle cholinesterases (ChE) were compared with those of the laboratory reared control fish and the fish obtained from a less polluted water body, Bathalagoda reservoir (reference site). The results revealed that biomarker levels of the fish collected from the reference site were not significantly different from the controls. Hepatic EROD and GST activities in fish from Bolgoda Lake were induced 4.2-16.6 folds and 1.4-3.3 folds respectively compared with the control fish. Analysis of bile in the lake fish revealed recent uptake of naphthalene, pyrene and benzo(a)pyrene type polycyclic aromatic hydrocarbons (PAHs). The induction of EROD activities in feral fish reflects the exposure of fish to aryl hydrocarbon receptor agonists including PAHs present as pollutants in the Bolgoda Lake. Cholinesterase activity in the fish inhabiting one sampling site of Bolgoda Lake was lower (22-40% inhibition) than the activity measured in the control fish indicating the presence of anticholinesterase pollutants in the area. Hepatic metallothionein levels in the lake fish were higher (1.9-3.2 folds) in comparison to the controls indicating metal exposure. The results support the potential use of these biomarkers in Nile tilapia in assessing pollution in tropical water bodies.

Rapid comparison of properties on protein surface

PubMed Central

Sael, Lee; La, David; Li, Bin; Rustamov, Raif; Kihara, Daisuke

2008-01-01

The mapping of physicochemical characteristics onto the surface of a protein provides crucial insights into its function and evolution. This information can be further used in the characterization and identification of similarities within protein surface regions. We propose a novel method which quantitatively compares global and local properties on the protein surface. We have tested the method on comparison of electrostatic potentials and hydrophobicity. The method is based on 3D Zernike descriptors, which provides a compact representation of a given property defined on a protein surface. Compactness and rotational invariance of this descriptor enable fast comparison suitable for database searches. The usefulness of this method is exemplified by studying several protein families including globins, thermophilic and mesophilic proteins, and active sites of TIM β/α barrel proteins. In all the cases studied, the descriptor is able to cluster proteins into functionally relevant groups. The proposed approach can also be easily extended to other surface properties. This protein surface-based approach will add a new way of viewing and comparing proteins to conventional methods, which compare proteins in terms of their primary sequence or tertiary structure. PMID:18618695

Rapid comparison of properties on protein surface.

PubMed

Sael, Lee; La, David; Li, Bin; Rustamov, Raif; Kihara, Daisuke

2008-10-01

The mapping of physicochemical characteristics onto the surface of a protein provides crucial insights into its function and evolution. This information can be further used in the characterization and identification of similarities within protein surface regions. We propose a novel method which quantitatively compares global and local properties on the protein surface. We have tested the method on comparison of electrostatic potentials and hydrophobicity. The method is based on 3D Zernike descriptors, which provides a compact representation of a given property defined on a protein surface. Compactness and rotational invariance of this descriptor enable fast comparison suitable for database searches. The usefulness of this method is exemplified by studying several protein families including globins, thermophilic and mesophilic proteins, and active sites of TIM beta/alpha barrel proteins. In all the cases studied, the descriptor is able to cluster proteins into functionally relevant groups. The proposed approach can also be easily extended to other surface properties. This protein surface-based approach will add a new way of viewing and comparing proteins to conventional methods, which compare proteins in terms of their primary sequence or tertiary structure.

GPS Observations in Anatahan Island, Northern Mariana Islands, Before and After the Eruption of May 10, 2003

NASA Astrophysics Data System (ADS)

Kato, T.; Matsushima, T.; Nakada, S.; Watanabe, T.; Tabei, T.; Camacho, J. T.; Chong, R.

2003-12-01

A GPS observation project in the Northern Mariana Islands started in 1992 by a joint team of Japan, US and Saipan, CNMI. We have repeated surveys in the area for several times until 2003. Previous results until 1999 showed clear evidence of back arc spreading at the Mariana Trough with velocities of 4-6cm/yr with respect to the Philippine Sea plate. There was no significant volcanic activity in this time periods. Anatahan Island erupted about three months after the latest resurvey of January 2003. In order to investigate crustal deformations of the island related to this eruption, we established a permanent site in Anatahan (ANAT). The site is located about 7km WNW of the active crater in the eastern caldera. Solar panel and a lead battery are used for power and a small PC is used for automatic data archive. A special stainless pillar was designed to set up right above the pre-occupied benchmark. We also established a new permanent site in Saipan on the roof of EMO (EMO1). For a tie to the old site in Saipan, we conducted a survey at MPLC site that have been repeatedly occupied. For a preliminary analysis, we used data sets of 1994, 1998, 1999 and January and July of 2003 for a baseline MPLC - ANAT. The obtained results suggest that Anatahan has linearly drifted to northwest relative to Saipan at least until January 2003 with a rate of about 6.5mm/yr. There was no clear long-term vertical motion of Anatahan Island until January 2003. Comparison of position of ANAT relative to MPLC between January and July, 2003 suggests about 19cm subsidence of the island. Horizontal displacement may not be significant though a few centimeters of offset toward north could be visible. Large subsidence may be due to the spouting of magma. In order to monitor the crustal deformation during the volcanic activity, we are continuing GPS tracking at the established two permanent sites for a while.

Active site nanospace of aminoacyl tRNA synthetase: difference between the class I and class II synthetases.

PubMed

Dutta, Saheb; Choudhury, Kaberi; Banik, Sindrila Dutta; Nandi, Nilashis

2014-03-01

The present work is aimed at understanding the origin of the difference in the molecular organization of the active site nanospaces of the class I and class II aminoacyl tRNA synthetases (aaRSs) which are tunnel-like structures. The active site encloses the cognate amino acid (AA) and the adenosine triphosphate (ATP) to carry out aminoacylation reaction. Comparison of the structures of the active site of the class I and class II (aaRSs) shows that the nanodimensional tunnels are curved in opposite directions in the two classes. We investigated the origin of this difference using quantum mechanical computation of electrostatic potential (ESP) of substrates, surrounding residues and ions, using Atoms in Molecule (AIM) Theory and charge population analysis. We show that the difference is principally due to the variation in the spatial charge distribution of ATP in the two classes which correspond to extended and bent conformations of ATP. The present computation shows that the most feasible pathway for nucleophilic attack to alphaP is oppositely directed for class I and class II aaRSs. The available crystal structures show that the cognate AA is indeed located along the channel favorable for nucleophilic attack as predicted by the ESP analysis. It is also shown that the direction of the channel changes its orientation when the orientation of ATP is changed from extended to a bent like structure. We further used the AIM theory to confirm the direction of the approach of AA in each case and the results corroborate the results from the ESP analysis. The opposite curvatures of the active site nanospaces in class I and class II aaRSs are related with the influence of the charge distributions of the extended and bent conformations of ATP, respectively. The results of the computation of electrostatic potential by successive addition of active site residues show that their roles on the reaction are similar in both classes despite the difference in the organization of the active sites of class I and class II aaRSs. The difference in mechanism in two classes as pointed out in recent study (S. Dutta Banik and N. Nandi, J. Biomol. Struct. Dyn. 30, 701 (2012)) is related with the fact that the relative arrangement of the ATP with respect to the AA is opposite in class I and class II aaRSs as explained in the present work. The charge population difference between the reacting centers (which are the alphaP atom of ATP (q(p)) and the attacking oxygen atom of carboxylic acid group (q(o)), respectively) denoted by delta(q), is a measure of the propensity of nucleophilic attack. The population analysis of the substrate AA shows that a non-negligible difference exists between the attacking oxygens of AA in class I (syn) and in class II (anti) which is one reason for the lower value of delta(q) in class II relative to class I. The population analysis of the AA, ATP, Mg+2 ions and active site residues shows that the difference in delta(q) values of the two classes is substantially reduced. When ions and residues are considered. Thus, the bent state of ATP, Mg+2 ions and active site residues complements it cognate AA to carry out the nucleophilic reaction in class I as efficiently as occurs in class I (with the extended state of ATP, single Mg+2 ion and active site residues). This could be one reason for the two different conformations of ATP in the two classes. The mutual arrangements of AA and ATP in each aaRS are guided by the spatial charge distribution of ATP (extended and bent). The present work shows that the construction of nanospace complements the arrangement of the substrate (AA and ATP).

Composition of Façon de Venise glass from early 17th century London in comparison with luxury glass of the same age

NASA Astrophysics Data System (ADS)

Cagno, S.; De Raedt, I.; Jeffries, T.; Janssens, K.

SEM-EDX and LA-ICP-MS analyses were performed on a set of early 17th century London glass fragments. The samples originate from two archaeological sites (Aldgate and Old Broad Street) where glass workshops were active in this period. The great majority of the samples are made of soda glass. Two distinct compositional groups are observed, each typical of one site of provenance. The samples originating from the Old Broad Street excavation feature a silica-soda-lime composition, with a moderate amount of potash. The samples from Aldgate are richer in potassium and feature higher amounts of trace elements such as Rb, Zr and Cu. The distinction between the two groups stems from different flux and silica sources used for glassmaking. A comparison with different European glass compositions of that time reveals no resemblance with genuine Venetian production, yet the composition of the Old Broad Street glass shows a close similarity to that of fragments produced `à la façon de Venise' in Antwerp at the end of the 16th century. This coincides with historical sources attesting the arrival of glassworkers from the Low Countries in England and suggests that a transfer of technology took place near the turn of the century.

Fall 1994 wildlife and vegetation survey, Norton Air Force Base, California

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

Not Available

The fall 1994 wildlife and vegetation surveys were completed October 3-7, 1994, at Norton Air Force Base (AFB), California. Two biologists from CDM Federal Programs, the U.S. Environmental Protection Agency (EPA) regional biologist and the Oak Ridge National Laboratory (ORNL) lead biologist conducted the surveys. A habitat assessment of three Installation Restoration Project (IRP) sites at Norton Air Force Base was also completed during the fall survey period. The IRP sites include: Landfill No. 2 (Site 2); the Industrial Wastewater Treatment Plant (IWTP) area; and Former Fire Training Area No. 1 (Site 5). The assessments were designed to qualitatively characterizemore » the sites of concern, identify potential ecological receptors, and provide information for Remedial Design/Remedial Action activities. A Reference Area (Santa Ana River Wash) and the base urban areas were also characterized. The reference area assessment was performed to provide a baseline for comparison with the IRP site habitats. The fall 1994 survey is the second of up to four surveys that may be completed. In order to develop a complete understanding of all plant and animal species using the base, these surveys were planned to be conducted over four seasons. Species composition can vary widely during the course of a year in Southern California, and therefore, seasonal surveys will provide the most complete and reliable data to address changes in habitat structure and wildlife use of the site. Subsequent surveys will focus on seasonal wildlife observations and a spring vegetation survey.« less

A method for the automated detection phishing websites through both site characteristics and image analysis

NASA Astrophysics Data System (ADS)

White, Joshua S.; Matthews, Jeanna N.; Stacy, John L.

2012-06-01

Phishing website analysis is largely still a time-consuming manual process of discovering potential phishing sites, verifying if suspicious sites truly are malicious spoofs and if so, distributing their URLs to the appropriate blacklisting services. Attackers increasingly use sophisticated systems for bringing phishing sites up and down rapidly at new locations, making automated response essential. In this paper, we present a method for rapid, automated detection and analysis of phishing websites. Our method relies on near real-time gathering and analysis of URLs posted on social media sites. We fetch the pages pointed to by each URL and characterize each page with a set of easily computed values such as number of images and links. We also capture a screen-shot of the rendered page image, compute a hash of the image and use the Hamming distance between these image hashes as a form of visual comparison. We provide initial results demonstrate the feasibility of our techniques by comparing legitimate sites to known fraudulent versions from Phishtank.com, by actively introducing a series of minor changes to a phishing toolkit captured in a local honeypot and by performing some initial analysis on a set of over 2.8 million URLs posted to Twitter over a 4 days in August 2011. We discuss the issues encountered during our testing such as resolvability and legitimacy of URL's posted on Twitter, the data sets used, the characteristics of the phishing sites we discovered, and our plans for future work.

Comparison of mosquito control programs in seven urban sites in Africa, the Middle East, and the Americas.

PubMed

Impoinvil, Daniel E; Ahmad, Sajjad; Troyo, Adriana; Keating, Joseph; Githeko, Andrew K; Mbogo, Charles M; Kibe, Lydiah; Githure, John I; Gad, Adel M; Hassan, Ali N; Orshan, Laor; Warburg, Alon; Calderón-Arguedas, Olger; Sánchez-Loría, Victoria M; Velit-Suarez, Rosanna; Chadee, Dave D; Novak, Robert J; Beier, John C

2007-10-01

Mosquito control programs at seven urban sites in Kenya, Egypt, Israel, Costa Rica, and Trinidad are described and compared. Site-specific urban and disease characteristics, organizational diagrams, and strengths, weaknesses, obstacles and threats (SWOT) analysis tools are used to provide a descriptive assessment of each mosquito control program, and provide a comparison of the factors affecting mosquito abatement. The information for SWOT analysis is collected from surveys, focus-group discussions, and personal communication. SWOT analysis identified various issues affecting the efficiency and sustainability of mosquito control operations. The main outcome of our work was the description and comparison of mosquito control operations within the context of each study site's biological, social, political, management, and economic conditions. The issues identified in this study ranged from lack of inter-sector collaboration to operational issues of mosquito control efforts. A lack of sustainable funding for mosquito control was a common problem for most sites. Many unique problems were also identified, which included lack of mosquito surveillance, lack of law enforcement, and negative consequences of human behavior. Identifying common virtues and shortcomings of mosquito control operations is useful in identifying "best practices" for mosquito control operations, thus leading to better control of mosquito biting and mosquito-borne disease transmission.